# WCGrid News and Talking Points!!



## Arjai (Nov 13, 2014)

The goal is to post project updates along with interesting tidbits / opinions thrown in.



Suggestions are welcome, criticism, is not.  PM me with stuff you'd like to see, and I will possibly respond.

Finalized Format, Ver 1.0.



Spoilers contain links to the WU reports published here, in this Forum. Links to original content is contained in each post, near the end.



Spoiler: WCG Specific Stuff/ BIONC Stuff



*Decades of Discovery: Here’s to the next 10 years of humanitarian science*


*16 Nov 2014*
*Release Notes for BOINC 7.4*
*1/8/2015 *
*World Community Grid Update*
*16 Jan 2015*
*World Community Grid Update - February 2015*
*20 Feb 2015*
*Database Upgrade: Saturday, February 28, 2015 at 03:00:00 UTC*
*24 Feb 2015*
*Top distributed computing projects still hard at work fighting the world's worst health issues*
*March 9, 2015*
*Top distributed computing projects still hard at work fighting the world's worst health issues ver. 1.2*
*March 9, 2015*
*New ways to visualize progress on your favorite research projects
	
*
*29 May 2014 
BOINC released a new version of it's Manager. 7.4.42*
*The past and the potential of World Community Grid: A Q&A with senior team *

*members.*
*14 Apr 2015 
System Updates: Sunday, April 26, 2015 at 01:00:00 UTC*
*Research task availability resumes following unexpected outage
	
*
*4 May 2015*
*Firmware Upgrade: Tuesday, May 5, 2015 at 14:00:00 UTC*


*4 May 2015*
*In 10 years, 'crowdsourced computing' has changed the world; now it's tackling Ebola*
*Wednesday *
*10 June 2015*
*Security upgrade, Monday, July 20, 2015*
*14 Jul 2015*
*Firmware upgrade: Saturday, August 8, 2015 at 01:00 UTC
	
*
*4 Aug 2015*
*Help World Community Grid make it onstage at SXSW 2016 *


*17 Aug 2015*





Spoiler: Computing for Clean Water



*Enhancing the potential for nanotechnology to improve access to clean water for millions
	

6 Jul 2015 *
*An exciting video about the recent Computing for Clean Water breakthrough.
	
*
*16 Jul 2015*
*Open science: sharing our clean water breakthrough data with all scientists
	
*
*5 Aug 2015*





Spoiler: CEP2



*Decade of discovery: doubling carbon-based solar cell efficiency*
*22 Oct 2014*
*A productive summer for the Clean Energy Project*


*23 Oct 2014
Computing for Clean Water on the road to publication
9 Feb 2015*
*The hard work of making discoveries useful*


*11 May 2015*
*Summer is a great time to focus on solar energy*


*2 Sep 2015*





Spoiler: Help Cure MD



*HELP CURE MUSCULAR DYSTROPHY*
*October 28, 2014*
*From simulation to prediction: advances in understanding proteins*


*26 Nov 2014 *





Spoiler: Mapping Cancer Markers



*Early-stage results from the Mapping Cancer Markers team *
*27 Oct 2014*
*Using one cancer to help defeat many: Mapping Cancer Markers makes progress*
*12 Feb 2015*
*One step closer to identifying lung cancer biomarkers
	
*
*19 Aug 2015*





Spoiler: Help Fight Childhood Cancer



*Decade of discovery: achieving a breakthrough in childhood cancer *


*28 Oct 2014*
*Surprising new prospects help advance the fight against neuroblastoma*
*20 Jan 2015*





Spoiler: Uncovering Genome Mysteries



*Community Grid Fosters Microbial Discovery*
*October 22, 2014*
*Sydney Scientists Are Linking Home Computers Around The World To Create A Huge Super Processor*
CHRIS PASH,*OCT 22 2014*
*Citizen IBM Uncovering Genome Mysteries*
*October, 21st 2014*
*Seven quadrillion comparisons later, Uncovering Genome Mysteries is just getting started*
*26 Feb 2015*
*Seven quadrillion comparisons later, Uncovering Genome Mysteries is just getting started
	

 v1.2*
*26 Feb 2015 ?March update?*





Spoiler: Fight Aids @ Home



*Teamwork yields experimental support for FightAIDS@Home calculations*
*6 Nov 2014*
*The end of the beginning is near for FightAIDS@Home*
*20 Feb 2015 *
*Pioneering new techniques in the fight against HIV
	
*
*30 Sep 2015*





Spoiler: Help Defeat Cancer



*Decade of discovery: New precision tools to diagnose and treat cancer*


*3 Nov 2014*
*Help Defeat Cancer*
*15 Dec 2014*





Spoiler: Discovering Dengue Drugs-Together



*Decade of Discovery: A new drug lead to combat dengue fever
	
*
*10 Nov 2014*





Spoiler:  Drug Search for Leishmaniasis 



*Finding new solutions for a neglected tropical disease*


*28 Nov 2014*
*Exceptional early results in the fight against Leishmaniasis*
*12 Jul 2015 *





Spoiler:  Outsmart Ebola Together



*Help researchers find an Ebola cure
	
*
*3 Dec 2014
Outsmart Ebola Together! News articles.
12/3 and 12/8/14*
*Outsmart Ebola Together*
*12/19/2014 *
*A milestone and a roadmap: progress in the fight against Ebola*
*5 May 2015*
*Finding new avenues to attack Ebola *
*6 Oct 2015 *





Spoiler: GO Fight Against Malaria



*Making progress against two of the world’s deadliest diseases
9 Feb 2015*
*Post grid calculations continue to yield progress and inspire new methods against deadly diseases*
*5 Jun 2015*





Spoiler: Schistosoma



*Turning virtual results into real-world treatments for schistosoma
22 Apr 2015*





Spoiler: Help Cure Cancer



*End of the Help Conquer Cancer project
	
*
*29 May 2013 *
*Analyzing crystals to help fight cancer
	
*
*28 Aug 2015*



These Spoiler's are for News events in 2015 and before, to the start of this thread. There was an issue with editing this post, and by the time I had editing power, again, It was too daunting a task to update. I may tackle it, someday, but it becomes more of an issue as time goes on. We'll see if at some point, I can find time to at least start to update it!!


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## Arjai (Nov 13, 2014)

*Decade of discovery: doubling carbon-based solar cell efficiency*

*22 Oct 2014*



> Since launching on World Community Grid in 2008, The Clean Energy Project has screened more than two million organic molecules, with the help of our volunteers – _the most extensive investigation of quantum chemicals ever performed._






> The Harvard team – who so far have been provided with the _equivalent of 17,000 years of computing time_ – continues to investigate the most promising candidates for use in cheaper, more efficient and flexible solar cells.



Very good work has been done and it is amazing the quantity of data in such a short time. I am sure to revisit this theme again, I find it both amazing and encouraging that world wide people are volunteering their computers for this work! Bravo, World. 

The rest of the story (I plan to borrow this phrase from Paul Harvey, indefinitely)


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## Arjai (Nov 13, 2014)

*Get competitive for good with our 10th anniversary challenge*

*22 Oct 2014* 



> The challenge is to recruit as many friends as possible to World Community Grid to power another decade of scientific success. Put simply, the more friends you recruit – the higher your chances of becoming a World Community Grid Champion.
> 
> And there are some great prizes up for grabs.




The rest of the story


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## Arjai (Nov 13, 2014)

*A productive summer for the Clean Energy Project*






*23 Oct 2014* 

Another update from CEP2.



> As you have probably seen in the forums, we have had a redesign of the structure of the work units. We want to thank everyone for their patience while we sorted out all the “teething” problems, but they now seem to be working well. The reason for these changes was to allow us to try and move onto slightly different families of molecules which we have identified as being particularly interesting. It is important for the CEP to be constantly updating the molecular libraries so we can really live on the cutting edge, and hopefully discover the next “blockbuster” Organic Photovoltaic molecule (the type of molecule the CEP is looking for). To do this, we have to push up against the limits of what is possible on the grid, and we really appreciate the patience of the crunchers when we occasionally push too hard!



I like their attitude!! Go BIG, or GO HOME!! 

The Rest of the Story


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## Norton (Nov 13, 2014)

Sub'd 

Suggestion- how about links to the articles/items you're posting in the OP? Spoilered and arranged by date/title/etc..

Example:


Spoiler:  WCGrid News and Talking Points archive



- 10/22/2014 *Decade of discovery: doubling carbon-based solar cell efficiency*
http://www.techpowerup.com/forums/threads/wcgrid-news-and-talking-points.207154/#post-3192643
- mm/dd/yyyy *Title*
link
- mm/dd/yyyy *Title*
link


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## Arjai (Nov 13, 2014)

*HELP CURE MUSCULAR DYSTROPHY*

*October 28, 2014*

An update from the Project that ended, Phase 2, last year.



> Phase 1 of Help Cure Muscular Dystrophy has ended in June 2007 and Phase 2 has been launched in may 2009 and ended in the fall 2013.
> 
> The first and second phase of the project is supported by World Community Grid and by Decrypthon (a partnership between AFM (French Muscular Dystrophy Association), CNRS (French National Center for Scientific Research) and IBM).





> MORE ACCURATE PREDICTIONS OF INTERACTION SITES
> We previously developed a tool, Joint Evolutionary Tree (JET) for the prediction of protein-protein interfaces [Engelen et al. 2009]. JET assumes that interaction sites are formed by a highly conserved core, surrounded by multiple concentric layers of less conserved residues, but with specific physico-chemical properties. Although this assumption is verified in the majority of interfaces, there are some cases where the interaction site only extends in a preferred direction from the retained core. In order to refine the definition of interaction sites predicted by JET, we have introduced a geometric criterion to describe the protein surface and have coupled this with conservation and physico-chemical properties. The new version of JET encourages extensions of interaction sites to protruding areas in the protein that appear to be highly exposed to the solvent. Depending on the system studied, JET is now able to automatically determine the combination of the most relevant criteria. These changes have significantly improved the performance of JET on different types of protein [Laine et al complexes. 2013- post Berlin]. We are currently setting up a database for all PDB structures, including those structures studied on the WCG grid in the HCMD2 project.



A bit technical but, it essentially means that they have found a way to use all the data produced by WCG, despite earlier failures described in the article, here.



> 4) Carry out a refined analysis of the large database of protein interactions that you generated (!) to characterize interaction networks and binding promiscuity. During stage two of the Help Cure Muscular Dystrophy project (HCMD2), the resources of the World Community Grid (WCG) were used to dock all possible protein pairs within a set of 2200 proteins, potentially important for understanding and treating
> neurodegenerative diseases. This data will be analyzed to characterize key “hub” proteins and network structures, first, with the existing energetic and residue conservation data and then with the new methods resulting from 1-3.



As a layman, and an intelligent one, I can sort of grasp the concept and experiments. What I truly understand? This project is becoming a Grand Success!!


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## Arjai (Nov 13, 2014)

Norton said:


> Sub'd
> 
> Suggestion- how about links to the articles/items you're posting in the OP? Spoilered and arranged by date/title/etc..
> 
> ...


Might make for a rather large opening post....But, also a one stop shopping spot. In fact, I may just link to my posting, that contains the link to the original story. Deal?


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## Norton (Nov 13, 2014)

Arjai said:


> Might make for a rather large opening post....But, also a one stop shopping spot. In fact, I may just link to my posting, that contains the link to the original story. Deal?



That's what I'm suggesting, a link to your postings 

Using spoilers will allow the OP to stay reasonably shorter


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## Arjai (Nov 13, 2014)

*Early-stage results from the Mapping Cancer Markers team*

*27 Oct 2014*



> Thanks to your help, the Mapping Cancer Markers team is nearly finished with benchmarking their first set of genetic markers.





> The Mapping Cancer Markers (MCM) team would like to extend a huge _thank you_ to World Community Grid members everywhere. As of October 27, 2014, we have surpassed 89,000 years of computation, a goal that simply would not be possible without your help.



Que my amazing face!



> The first half of the “benchmarking” experiment involves determining the performance of markers as the size of the signature changes. For instance, when we compare successful 5-marker signatures against 20-marker signatures, which markers are consistently useful? Which ones increase or diminish in predictive power? Is there an optimum size for signatures? And most importantly, can we identify seemingly minor players that are critical, but not yet in clinical use that can discriminate between normal and disease states?





> In the above network, 20 out of 24 important proteins we have identified on World Community Grid (right hand side) can be linked through known protein interactions and 56 other proteins (left hand side).



I love it when our computed research drives the researchers in new directions with the results. 

The Rest of the Story.


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## Arjai (Nov 13, 2014)

*Decade of discovery: achieving a breakthrough in childhood cancer *





*28 Oct 2014*



> Through the Help Fight Childhood Cancer project, World Community Grid volunteers powered the screening of over three million drug candidates for neuroblastoma – a common and dangerous form of childhood cancer. Through this screening, researchers identified seven drug candidates that showed great potential for drug development – a breakthrough that could save many young lives.





> Over the course of two years, World Community Grid volunteers helped the researchers screen three million molecules - a search that would have taken more than 55,000 years on a single computer. Following this testing, in February this year the researchers announced the discovery of seven promising molecules that proved effective at activating the self-destruct function and destroying neuroblastoma cancer tumors when tested on mice, without any apparent side effects on healthy tissue.
> 
> This was a significant breakthrough - particularly because over the course of the last 20 years, very little progress has been made in improving the cure rate for this deadly disease. What makes this discovery even more important is the fact that it could aid the research of many adult cancers including breast, lung, pancreatic, prostate and colon cancers.
> 
> ...



Exciting news!! And a possible new project in the works!!


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## Arjai (Nov 13, 2014)

*Community Grid Fosters Microbial Discovery*

*October 22, 2014*



> An international team of volunteers is putting their spare computing power to work unlocking the secrets of microbes from around the world. By plugging in to IBM’s World Community Grid, contributors are creating a supercomputer that can carry out genetic comparisons of a wide variety of tiny organisms that are too small to see with the naked eye. But don’t let their size fool you, the smallest of earth’s lifeforms have profound implications for human health, agriculture and industry.
> 
> The Uncovering Genome Mysteries project is administered by University of New South Wales (UNSW) in Australia and the Oswaldo Cruz Institute of Brazil. The project seeks to make about 20 quadrillion comparisons of 200 million proteins underlying a wide variety of lifeforms, such as microorganisms found on seaweeds from Australian coastlines and in the Amazon river. The computing involved in such an immense undertaking would take 40,000 continuous years on a typical PC, but the capacity of the World Community Grid will reduce the task to mere months.












News article from HPC


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## Arjai (Nov 13, 2014)

*Sydney Scientists Are Linking Home Computers Around The World To Create A Huge Super Processor*

CHRIS PASH, *OCT 22 2014*



> The team at the University of NSW are using an international group of volunteers sharing their spare computer capacity to create a research supercomputer.
> 
> The project has the aim of making 20 quadrillion, or 20,000 million million, comparisons of genes from a variety of tiny life-forms invisible to the naked eye.





> “But we know very little about them. Scientists have studied less than 1% of microbial diversity around the globe. Valuable discoveries await us if we can learn about the remaining 99%.”
> 
> The Uncovering Genome Mysteries project is hosted on IBM’s World Community Grid.





> With enough volunteers the project could be completed within months. But it would take 40,000 years for a single PC to make 20 quadrillion computations.
> 
> Microbes are vital to sustaining life on Earth, producing half of the oxygen we breathe, soaking up carbon dioxide and recycling nutrients.



_Half the AIR we breath?_ Hmmm...learned sumptin today!



Business Insider, Australia article


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## Arjai (Nov 13, 2014)

*Citizen IBM Uncovering Genome Mysteries*

*October, 21st 2014*



> Our understanding of life on earth has grown enormously since the advent of genetic research. A decade ago, the Human Genome Project added humans to the list of a
> dozen organisms whose genomes had been completely sequenced. Today’s rapid
> DNA sequencing technologies have decoded the genomes of thousands of additional organisms, including many microorganisms that previously could not be studied via conventional methods.





> Today, we’re launching _Uncovering Genome Mysteries_ on World Community Grid to examine nearly 200 million proteins from a wide variety of life forms – including microorganisms found on seaweeds from Australian coastlines and in the Amazon river. Through this work, we will learn more about the functions of millions of genes and the proteins they encode, enabling scientists to better understand complex microbial systems, identify how organisms interact with one another, and analyze how microorganisms change under environmental stresses, such as climate change.





> _Wim Degrave, Ph.D., of Oswaldo Cruz Foundation (Fiocruz), and Torsten Thomas, Ph.D., of the University of New South Wales, lead the Uncovering Genome Mysteries project._



A wide ranging project that could help solve a whole Bunch 'O Things!!


Citizen IBM article
_
_


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## Arjai (Nov 13, 2014)

*Decade of discovery: New precision tools to diagnose and treat cancer*





*3 Nov 2014*



> When it comes to cancer, a doctor's diagnosis affects how aggressively a patient is treated, which medications might be appropriate and what levels of risk are justified. New precision medicine techniques are enabling physicians and scientists to refine diagnoses by identifying changes and patterns in individual cancers at unprecedented levels of granularity - ultimately improving treatment outcomes for patients.





> To study the feasibility of automating tissue microarray analysis, we partnered with IBM's World Community Grid in 2006 to launch the Help Defeat Cancer project. At the time, we were pioneering a new approach that nobody else was investigating, and it was met with tremendous skepticism by many of our colleagues.
> 
> However, with the support of more than 200,000 World Community Grid volunteers from around the globe who donated over 2,900 years of their computing time, we were able to study over 100,000 patient tissue samples to search for cancer signatures.





> Thanks to World Community Grid and the Help Defeat Cancer project, we demonstrated the success of using computer-based analysis to automatically investigate and classify cancer specimens based on expression signature patterns. We were able to develop a reference library of cancer signatures that can be used to systematically analyze and compare tissue samples across large patient cohorts.



Awesome Face!!

More Awesome, Here...


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## Arjai (Nov 13, 2014)

*Teamwork yields experimental support for FightAIDS@Home calculations
	

	
	
		
		

		
		
	


	


*

*6 Nov 2014*



> _The "exo-site" discovered in HIV protease (shown here in green), showing the original bound 4d9 fragment (shown here as red and orange sticks) and the volume (shown as the orange mesh) that is being targeted by FightAIDS@Home. (image credit: Stefano Forli, TSRI)_
> 
> Our lab at the Scripps Research Institute, La Jolla, is part of the HIV Interaction and Viral Evolution (HIVE) Center - a group of investigators with expertise in HIV crystallography, virology, molecular biology, biochemistry, synthetic chemistry and computational biology. This means that we have world-class resources available to verify and build upon our computational work, including the nuclear magnetic resonance (NMR) facility at the Scripps Research Institute, Florida. NMR is a technique for determining the molecular structure of a chemical sample, and therefore is very useful for validating some of the predictions made during the computational phase ofFightAIDS@Home.





> In fact, the first results from the NMR experiments validated the exo site we so thoroughly investigated in FightAIDS@Home. As a result, we now have experimental evidence that a small molecule binds to the exo site in solution with structural effects that seem to perturb the dynamic behavior of protease, even with a known inhibitor in the active site.



OK? Got it? 

More scientific gobbledy gook to try and wrap your head around, HERE!

The upshot, context, is, We are awesomely providing these guys with the stuff they want. They are very Thankful.


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## Arjai (Nov 13, 2014)

*Decade of Discovery: A new drug lead to combat dengue fever
	

	
	
		
		

		
		
	


	


*

*10 Nov 2014*



> Dengue fever, also known as “breakbone fever”, causes excruciating joint and muscle pain, high fever and headaches. Severe dengue, known as “dengue hemorrhagic fever”, has become a leading cause of hospitalization and death among children in many Asian and Latin American countries. According to theWorld Health Organization (WHO), over 40% of the world’s population is at risk from dengue; another study estimated there were 390 million cases in 2010 alone.





> Despite the fact dengue represents a critical global health concern, it has received limited attention from affluent countries until recently and is widely considered to be a neglected tropical disease. Currently, no approved vaccines or treatments exist for the disease. We launched Discovering Dengue Drugs - Together on World Community Grid in 2007 to search for drugs to treat dengue infections using a computer-based discovery approach.





> We have recently made an exciting discovery using insights from Discovering Dengue Drugs - Together to guide additional calculations on our web portal for advanced computer-based drug discovery, DrugDiscovery@TACC. A molecule has demonstrated success in binding to and disabling a key dengue enzyme that is necessary for the virus to replicate.





> Furthermore, it also shows signs of being able to effectively disable related flaviviruses, such as the West Nile virus.



BONUS!!! 

The Rest of the Story

The Discovering Dengue Drugs research team has published a paper describing a new drug candidate that was discovered with the help of World Community Grid volunteers.


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## Arjai (Nov 18, 2014)

*Decades of Discovery: Here’s to the next 10 years of humanitarian science*





*16 Nov 2014*



> We’ve reached the end of our six-week decade of discovery celebrations - marking 10 years of scientific success. Since October, we’ve been revisiting key projects from the last decade and highlighting some of the fantastic achievements that you’ve helped make possible. We’ve also been running a competition to encourage more people to join World Community Grid. We’d like to thank you again for your support and remind you why it’s so important to keep spreading the word...





> All these cutting-edge projects would not have been possible without the computing power donated by volunteers like you. In order to power more humanitarian research projects like these, it’s vitally important that we continue to raise awareness and get more people to join World Community Grid.





> *Thank you again for your continued support and stay tuned for the launch of another significant project on World Community Grid in the coming weeks.*



I can't wait!! I can't WAIT!!!  

The full Story, Here.


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## Arjai (Nov 27, 2014)

*From simulation to prediction: advances in understanding proteins*





*26 Nov 2014 *



> *Summary*
> The Help Cure Muscular Dystrophy project finished its grid calculations last year. Team leader Dr. Alessandra Carbone has posted an update explaining her colleagues’ ongoing work on understanding and modeling the complex protein-protein interactions that lie behind diseases such as muscular dystrophy.





> Dr. Carbone’s post gives another great example of how the work done on World Community Grid continues to have value for researchers long after the grid phase of the project is complete.
> 
> For further details, read Dr. Carbone’s update on her project website.



https://secure.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=137
Dr.Carbone's Link to her project site.

More from Dr. Carbone's report....



> COEVOLUTION ANALYSIS AND PROTEIN-PROTEIN INTERACTIONS
> We planned to obtain extra evidence of protein-protein interactions, and a better understanding of their nature, by exploiting information coming from co-evolution of residues at the interface of the two proteins. Novel kinds of interaction between potential partners, identified on interaction surfaces by coevolution analysis, are currently under investigation. We also developed a very fast version of the algorithm for the analysis of co-evolution "Blocks In Sequences" (BIS) [Dib & Carbone 2012]. Today, this implementation allows us to analyse long genomic sequences, such as complete viral genomes and to study the interaction of sets of proteins. *This was previously impossible* and it allows us to identify contacts among multiple proteins for which no interaction information was available. _Using this approach, we considered the entire coding portion of the genome of hepatitis C virus (HCV) and identified, with BIS, all potential points of contact between the 10 proteins of this virus._ In collaboration with F. Penin we are currently analyzing the interaction data.



Emphasis, mine. This IS exciting!!


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## Arjai (Nov 29, 2014)

*Finding new solutions for a neglected tropical disease*





*28 Nov 2014*



> The last year of work really helps emphasize the tremendous scale of our project. World Community Grid volunteers generated approximately 4TB of data, consisting of more than 1.5 billion records, which store information about interaction energies between a set of _Leishmania_ proteins and a library of 600,000 compounds.



*1.5 BILLION*, _Billion people_, _Billion!! _



> Based on the preliminary results, we are optimistic about finding a good candidate to treat leishmaniasis, which can be improved with further computational and experimental validations. We are preparing for a second phase of the project, which involves an extra selection filter using an adapted MD protocol to avoid false positives and consequently detect molecular hits that can behave similarly to real life. With the help of all the volunteers we hope to identify at least one new molecule capable of fighting against a neglected disease that urgently needs more effective and non-toxic chemical treatments.



Could this be the "NEW" project being rumored about? BTW, I'm all in on this one!!



> Working with World Community Grid for over three years has been a fantastic experience. Since the beginning of the project in September 2011, we have maintained a tight relationship with the team at World Community Grid. And of course, the volunteers who donated their computing time made this entire project possible—we can’t say thank you enough for that generosity.





> Finally, we started communication with Dr. Olson´s Lab at The Scripps Research Institute in La Jolla, California. They have a lot of experience in drug discovery, and are the developers of AutoDock Vina, the program we use in the DSFL project. Their BEDAM program may allow us to filter our results further based on thermodynamic parameters.



WCG Collaboration, Nice! 

The rest of the Story, with more detail, Here!


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## twilyth (Nov 29, 2014)

Cool.  Thanks @Arjai. Even if they aren't the current beta, it means they're going to be another project coming soon hopefully.


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## manofthem (Nov 30, 2014)

This is very cool. I don't know how I've missed this thread until just this second, but I'm lovin' it! 
Great Work @Arjai


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## Arjai (Nov 30, 2014)

manofthem said:


> This is very cool. I don't know how I've missed this thread until just this second, but I'm lovin' it!
> Great Work @Arjai


See, I AM doing something!! Even @manofthem noticed!!


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## Arjai (Dec 6, 2014)

*Help researchers find an Ebola cure
	

	
	
		
		

		
		
	


	


*

*3 Dec 2014*



> The current outbreak of the Ebola virus is the largest in history, and has been described by the World Health Organization as *"the most severe acute public health emergency seen in modern times”.*





> Currently, there are no approved treatments or vaccines for this deadly disease. In response to this urgent need, I reached out to my colleagues around the world to create the Viral Hemorrhagic Fever Immunotherapeutic Consortium, a collaborative effort of the world’s top Ebola experts to pool our knowledge and skills to find a cure as quickly as possible.





> Today, we’re launching Outsmart Ebola Together to accelerate the search for a cure. Outsmart Ebola Together is a collaboration between The Scripps Research Institute and IBM’s World Community Grid to screen millions of chemical compounds, searching for ones that can disable the Ebola virus.





> *World Community Grid volunteers are critical to the success of Outsmart Ebola Together.* If you have a computer or Android device, you can help too. Join World Community Grid today to donate your spare computing power to searching for Ebola treatments with our team.




Let's DO THIS!!!


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## Arjai (Dec 6, 2014)

Anybody sporting these Ebola WU's yet? Is it still in Beta? I seem to have very limited success getting Beta's...


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## FordGT90Concept (Dec 6, 2014)

I checked my two computers and no Ebola is tasked.


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## [Ion] (Dec 6, 2014)

Arjai said:


> Anybody sporting these Ebola WU's yet? Is it still in Beta? I seem to have very limited success getting Beta's...


Yeah I have 63 pages of them


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## t_ski (Dec 6, 2014)

^^^ That's where they all went...


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## manofthem (Dec 6, 2014)

t_ski said:


> ^^^ That's where they all went...





I've had a few beta OETs on my main rig today, not sure about the others.


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## [Ion] (Dec 6, 2014)

t_ski said:


> ^^^ That's where they all went...



Gotta get work.....not my fault the WCG scheduler is giving me some


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## Peter1986C (Dec 6, 2014)

I had some OET WUs.


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## Norton (Dec 6, 2014)

I have 4 wu's completed with 5 pages of them waiting to run


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## Arjai (Dec 6, 2014)

Well, just discovered why i wasn't getting any OET WU's. At some point I reconfigured my projects page, for whatever reason, and did not reset it to all projects. So, I should get some, either this evening or tomorrow, after I have run some and make room for them!

OOPS!


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## Peter1986C (Dec 7, 2014)

It was not auto-added to our profiles because it has the same special requirements thing that CEP has.


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## Arjai (Dec 17, 2014)

Four articles written about *Outsmart Ebola Together!
12/3 and 12/8/14*

Mashable

KBPS San Diego

CNN Money

International Business Times

Boinc pointed to an ABC NEWS site but, searching their site yielded no results. So, to make four, I included the article from San Diego.


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## Arjai (Dec 17, 2014)

*Help Defeat Cancer *

*15 Dec 2014*



> Dear World Community Grid volunteers,
> 
> Since our last Help Conquer Cancer (HCC) project update, we have continued to analyze the results that you generated. Here, we provide an update on that analysis work, and new research directions the project is taking.





> Volunteers for the HCC project received raw protein crystallization images and processed each image into a set of over 12,000 numeric image features. These features were implemented by a combination of image-processing algorithms, and refined over several generations of image-processing research leading up to the launch of HCC.





> This traditional method of building an image classifier involves two types of learning: the crystallographer or image-processing expert (human), who studies the image and designs features, and the classifier (computer model), that learns to predict image labels from the designed features. The image classifier itself never sees the pixels;





> More recently, we have applied a powerful computer-vision/machine-learning technology that improves this process by closing the feedback loop between pixels, features and the classifier: deep convolutional neural networks (CNNs). _These models learn their own features directly from the image pixels; thus, they could complement human-designed features._





> Figure 3 (below) shows CrystalNet's crystal-detection performance across 10 image classes in the test set. CrystalNet produces an area under curve (AUC) 0.9894 for crystal class classification. At 5% false positive rate, our model can accurately detect 98% of the positive cases.











> Recently, however, HWI crystallographers were able to compile and share with us a complete record of all crystallization-trial proteins produced by the North-Eastern Structural Genomics (NESG) group. This dataset represents approximately 25% of all proteins processed by HCC volunteers on World Community Grid.





> With more complete protein/cocktail information, combined with more accurate image labels from improved deep neural-net image classifiers, we anticipate greater success mining our protein-crystallization database. Work is ongoing.



Love to see our work creating interesting new processes to help with solving the sheer numbers we have given them!! 

Complete news article, including _even more_ confusing terms, can be found, HERE!


----------



## Arjai (Dec 20, 2014)

*Outsmart Ebola Together*

*12/19/2014 
*


> ...The Ebola project, which debuted on the grid the first week of December, completed in one week what it would have taken a PC with a single processor about 35 years to accomplish.




Time magazine article about OET and WCG. I have no time to read it right now. But, you can!! Click HERE.


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## Arjai (Jan 9, 2015)

*Release Notes for BOINC 7.4*
*1/8/2015 *

*Changes in 7.4.36*

*Attaching to World Community Grid*
*Back-up projects (0 Resource Share)*
*Better detection of notice  UPDATES (reduces the number of system notifications)*
*Suspending GPUs should not suspend Bitcoin Miners*
*Increasing the maximum number of coprocessor devices to 64*
*Updates to OpenSSL(1.0.1j) and LibCurl(7.39.0)*
Yea, NOW I can BitCoin and Crunch!!

Oh, here's a link....

And the Download page


----------



## Peter1986C (Jan 11, 2015)

GPU mining XBT has been infeasible for some time now. Even special equipment is often not efficient enough to no lose money on the process with current value.


----------



## twilyth (Jan 11, 2015)

Very true.  And bitcoin hardware makers tend to run their machines for a few months before releasing them to the general public.  When you factor in the rate at which the difficulty grows each month, you're lucky to get a few months worth of processing out of them before you start running at a loss.  And if you factor in the cost of the hardware, you're probably running at loss to begin with.  Now with prices a fraction of what they were a year ago, it difficult if not impossible to make a profit - at least for an individual trying to do this.


----------



## Peter1986C (Jan 17, 2015)

World Community Grid Update - January 2015
	

	
	
		
		

		
		
	


	






By: Keith Uplinger
World Community Grid

16 Jan 2015




Summary An update about technical activities at World Community Grid in January 2015. 
	

	
	
		
		

		
		
	


	







A brief update on some of the upcoming technical activity at World Community Grid:

In the next few weeks we will experience a few outages to upgrade our environment. First, we will be doing an upgrade to the network infrastructure with some new equipment, *which will cause the entire website to go down for a few hours*. We will also be upgrading our database servers next weekend. With this extra server capacity we will be exploring how to get the stats updates to run quicker.

On the application side of things, we are working on onboarding *a few new science applications as well as fixing a few issues with current projects.* As many of our members know, we do not release information about upcoming projects, so unfortunately I can not give details about these.

For the Outsmart Ebola Project, we are working to add mid job checkpointing to the VINA application. During our last BETA test, we identified that the checkpointing was causing more than the usual number of invalids compared to checkpointing at the job level. The reason for doing this is the next set of work units from the researchers are what are flexible docking work units and they can run long. Average job runtime for flexible work units is closer to 6 hours, where rigid jobs were running closer to 15 minutes. Once this is completed and we get a successful beta test, we will be starting the Outsmart Ebola Together project with a more consistent flow of work units.

The Uncovering Genome Mysteries project has an issue where it writes to the disk very frequently. At this time we are alpha testing some changes that will prevent this from happening. The current version in alpha does have a known issue and is being investigated, as it was causing invalid errors. Once we have a suitable version of the application, we will promote it to beta testing to make sure the changes are valid.

The VINA application on Android has seen an increase in errors due to the latest version of Android OS. It is causing a PEI exception to be thrown. We are working with Berkeley to get this resolved and tested in our environment. Currently we have recompiled the science application to run with PEI. Berkeley is also working on releasing a version of the BOINC client that will work properly with Android Lollipop.

As always, thank you for participating in World Community Grid and contributing to the humanitarian research projects that have benefitted from your generosity!

Source


-


----------



## Peter1986C (Jan 21, 2015)

*Surprising new prospects help advance the fight against neuroblastoma
	

	
	
		
		

		
		
	


	


*




By: Dr. Akira Nakagawara, MD, PhD
CEO of the Saga Medical Center KOSEIKAN and President Emeritus, Chiba Cancer Center

20 Jan 2015




Summary Prof. Nakagawara, lead researcher of the Help Fight Childhood Cancer project, updates us on the project's status after a remarkable year that included the publication of a breakthrough paper in 'Cancer Medicine'. World Community Grid results have revealed even more potential treatment mechanisms than the team previously thought, and paved the way for a second phase of the project. 
	

	
	
		
		

		
		
	


	










Last year saw many successes for the Help Fight Childhood Cancer (HFCC) project in particular and the effort to overcome neuroblastoma in general. HFCC was a joint effort by personnel at the Chiba Cancer Center Research Institute (which I led) and Chiba University, (led by Dr. Hoshino and Dr. Tamura). Its primary goal was to identify small chemical compounds which target the particular sites of the proteins important in regulating the tumor cell growth and aggressiveness. Then, if the compounds we identified had the ability to kill the neuroblastoma tumor cells both in vitro and in vivo, the second goal was to develop new drugs to treat the patients with aggressive neuroblastoma using the structural information of the chemical compounds we identified. Thanks to your help, we have made significant progress toward both of those goals. We greatly appreciate all of the World Community Grid volunteers for their enormous enthusiasm to help cure and support children with cancer.

*Overview of our recent progress*

As we reported last year, we had great success in identifying some promising anti-cancer compounds, and have published the first round of our results in the journal _Cancer Medicine_. However, these were only a subset of the promising results that we have found. So far, World Community Grid members have helped us identify anti-cancer potential in small chemical compounds that work in three different ways:


*1.TrkB receptor antagonists:*
These were the subject of our _Cancer Medicine_ paper. We used your AutoDock computations to identify 7 chemicals from a library of 3 million chemical compounds. Those chemicals showed very low IC50 values (low values indicate a measurement of more effectiveness) killing neuroblastoma cells in vitro. We then selected the 2 chemicals with the lowest IC50 values, and found that they significantly suppressed the zenografted tumor growth in nude mice. Dr. Hoshino's group at Chiba University is currently generating new small chemical compounds based on the structure of the candidate compounds you helped us identify. These are chemical compounds with much lower IC50 value to kill the neuroblastoma cell, and are based on the structure of those identified by World Community Grid.

The primary short-term challenge for this aspect of our research is finding a pharmaceutical company that can collaborate with us in turning these promising compounds into a medication. This has been difficult because although neuroblastoma is terrible, in absolute terms it is still a very small market, and few companies are interested in devoting development resources to it.

*2. TrkB receptor agonists:*
As a byproduct of World Community Grid computations, we happened to find the agonists of TrkB which appear to function similarly to Brain-derived neurotrophic factor (BDNF), which is a physiological ligand of TrkB. This could provide another avenue of attack against neuroblastoma. The functional analysis of these results is going on now in my laboratory.

*3. Antagonists inhibiting the binding sites of ALK receptor and ShcC adaptor protein:*
We have previously found that both the ALK receptor and its adaptor protein ShcC are markers for aggressiveness in neuroblastoma. The ALK protein interacts with the ShcC protein at two binding sites. Therefore, we were looking to block those sites by identifying small chemical compounds which interrupt the binding sites. Calculations done on World Community Grid successfully identified several compounds for the two binding sites which kill neuroblastoma cells in vitro with low IC50 values. We are currently analyzing the molecular pathway by which those compounds kill the tumor cells.

For these compounds, we collaborated with Dr. Sakai's group at the National Cancer Center Research Institute in Tokyo. The student who was working on this project has left the lab, so we are now looking for the new researcher who is interested in this project.

*Sharing our research*

The process of making this data public is currently ongoing - the TrkB antagonists were the subject of our paper in _Cancer Medicine_ in 2014, and that raw data is publicly available. We are still working on the other data on TrkB agonists and ALK/ShcC antagonists. We presented our Phase 1 results at several conferences in Japan, as well as at the ANR (Advances in Neuroblastoma Research) meeting held in Germany in 2014. That raw data is not yet publicly available.

*Next steps*

As I mentioned last July, I moved from Chiba to Saga and took up a position at the Saga Medical Center KOSEIKAN, whose hospital was founded in 1834 during the Edo Days of Japan. Therefore, the HFCC team is now a collaboration between the Graduate School of Medicine, Chiba University, and the Saga Medical Center KOSEIKAN. The home page of HFCC will soon be moved from the Chiba Cancer Center to the Saga Medical Center KOSEIKAN.

Phase 1 of HFCC targeted neuroblastoma, and we are now developing a Phase 2 that will target many more childhood cancers. This future work will include a new team from Hong Kong University led by Dr. Godfrey C.F. Chan, a pediatric oncologist. We hope to bring the next phase of this project to World Community Grid soon.

Once again, thank you to the whole World Community Grid team, and to all the volunteers, for making this research possible. With your help, we are much closer to finding effective treatments for a devastating childhood disease.

---------------------

Source: http://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=413

---------------------


----------



## twilyth (Jan 21, 2015)

The BDNF connection is interesting since it has been implicated in depression and IIRC there is some research that implies that the way serotonin uptake inhibitors really work is via BDNF.  Reductions in BDNF seem to result in atrophy of the hippocampus which facilitates the creation of memories.  Persistent stress seems to reduce BDNF levels which results in depression as per the HPA axis theory.


----------



## Peter1986C (Feb 20, 2015)

*The end of the beginning is near for FightAIDS@Home*







_By: The FightAIDS@Home research team_

*20 Feb 2015  *




Summary Thanks to the incredible generosity of World Community Grid volunteers, the FightAIDS@Home project team has finished with an important stage of their project. The research team has refocused on analyzing their existing results and preparing for the end of this historic grid computing stage. 
	

	
	
		
		

		
		
	


	







FightAIDS@Home has been running on World Community Grid in some form almost since the beginning of World Community Grid itself: our project launched in 2005. Thanks to the enormous and ongoing support of our worldwide community of volunteers, we have expanded the scope of our research and explored new targets and drug candidates that we simply could not imagine at the outset. It hardly seems sufficient to say thank you for donating over 330,000 years of processing time to support our research, but once again, from all of us to all of you: thank you. Clearly we could not do this research without you.

With your help, we have reached a new milestone: no new AutoDock (AD) or AD Vina docking experiments are currently being generated. Put another way: we’re done creating new work tasks. The AutoDock queue is now empty, and the AD Vina queue has more than a year's worth of jobs left. Most of our efforts have shifted towards analysis.

The analysis of the FightAIDS@Home data has several levels of difficulty due to the sheer amounts of data, which are comprised of several structures of any drug target as well as millions of small molecules, resulting in hundreds of millions of data points. We are attempting to use a couple of approaches to mine this data, one of which includes examining amino-acids involved in top-ranked dockings. Another approach is to investigate the atomic coordinates of important interactions (pharmacophore) between the protein and the small molecule that was docked. Figures 1 and 2 (below) illustrate a simple example of inhibitor TL3 (Figure 1) and the predictions of 1 experiment (Figure 2, ~5.5 million dockings on 1 protein structure). Of course, these evaluations must be done with a large set of known inhibitors and across myriad protein structures. Once these methods pass a high level of confidence, molecules will be bought and sent to collaborators to be tested.



 _*
Figure 1.* Docked pose of known HIV-1 protease inhibitor TL3 in an HIV-1 protease structure (not shown)._ Spherical representations (accompanied with dots, orange for TL3, green for a water molecule) represent important locations for protein-ligand interactions that are used to evaluate if a molecule may be a good drug candidate. The green sphere represents the location of an important ("flap") water molecule often observed in HIV-1 protease co-crystal structures. The 2 orange spheres directly below the green sphere represent two locations of an interaction with significant amino acids (Asp25) of HIV-1 protease.





 
_*Figure 2.* Same docked pose of TL3 in HIV-1 protease as Figure 1 with top percentage of interactions from 1 experiment (pink spheres) and several predictions (transparent surfaces) for important protein-ligand interactions._ Note that the water molecule (green) and the 2 orange interactions below it are always predicted.

http://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=420Link


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## Arjai (Feb 24, 2015)

*Using one cancer to help defeat many: Mapping Cancer Markers makes progress*
12 Feb 2015



> Results from the first stage of the Mapping Cancer Markers project are helping the researchers identify the markers for lung cancer, as well as improve their research methodology as they move on to analyze other cancers.
> 
> Once again, the Mapping Cancer Markers (MCM) team would like to extend a huge _thank you_ to the World Community Grid members. Although we publish this _thank you_ each update, we are truly grateful for your contribution to this project.
> 
> ...









> _Figure 1: An iterative strategy for biomarker discovery. Work units are processed on World Community Grid. The results are analyzed via a Streams pipeline. This generates a list of high-scoring genes, which combined with biological network information (NAViGaTOR) are used to design new MCM work units targeting areas of interest in signature space._



Full Story


----------



## Arjai (Feb 24, 2015)

*World Community Grid Update - February 2015*
*20 Feb 2015*



> In the past month, you may have noticed a few things that have been completed or updated with the World Community Grid website and servers. We were able to release the Outsmart Ebola Together (OET) application withupdated checkpointing code. This has resulted in an increased flow of work units to our members. At the current pace, we have plenty of work to last us for awhile. We have also released the updated Android application that runs on 4.1+ only. This was released for both the OET and FightAIDS@Home(FAAH) projects.
> 
> We have also successfully completed two hosting environment changes. The first one was for our network infrastructure, and the second one was an update to our database servers. Members have already noticed the increase in speed for daily stats updates, as a result of phase 1 of this upgrade.



More Techy stuff!!


----------



## manofthem (Feb 24, 2015)

Great posts @Arjai! 

Just read (skimmed really) through those articles, and those are exciting updates. 

I have noticed an increase in OET wus lately. Also, I didn't know that UGM did a lot of writes to disk, but apparently they're working on a solution to fix that. Pretty cool stuff.


----------



## Arjai (Feb 24, 2015)

*Making progress against two of the world’s deadliest diseases*
9 Feb 2015



> SummaryThe GO Fight Against Malaria team has just published a paper in which they describe an unexpected benefit of their research: they’ve identified two compounds that could advance the future development of new drugs to treat tuberculosis, including drug-resistant tuberculosis. These results open up a new front in the fight against tuberculosis, which is constantly evolving to resist existing treatments.










> _New fragment-sized inhibitors of the TB drug target called "InhA" were discovered in GO FAM experiment 5. The cyan ball-and-stick molecule in the center shows the predicted binding mode of the most potent inhibitor we discovered, while the InhA enzyme it inhibits (which was the target of the docking calculations) is shown in grey._





> *Paper Title:*
> 
> "A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA"
> 
> ...



Nice!!

More Story here


----------



## Arjai (Feb 24, 2015)

*Computing for Clean Water on the road to publication*
9 Feb 2015
*
*



> SummaryThe Computing for Clean Water team has written a paper describing the results of their research on World Community Grid. They’ve described the novel flow effect that all you volunteers helped discover. Their paper is currently under consideration at a prestigious journal.










> The scientific process has many phases, and one of the most challenging of these is publishing results. What often amounts to years of a scientist’s working life has to be distilled to just a few pages, and done so in a way that is both clear and compelling - at least for other experts in the field. The team behind Computing for Clean Water worked for many months last year on drafting and polishing such an article, which sums up several years of work. Indeed, if we included all the processing time that you, the volunteers, have contributed to the project with your PCs and laptops, we could argue that the article represents many thousands of years of collective effort!





> We have been waiting several months now to see whether we are amongst the lucky few, or whether we will have to revise our article and perhaps consider submitting it to a less demanding journal. Ultimately, the goal is to get the information out there so other people can benefit from it. So there is always a balance between wanting to ensure the broadest possible audience for our results by publishing in a top journal, and simply ensuring that the information is accessible to other scientists, by publishing in a more lenient one. In the case of Computing for Clean Water, it’s fair to say that the whole team behind this project feels an additional responsibility to the large community of volunteers, to do the best possible job of promoting their diligent efforts.
> 
> So thanks again to all the volunteers on Computing for Clean Water for your help and for your patience with this process. Rest assured that you will be the first to know when and where the results will be published.



Best of Luck, to them!!

Rest of the story...


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## Arjai (Feb 26, 2015)

*Database Upgrade: Saturday, February 28, 2015 at 03:00:00 UTC*
*24 Feb 2015*
*
Word for Word:

Summary
Database upgrades will be performed Saturday, February 28th.
	

	
	
		
		

		
		
	


	








World Community Grid will be performing a database upgrade starting Saturday, February 28, 2015 at 03:00:00 UTC. The window for this maintenance activity is estimated to be 16 hours, although we anticipate the actual outage time will be less.

During this database upgrade, volunteer devices may not be able to fetch new research tasks or return completed work for a period of time. However the World Community Grid website will be available.

No action is required by the members, as the BOINC/World Community Grid software application will automatically reconnect to our servers once the upgrade is over.

Thank you again for your participation in World Community Grid!
*
_So, Yea. Let's get those buffers pumped up an extra day. AND Be sure to Manually update Friday Night, or Day, if'n you prefer that! 
_
Proof.
*
*


----------



## Arjai (Feb 27, 2015)

*Seven quadrillion comparisons later, Uncovering Genome Mysteries is just getting started*
*26 Feb 2015*
*




*


> ...The project expects to examine more than 200 million proteins, the majority of which were generated in environmental and ecological studies ranging from bacteria in marine ecosystems in Australia, to Amazon River samples from Brazil. Similarity data from these comparisons will lead to a better understanding of metabolic and structural functions of the predicted proteins in databases, and uncover many new features and cellular processes in microorganisms. Of the expected 20 quadrillion (20,000,000,000,000,000) comparisons in the project, about 36% have been completed thus far, equivalent to almost 8,000 CPU-years of computation.






> Volunteers participating in the UGM project process work units that contain sets of protein sequences predicted from a variety of organisms, and compare those against each other. Every time a significant similarity between two sequences is detected, a line of output is written that contains the coordinates and information on the statistical significance of the similarity. All of the output data together allow us to trace functional predictions of unknown sequences when they are similar to sequences with known functions, and indicate how organisms and their biochemistry, metabolic functions, and other cellular processes relate to one another.





> ...Many applications in health, environment, and agriculture can be attributed to making use of such data. For example, they enabled the development of new strategies to fight pathogens that threaten human and animal health, and development of diagnostics, treatments, and preventions through appropriate design of vaccines. But there are many other applications to be discovered, in agriculture, industry or the environment, through the study of the wide variety of proteins and enzymes.



An awesome undertaking, already making waves!!

Even more good news, here!!


----------



## manofthem (Feb 27, 2015)

Arjai said:


> *Database Upgrade: Saturday, February 28, 2015 at 03:00:00 UTC
> 24 Feb 2015
> 
> Word for Word:
> ...



Wow, 16hrs!  You're right bud, jump the buffer


----------



## twilyth (Mar 14, 2015)

New article on WCG - https://sciencesprings.wordpress.co...g-the-worlds-worst-health-issues-in-it-world/



> Like Dr. Saphire, he prefers the massive number of CPUs available via WCG over an in-house supercomputer. “We have very good computing resources here, but we’re not the only people who use the computing resources at Scripps. We can only get 300 CPUs at any given time, whereas on the World Community Grid we can get tens of thousands of CPUs to use at any given time. So it’s a major boost. We would never even try to do the scope of the kinds of dockings we do using just our local institutional resources,” he said.



The membership numbers it cites though are completely wrong.  We don't have 700k members but less than half a million and of those, only 70k are active - with the numbers on a downward trend.


----------



## DinaAngel (Mar 14, 2015)

I will help fold soon!


----------



## twilyth (Mar 14, 2015)

DinaAngel said:


> I will help fold soon!


Protein folding is a different project although WCG has done some related projects in the past.


----------



## krusha03 (Mar 14, 2015)

DinaAngel said:


> I will help fold soon!


But it's a waste not to get those 12 threads crunching when idle


----------



## DinaAngel (Mar 15, 2015)

why cant i seem to get my gpus to do the cancer project, it said it was the one who had it enabled. also whats optimal work strength?


----------



## krusha03 (Mar 15, 2015)

DinaAngel said:


> why cant i seem to get my gpus to do the cancer project, it said it was the one who had it enabled. also whats optimal work strength?


Afaik there arent any GPU projects only CPU


----------



## manofthem (Mar 15, 2015)

DinaAngel said:


> why cant i seem to get my gpus to do the cancer project, it said it was the one who had it enabled. also whats optimal work strength?





krusha03 said:


> Afaik there arent any GPU projects only CPU



@krusha03 is correct, there is no gpu work for WCG. The previous HCC gpu work ended around May '13, and as of yet there hasn't been any additional gpu enabled project.

The next best thing is to fire up F@H which takes full advantage of gpu. Drop by the F@H team thread if you're interested, simple setup.


----------



## twilyth (Mar 16, 2015)

DinaAngel said:


> why cant i seem to get my gpus to do the cancer project, it said it was the one who had it enabled. also whats optimal work strength?


There's a chance that the Ebola project might have gpu work at some point.  They have a dedicated computer science PhD working on their next phase.  I think in many cases, people don't really have the coding knowledge or experience to put together something suited to high performance computing where you can take advantage of massive parallelization.  But if OET can be set up that way, at least we know that they have someone on staff with the chops to do it.


----------



## manofthem (Mar 16, 2015)

twilyth said:


> There's a chance that the Ebola project might have gpu work at some point.  They have a dedicated computer science PhD working on their next phase.  I think in many cases, people don't really have the coding knowledge or experience to put together something suited to high performance computing where you can take advantage of massive parallelization.  But if OET can be set up that way, at least we know that they have someone on staff with the chops to do it.



That would be fantastic if so! let's hope he can do it, they decide to do it, and we get them!


----------



## Arjai (Mar 17, 2015)

*Top distributed computing projects still hard at work fighting the world's worst health issues
By Andy Patrizio*
ITworld | *March 9, 2015*



> This past fall saw the worst Ebola outbreak ever ravage western Africa, and while medical researchers are trying to find a drug to treat or prevent the disease, the process is long and complicated. That's because you don't just snap your fingers and produce a drug with a virus like Ebola.





> Thanks to thousands of strangers, Ebola researchers are getting the help and computing power they need to shave off the time needed to find new drugs by a few years.





> There is a wide variety of programs, and one of them is aimed at finding drugs to help stop Ebola. It's part of the World Community Grid (WCG), run by IBM and using software developed at the University of California at Berkeley.





> In the case of Ebola, WCG has partnered with The Scripps Institute, a biomedical research group in La Jolla, Calif., to launch Outsmart Ebola Together. The project will target multiple hemorrhagic viruses in the Ebola family, according to Dr. Erica Saphire, the researcher heading the program at Scripps.





> Dr. Art Olson, professor in a department of integrative computational and structural biology at Scripps, has used WCG for the FightAIDS@Home project since 2005, and before that with a now-defunct company called United Devices back in 2000 in one of the first distributed biomedical computing project.





> Like Dr. Saphire, he prefers the massive number of CPUs available via WCG over an in-house supercomputer. "We have very good computing resources here, but we're not the only people who use the computing resources at Scripps. We can only get 300 CPUs at any given time, whereas on the World Community Grid we can get tens of thousands of CPUs to use at any given time.





> A recently disclosed project from the Help Fight Childhood Cancer group at WCG found compounds to cure childhood neuroblastoma, a cancer of the nervous system. Done in conjunction with a group in Japan, they found 7 drug candidates with a 95% likelihood of curing the cancer.





> So it could be that your idle PC may one day save your life.



Nice article about the success of WCG and the work of another, smaller, DC program.

Read it all, Here!


----------



## Arjai (Mar 27, 2015)

*Seven quadrillion comparisons later, Uncovering Genome Mysteries is just getting started
	

	
	
		
		

		
		
	


	


*
*
26 Feb 2015 ?March maybe?
*


> *Summary*
> The Uncovering Genome Mysteries research team has started analyzing results from their massive ongoing project, which is comparing proteins between diverse organisms from around the world. Better understanding of similarities between proteomes should help scientists develop sustainable technologies, renewable materials, productive crops, and new treatments for stubborn diseases.






> The project expects to examine more than 200 million proteins, the majority of which were generated in environmental and ecological studies ranging from bacteria in marine ecosystems in Australia, to Amazon River samples from Brazil.





> Of the expected 20 quadrillion (20,000,000,000,000,000) comparisons in the project, about 36% have been completed thus far, equivalent to almost 8,000 CPU-years of computation.



Incredibly _AWESOME_, no?



> This project involves cooperation between World Community Grid; the laboratory of Dr. Torsten Thomas and his team in the School of Biotechnology and Biomolecular Sciences & Centre for Marine Bio-Innovation at the University of New South Wales, Sydney, Australia; and the laboratory for Functional Genomics and Bioinformatics of Dr. Wim Degrave and his team at the Oswaldo Cruz Foundation – Fiocruz, in Brazil.





> The data resulting from those calculations are starting to be processed at Fiocruz and the University of New South Wales, and will later be presented in a database that will allow researchers to study the relationships between the proteins of all living things, to help develop a much better understanding of organisms in their (biodiverse) environment.





> For example, these might function as insecticides, antibiotics or enzymes that can degrade and eliminate waste or industrial pollutants such as oil or organic chemicals. Enzymes can aid in the synthesis and production of “green chemicals” and biotransformation systems, but also in the production of renewable energy such as bio-alcohols, or in more sophisticated systems through synthetic biology, where the engineering of microorganisms can optimize the production of biopharmaceuticals, green plastics and biofuels.



Yes, I like this. 



> We deeply thank the World Community Grid volunteers who are contributing to this massive effort.



I think I speak for all of us here at TPU, in Thanks to you all for doing such a daunting task that will do nothing more than make this a better place to live, and to live healthy.   

Read ALL about it, Here!


----------



## Arjai (Mar 27, 2015)

*Top distributed computing projects still hard at work fighting the world's worst health issues*

By Andy Patrizio
ITworld*|*March 9, 2015



> This past fall saw the worst Ebola outbreak ever ravage western Africa, and while medical researchers are trying to find a drug to treat or prevent the disease, the process is long and complicated. That's because you don't just snap your fingers and produce a drug with a virus like Ebola.





> Thanks to thousands of strangers, Ebola researchers are getting the help and computing power they need to shave off the time needed to find new drugs by a few years.





> There is a wide variety of programs, and one of them is aimed at finding drugs to help stop Ebola. It's part of the World Community Grid (WCG), run by IBM and using software developed at the University of California at Berkeley.





> *The Ebola hunt*
> In the case of Ebola, WCG has partnered with The Scripps Institute, a biomedical research group in La Jolla, Calif., to launch Outsmart Ebola Together. The project will target multiple hemorrhagic viruses in the Ebola family, according to Dr. Erica Saphire, the researcher heading the program at Scripps.





> Dr. Saphire said the FightAIDS@Home group at Scripps often gets done in a few months what would have taken 10 years otherwise and wants to put the three million devices of WCG to work. "With this massive computational power, we're asking what can we understand that we've never understood before," she said. "It's the most fundamentally important thing my lab has ever done. It's also the biggest."






> Scripps is a large, well-funded institute and could easily afford supercomputers, but Dr. Saphire said WCG is a better option. "It turns out that having hundreds of thousands of computers in parallel accelerates things more than having a supercomputer here," she said.






> *Success stories*
> Dr. Art Olson, professor in a department of integrative computational and structural biology at Scripps, has used WCG for the FightAIDS@Home project since 2005, and before that with a now-defunct company called United Devices back in 2000 in one of the first distributed biomedical computing project.





> Like Dr. Saphire, he prefers the massive number of CPUs available via WCG over an in-house supercomputer. "We have very good computing resources here, but we're not the only people who use the computing resources at Scripps. We can only get 300 CPUs at any given time, whereas on the World Community Grid we can get tens of thousands of CPUs to use at any given time. So it's a major boost. We would never even try to do the scope of the kinds of dockings we do using just our local institutional resources," he said.





> There are other WCG successes besides Scripps. Dr. Berstis said one success story was simulations of carbon nanotubes. Water flows through the tubes 10,000 times more efficiently than thought, so there are now experiments to find less expensive methods of filtering or desalinating water than using the very expensive reverse osmosis filters.


Remember this? All the science talk from these guys made my head spin!! 



> A recently disclosed project from the Help Fight Childhood Cancer group at WCG found compounds to cure childhood neuroblastoma, a cancer of the nervous system. Done in conjunction with a group in Japan, they found 7 drug candidates with a 95% likelihood of curing the cancer.


Absolutely, an Incredible Project Success!! 



> Finally, there was a cancer project that looked at images of biopsies with machine optical scanning. Eventually an algorithm was developed that helped analyze those images to determine if cancer cells are present. "They are as good as humans now so it will help identify if there is cancer present or not much faster," said Dr. Berstis.


Love, LOVE, it!! 



> ...CDx needed a cheap system that can process 590GB of image data generated per pathology slide, and patients can have multiple slides, in less than four minutes....





> Employees leave their computers on when they go home at night. The client PCs tell the servers their computing capabilities and the servers decide which computers get what kinds of workloads. Faster computers get the higher priority in doing the next task, said Robert Tjon, vice president of engineering and developer of the grid.





> "One hundred percent utilization of the computer resources will keep the cost of the overall grid down in terms of space, heat, power, and manpower to keep the system up. We also like the fact that Intel invests billions to make the computer cheaper and faster and we only have to pay the price of a regular, popular consumer item," he said.
> 
> So it could be that your idle PC may one day save your life.



A lot of US, already know this stuff. However, it is nice to see more, and more, news sites pick this up. Spreadin' the WORD!!
Amen!!


The WHOLE of it, Aqui!




P.S. I thought this was a little familiar! I think I quoted the post better this time, though!


----------



## krusha03 (Mar 27, 2015)

I love when i read there is an actual progress by the work being done by our PCs


----------



## Arjai (Apr 6, 2015)

Not sure if many of you are aware of the *Research Page on WCG*.

It shows the amount of progress on each active Project.

It can be found, Here!


----------



## manofthem (Apr 6, 2015)

Arjai said:


> Not sure if many of you are aware of the *Research Page on WCG*.
> 
> It shows the amount of progress on each active Project.
> 
> It can be found, Here!



Thanks for the link, didn't know about that. Seems I should get back in on some CEP2 live before it closes out. It looks like I have some time but I only have like 180 days on that project, not much at all.


----------



## Peter1986C (Apr 6, 2015)

Arjai said:


> Not sure if many of you are aware of the *Research Page on WCG*.
> 
> It shows the amount of progress on each active Project.
> 
> It can be found, Here!


I know about it, but thanked you because it is good that you brought it up.


----------



## Arjai (Apr 8, 2015)

This has been floating around the "Notices" tabs on my machines. Thought to myself, "Self, why not add a post to the Talking Points?"

So, here we are!

BOINC released a new version of it's Manager. 7.4.42.

The Notes....



> *Changes in 7.4.42*
> 
> Update localizations
> Screensaver fix for when the client is suspended
> ...


 How's about that?!?! 



Get it here, while it's still got the fresh BOINC smell to it!!
http://boinc.berkeley.edu/wiki/Release_Notes


----------



## Arjai (Apr 15, 2015)

*The past and the potential of World Community Grid: A Q&A with senior team *



*members.*

*14 Apr 2015 *



> *Summary*
> World Community Grid senior scientist Viktors Berstis and technical lead Keith Uplinger participated in a Question & Answer session with one of the winners of the Decade of Discovery recruitment competition held last November.



Long and Interesting talk, HERE


----------



## twilyth (Apr 15, 2015)

Oh wow - they talked to one user - woo-hoo.

Now maybe if they conducted another survey with feedback from the community as to what should actually go into the survey, I might be impressed.  But if they think that stunts like this are going to make any difference in terms of people leaving, my guess is that they're going to be severely disappointed.


----------



## Arjai (Apr 16, 2015)

Um, OK. So, maybe that was not the most interesting interview. However, I do kind of like the outside the box thinking process. I would like to leave it to the scientist's to invent the Ideas, rather than a couple of WCG cronies. Either way, it is something WCG has not done before. That I know of, in my short WCG life. That said, perhaps they can improve upon it, now that the first one is under their belt.

As far as numbers...WCG has yet to become sexy.

WCG should set up some sexy business cards, in multiple languages, to sell on their site. We, the unsexy Crunchers could drop them off with our kids, at the coffee shops or even drop them in the halls of the Mall you do your morning walks in. 

Kids today, or rather, in my little world, seem to have a disconnect with everything outside of their phone. Or, incessant complaining about that ugly girl at school.

I'm no marketing major but, somebody, somewhere, knows what kids today will think is sexy. iPhone's figured it out, get somebody to reach out to this generation, that is not a parental figure, and get them on board!

Rant over.


----------



## Heaven7 (Apr 16, 2015)

Arjai said:


> We, the unsexy Crunchers


Yup, that's us!  And proud of it, too. No need for sexy business cards (let me see one), but to get more people to join the WCG. Telling those kids their own phone will make more points crunching than their friend's could probably heat up the place... just my 2 cents.


----------



## twilyth (Apr 16, 2015)

There are a lot of reasons why participation in WCG is falling.  People are spending more time on their phones, which are really pretty power computers but WCG hasn't done much to promote the android app - at least not that I'm aware of.  But the main problem is that WCG has done nothing to cultivate a community.  Look at a site like Gaia online if you want to see how stimulate involvement.  WCG could do similar things like giving WCG "gold" to people who participate and then letting them use that to buy virtual goods on the site.  It would cost nothing except the development costs.

But IBM isn't willing to promote WCG and even less willing to spend any more money on it than they have to.  A lot of that has to do with the company itself not doing well.  Maybe if their bets on Watson and cloud services pays off they'll be more willing to throw some cash at WCG, but unless and until they do something, the number of active members is going to continue to decline.


----------



## Peter1986C (Apr 17, 2015)

- Computer knowledge needed.
- Juice is pricey for many folks.
- Science, but also DC is above the minds of the common folk.
- Too many tinfoilers say pills are just moneymakers.
- Too many of us are (afraid to be) called "that weirdo with his computer"


----------



## Arjai (Apr 25, 2015)

*Turning virtual results into real-world treatments for schistosoma
	

	
	
		
		

		
		
	


	


*

*22 Apr 2015




			Summary
		
Click to expand...

*


> The research team has combed through the grid computing results of Say No to Schistosoma, using several additional analytical techniques to help them select promising compounds. The three most promising substances are undergoing additional testing with the hope of identifying the most effective potential treatments for schistosomiasis.


*
*


> Thanks to World Community Grid volunteers who contributed to Say No to Schistosoma, we have selected compounds from the grid-based screening for further testing. We collaborated with various laboratories to perform further computer analysis of 24 compounds using several software tools.





> Quantitative Structure-activity relationship (QSAR) models were used to further evaluate the results. For more about QSAR, see here and here.





Spoiler



We wish to thank and acknowledge the help of World Community Grid volunteers and IBM for making this project possible. We are grateful that we can continue our efforts to find new treatments for schistosomiasis.


----------



## Arjai (Apr 25, 2015)

*System Updates: Sunday, April 26, 2015 at 01:00:00 UTC
	

	
	
		
		

		
			



*



> World Community Grid will be performing system updates starting *Sunday, April 26, 2015 at 01:00 UTC.* The window for this maintenance activity is estimated to be 8 hours, although we anticipate the actual outage time will be less. During the system updates, volunteer devices may not be able to fetch new research tasks or return completed work for a period of time.





> No action is required by the members, as the BOINC/World Community Grid software application will automatically reconnect to our servers once the update is over.





> *Thank you again for your participation in World Community Grid!*



Updates Completed! Yea!  4/5/2015 7:54 PM CT US


----------



## Arjai (May 5, 2015)

*Research task availability resumes following unexpected outage
	

	
	
		
		

		
		
	


	




4 May 2015
*



> Starting on May 3rd, no work units were distributed across all World Community Grid projects due to technical issues which have now been resolved.





> On May 3rd, World Community Grid experienced a technical issue with the scripts which generate research tasks to distribute to our volunteers. As a result, no new work units were available across all projects. We have now resolved this issue and members should be able to receive new tasks.br>
> We sincerely apologize for this unexpected outage and we will be modifying our work unit generation process accordingly and increase our monitoring going forward.
> 
> Thanks for your participation!



OK, see the next post...


----------



## Arjai (May 5, 2015)

*Firmware Upgrade: Tuesday, May 5, 2015 at 14:00:00 UTC*





*4 May 2015*



> World Community Grid will be performing a firmware upgrade starting*Tuesday, May 5, 2015 at 14:00:00 UTC.* The window for this maintenance activity is estimated to be 6 hours, although we anticipate the actual outage time to be very short.





> During this firmware upgrade, the website will become unavailable and volunteer devices will not be able to send or receive research tasks for a few short periods of time.
> 
> No action is required by the members, as the BOINC/World Community Grid software application will automatically reconnect to our servers once the upgrade is over.



I hope everybody has enough work now, to get through this mess!!


----------



## Peter1986C (May 5, 2015)

*A milestone and a roadmap: progress in the fight against Ebola*

*By: The Outsmart Ebola Together research team*

_5 May 2015 _ 





 Summary Thanks to the huge level of support from World Community Grid, the team at the Scripps Research Institute has already received most of the matching data for the first target protein of the Ebola virus. While this data is being analyzed, the search now moves to another related protein with potential to help the fight against hemorrhagic fevers. 
	

	
	
		
		

		
		
	


	







Outsmart Ebola Together, a long-term scientific project whose goal is to find new drugs for curing Ebola and related life-threatening viral hemorrhagic fevers, is still in its early stages, but we've already reached a major milestone. Our first target was the newly revealed receptor-binding site of the Ebola surface protein, GP. GP is the molecule Ebola virus uses to fuse with a human cell and force its way inside. Armed with a new model of the binding site, and with the vast resources of World Community Grid, we set out to test this site against drugs that could potentially bond with it and prevent Ebola infection. This stage of work is now close to complete:  we have received back from World Community Grid most of the data for the planned matchings of the Ebola surface protein against 5.4 million candidate chemical compounds.

We are now analyzing this data. Drugs that simulations predict will bind well with the Ebola surface protein will go on to a next round of experiments, conducted in the lab with actual proteins and actual drug molecules. Our analysis may also yield general insights about how classes of drugs interact with viral proteins.

Moreover, we are excited to announce that we are beginning work on a second target protein, the Lassa virus nucleoprotein.

Like Ebola, Lassa is a "Group V" virus: in other words, both are viruses that have at their core a genome composed of "negative-sense", single-stranded RNA. Both viruses produce a deadly hemorrhagic fever. While Lassa has received less publicity than Ebola, it is a more consistent killer. There are hundreds of thousands of cases of Lassa Fever every year in Western Africa, with tens of thousands of deaths. It is also the viral hemorrhagic fever most frequently transported out of Africa to the United States and Europe. There are no treatments approved for use in Lassa virus infection. Identification of a potent inhibitor of Lassa virus is imperative for public health.

The Lassa virus's nucleoprotein (NP) is so named because its first discovered function is to bind with, and so enclose and protect, the virus's central strand of RNA. However, Lassa NP is a complex beast that has other functions as well. In particular, our lab discovered that the NP (almost paradoxically) is also responsible for digesting double-stranded RNA (dsRNA) created by the virus itself. Having gained entry to a human cell, the Lassa virus must copy its single-stranded RNA in order to produce viral proteins and replicate itself. This requires creating double-stranded RNA. However, the virus must keep this work secret. The presence of double-stranded RNA in the cytoplasm is a clear sign of a viral infection, and human cells are smart enough to detect this, triggering an effective immune response. Hence the importance of the Lassa NP, which rips apart the virus's own dsRNA byproducts in order to keep its activities secret.

We approach Lassa NP armed with our lab's crystallographic structures, which clearly identify the shape of the NP and the site where the NP carries out its function of destroying double-stranded RNA. This site is a large cavity in the side of the protein; it is negatively charged, but is also bordered by a positively charged, protruding protein "arm". These distinctive features are key to the site's binding with dsRNA, and, we believe, should make it a good candidate for screenings against possible drugs.




Figure: Our lab's structure for the Lassa NP protein. Portions important to the protein's function of digesting double-stranded RNA include the "cavity" (glowing, particularly a manganese atom that helps bond RNA) and the adjacent "arm" (yellow).

We will now prepare this target protein for matchings against millions of drugs using the resources of the World Community Grid. As with our previous matchings against the Ebola surface protein, drugs that do well in this "virtual screening" will go on to further tests with actual proteins in the lab. While this work is difficult and carries no guarantees, we hope that it will lead to the discovery of a drug that can prevent the Lassa NP from hiding the virus's double-stranded RNA. We have already determined that doing this would allow human cells to detect and act against the Lassa virus more promptly and effectively, potentially saving lives.

It’s amazing to us that we’ve been able to receive so many results so quickly, and we want to say thank you to everyone in the World Community Grid family who helped make this possible. There is much work ahead, but it’s immensely encouraging to know that we have the resources available to carry it out.

_-----_

Source


----------



## twilyth (May 8, 2015)

It looks like we definitely have 3-4 more weeks of faah work.  Here's a post from one of the researchers.


----------



## Arjai (May 12, 2015)

*The hard work of making discoveries useful*




*11 May 2015* 



> *Summary*
> Even as World Community Grid computations continue, the team behind the Clean Energy Project is busy improving their database structure, making their results more accessible to the wider scientific community, and authoring papers to disseminate the methodology behind the project. _Also, look out for their new project website coming soon!_


 Emphasis, mine.



> The work Ed and Kewei have done on machine learning has been put into a paper which has just been submitted for review - we will keep you updated on how it progresses. Thanks to Ed and Kewei for putting this together. Ed and Miguel will present this work in a poster at the New England Machine Learning Day on May 18th, alongside the work they have done on sampling methods, which could improve the number of high-performance molecules that projects like the CEP produce.





> Kai has been working hard on putting together a new CEP website, which - whilst not ready for release quite yet - should be something exciting in the near future! The website will feature much more searching capacity (something made possible by the new database structure we have put in) and even more information about each molecule.





> One of our new undergraduates, Wendy, has just received funding to work in the lab this summer and will use this new database structure as part of her summer project....She will also be working with another of our new undergraduates, Claudia, on new ways to visualize the CEP data. Ed has worked with some experts in 3D rendering at Harvard to produce new animations that explain what the CEP is about; we are now looking to extend this idea into providing a new way to interact with the database.





> Sadly, Gregor has now finished his Masters studies with us, and left to go back to the ETH in Zurich....Ed is now putting two papers together based upon this work,...Thank you for all your hard work Gregor - come visit us soon!





> As ever, we are blown away by the support that all of you have given our project. We are so grateful for your continued support - we simply would not be able to do it without you!
> 
> Keep Crunching!!
> Your Harvard CEP Team



Nice update to a Project I see_ changing the way we get Energy_, in a *BIG* way, *Very Soon!!*

_Rock ON CEP!!


_


----------



## twilyth (May 12, 2015)

It looks like the FA@H project should run until the middle of June or so.  But as the post says, this is an estimate and assumes that we don't get a lot of people running only faah to make badges.  





My own guess is that all of the people who are really concerned about making a badge are already all in.  Plus there have been some posts by people saying that they'll quit the project as soon as they hit their goals to save wu's for people who are still working toward a goal.

This is one of the things I love about WCG.  There are so many people who want to help and will do whatever they can to help.  It's inspiring.  I just wish that WCG and IBM would realize this and do more to help stimulate a real community there - sort of like what we have here with our team.


----------



## Arjai (May 24, 2015)

*End of the Help Conquer Cancer project
	

	
	
		
		

		
		
	


	


*
*29 May 2013 
*
Blast from the past. First GPU Project End...



> *Summary*
> Thanks to the generous contribution of computing power from our members, the Help Conquer Cancer project has concluded.





> The Help Conquer Cancer project was launched on November 1, 2007 and was the first World Community Grid project that allowed our volunteers to contribute using their machines' graphics cards. While this project was active, World Community Grid members processed over 500 million results, which required nearly 115,000 CPU-years of computing power. This work would not have been possible without World Community Grid, because it would have taken hundreds of years to run using the computing resources available to the researchers at the Ontario Cancer Institute. Thanks to World Community Grid members, the computations were completed in less than 6 years.



500 Million Results.
115,000 CPU Years.
Less than 6 years runtime.

Awesome.

Let's hope for more GPU WU's.
Is this not enough of a testament to how well it works?

Reminisce.



.


----------



## twilyth (May 25, 2015)

I'm hoping that the next phases of Fight Aids and OET will be gpu oriented, but that's just a hope.  I haven't seen anything yet to suggest that.  But the power of gpgpu's in high performance computing (HPC) is so significant that it really can't be ignored any more.  Hopefully the researchers looking to use the grid have been developing the chops to use all of the resources wcg can offer.


----------



## Arjai (Jun 6, 2015)

*Post grid calculations continue to yield progress and inspire new methods against deadly diseases*

5 Jun 2015



> *Summary*
> The GO Fight Against Malaria project team has been making good use of the calculations which were conducted by our volunteers and that concluded in summer 2013. Their findings have sparked progress against not only malaria, but tuberculosis as well. They have one paper published and two more about to be submitted. They continue their work to publish their findings, after which they will resume the analysis on and experimental assessment of the massive amount of data generated by World Community Grid volunteers.






​


> Dear fellow World Community Grid volunteers,
> 
> The Global Online Fight Against Malaria (GO FAM) project was launched on the IBM World Community Grid on November 16, 2011. The first phase of the docking calculations was completed in July of 2013, and since then we have been busy analyzing, testing, publishing, and extending these results, which show promise against both malaria and tuberculosis. For a summary of the project, see our last project update from July 2014.





> *Update on: GO FAM experiment leads to the discovery of new hits against a key drug target for tuberculosis*
> 
> In our last update in July of 2014 (see the link above), we mentioned that we were halfway done writing our first research paper that utilized GO FAM results. On January 30, 2015, that paper was published in the _Journal of Chemical Information and Modeling_. In relation to this paper, we also created an animation of the predicted binding mode of the best inhibitor we discovered in that GO FAM experiment versus a critical drug target for treating tuberculosis.





> *Update on: Discovery of additional new hits against a target for drug-resistant tuberculosis*
> 
> Last July we discussed the initial progress from analyzing and testing the results of GO FAM experiment 9: specifically, the subset of these results that were generated against a key drug target for treating tuberculosis, which is an enzyme called “InhA.” We mentioned that derivatives of the best two “hits” we discovered had been designed in the Freundlich lab. Dr. Shao-Gang Li and Dr. Steven Paget have now synthesized several different “analogs” of these two new hits.





> *Creating a computational tool that predicts metabolic stability*
> 
> “Translational research” is the process of advancing research from the basic science (fundamental background studies) stage to the development of new drugs or other tools that can improve public health. A critical hurdle to the progress of translational research against many different diseases, including malaria, tuberculosis, cancer, and Alzheimer’s disease, involves proving that a compound is both effective and non-toxic in animal studies that serve as an early model/surrogate for the afflicted human patients.





> *Thank you to all our supporters*
> 
> We hope you’re as excited as we are to see the many different ways that your donated computing time has helped advance important scientific research. As is so often the case, the eventual impact of the research wasn’t known at the beginning, and we only arrived at these beneficial outcomes because you cared enough to support our project. On behalf of the entire team, thank you, and please check back for future updates!



OK, this is just a snippet of the original post on WCG.  Very interesting stuff coming out of this Project!


----------



## manofthem (Jun 6, 2015)

At times like these, I wish I had been able to do more for that project


----------



## Arjai (Jun 23, 2015)

*In 10 years, 'crowdsourced computing' has changed the world; now it's tackling Ebola*
*Wednesday 10 June 2015*

The "Independent" out of the UK posted an article about WCG's 10 Years.



> What do doctors, alien enthusiasts and you and I have in common? We can all play a crucial role in discovering cures for diseases. While some of the above may not have the expertise – or, indeed, brain power – to make scientific discoveries for themselves, all of our computers and mobile phones can help researchers while we sleep.









> Since the project's inception, volunteers on the WCG have powered two dozen research projects, donating more than a million years of computing time collectively, and performing more than 2.2 billion calculations for scientific research. In the case of Ebola, scientists are busy analysing how promising chemical compounds react when they encounter the virus....



More good stuff, HERE!


----------



## Arjai (Jul 7, 2015)

*Enhancing the potential for nanotechnology to improve access to clean water for millions
	

	
	
		
		

		
		
	


	


*
*
6 Jul 2015 
*


> *Summary*
> The Computing for Clean Water team has discovered how water can pass through tiny carbon nanotubes much more easily than previously predicted. This groundbreaking understanding of a fundamental physical process holds potential for improving access to clean water for millions through more efficient water filtration and desalination, as well as possible applications in clean energy and medicine. This discovery has been published in Nature Nanotechnology, the world's most prestigious nanotechnology journal.


*
*


> The size of the tubes allows water molecules to pass through, but blocks larger pathogens and contaminants, purifying the water. They are so small that the scientific community initially expected that water would move through them too slowly to be useful. However, earlier experiments showed that water sometimes passes through them much more easily than expected.






> Increased flow could mean a more efficient filter, but due to lack of sufficient computing power, until now there had been a wide gap between what scientists could understand from computer simulations, and what they could actually measure in experiments. Our research efforts focused on bridging this gap. By running massive computer simulations on World Community Grid with your help, we discovered that certain kinds of natural vibrations called phonons, under specific conditions, can lead to a 300%+ increased rate of diffusion (a kind of flow) of water through carbon nanotubes, compared to previous theoretical predictions.





> This work was a result of a global collaboration between researchers from China, Switzerland, Israel, the United Kingdom and Australia. Thanks to your participation, we were able to accomplish in just a few years what would have taken 40,000 years of computing on a single computer. On behalf of the entire team, I want to say thank you to the 150,000 World Community Grid volunteers who helped us run this research. This breakthrough belongs to you as well.







_Members of the Computing for Clean Water team: Zhiping Xu, Ming Ma Quanshui Zheng and Francois Grey​_More Awesome, Here!


----------



## Arjai (Jul 15, 2015)

*Exceptional early results in the fight against Leishmaniasis*

*12 Jul 2015 *



> *Summary*
> The Drug Search for Leishmaniasis team has completed in vitro lab testing of the 10 top-rated compounds identified during screening, and have found that 4 of those 10 have very interesting properties that could point the way to new therapies. The post-processing of results continues, with the hope of identifying even more promising compounds for future lab and in vivo testing.





> Last year, we updated you on the progress our team has made in filtering the computational results from our time on World Community Grid and identifying promising candidate compounds to test in the lab. Since then, we have completed the filtering process and identified over 100 compounds that the simulations predicted should bind effectively to the target PDB:3MJY protein in the Leishmaniasis parasite.





> Due to limited funding, we focused on the 10 compounds with the highest predicted rating, and found that 4 of them do in fact show positive results in in vitro tests, with one showing an exceptionally promising result. This means that in vitro the compounds kill the parasites efficiently while not affecting human cells.







Spoiler: Problem...



Due to the high success rate of our screen (i.e. 40% of the compounds we tested showed good _in vitro_ results), we think it would be very worthwhile to test the remaining compounds that we identified in our original screen, and we are still seeking funding to make that possible. In addition, the next step for the compounds already tested _in vitro_ is to move to _in vivo_ testing, and this process requires additional time and money. Unfortunately there are no crowdsourced initiatives like World Community Grid that can support actual in-lab testing!





> *Team news*
> 
> As our project carries on from year to year, it is inevitable that some team members will reach personal milestones along the way.
> 
> Andres Florez is finishing his PhD in Germany and is applying for a Post doc in Netherlands. Rodrigo Ochoa has finished his Master’s study and is currently working on measuring the stability of interactions between test compounds and the _Leishmania_ protein.





> As we continue with our research, we’re constantly reminded of how valuable it is to have received such support from World Community Grid volunteers. Thank you for helping the fight against Leishmaniasis; we hope to have future work that can benefit from volunteer computing as well.



Let's hope that this amazing breakthrough finds some money to get some more testing done!!

It would be a shame to have this sit on a shelf, while people are suffering!!


----------



## Arjai (Jul 15, 2015)

*Security upgrade, Monday, July 20, 2015*


*14 Jul 2015*



> *Summary*
> We will be updating our security certificates on Monday, July 20th, 2015. Volunteers using older versions of the software may need to upgrade.





> World Community Grid will be upgrading our SSL (security) certificates on*Monday, July 20th, 2015.* The majority of our volunteers will not be impacted by this change.





> Certain older versions of BOINC or World Community Grid software will not be compatible with our new certificates. After we upgrade the certificates, volunteers using older versions of the software may not be able upload, download, request or report research work. To ensure that you will not be impacted, please upgrade to the latest version of the software.





> If you need assistance, please post in the BOINC Agent Support forum.



Hmm, wonder what they mean by, "older versions"? As in, how older?


----------



## Norton (Jul 15, 2015)

Arjai said:


> *Security upgrade, Monday, July 20, 2015
> 14 Jul 2015*
> Hmm, wonder what they mean by, "older versions"? As in, how older?



Wondering if this will affect the software on my Linux rigs? They use 7.0.27 atm....


----------



## Arjai (Jul 16, 2015)

Norton said:


> Wondering if this will affect the software on my Linux rigs? They use 7.0.27 atm....


Most of the talk on the WCG Forum is about version 6.10.xx and earlier.

I have 6.12.33 on my Mint Lisa P4 Cruncher. Not sure about that either. I posted in their forum last night but, no time to check it. Gotta get my post done and hit the sack!!


----------



## Arjai (Jul 16, 2015)

*An exciting video about the recent Computing for Clean Water breakthrough.
	

	
	
		
		

		
		
	


	


*












> With the help of World Community Grid volunteers, researchers reveal their breakthrough discovery of how nanotechnology could be used to improve access to clean water for the 1 billion people around the world who lack it.


----------



## Arjai (Aug 5, 2015)

*Firmware upgrade: Saturday, August 8, 2015 at 01:00 UTC
	

	
	
		
		

		
		
	


	



4 Aug 2015*


> *Summary*
> A firmware upgrade will be performed on Saturday, August 8th.
> 
> 
> ...





> During this firmware upgrade, the website will become unavailable and volunteer devices will not be able to send or receive research tasks for a few short periods of time.
> 
> No action is required by the members, as the BOINC/World Community Grid software application will automatically reconnect to our servers once the upgrade is over. Thank you again for you participation in World Community Grid



Up the cache on Friday, don't wanna run out if they blow the grid!! 

EDIT Nothing official, haven't looked, but around 11 am Central, 8/8/15, I dumped, about 60 WU's, my sandbag, no problems. So, I believe the switch over is complete and working!! IBM, seems to be good about these things, Imagine that! 

EDIT.2 It's Official!! 





> [ The firmware updates have completed successfully at 0830 UTC. Thank you for your patience -Uplinger ]


----------



## Arjai (Aug 8, 2015)

*Open science: sharing our clean water breakthrough data with all scientists
	

	
	
		
		

		
		
	


	


*
*
5 Aug 2015
*


> *Summary*
> The Computing for Clean Water team is pleased to announce that the breakthrough paper we published online last month on the use of nanotechnology for more efficient water filtration will be available in the August print edition of Nature Nanotechnology. With our results published, we're now making the underlying data available to other interested scientists and discussing the attention our work has gotten, both from international experts in the field and from the world media.






> *Worldwide attention*
> 
> Finally, we have been overwhelmed by the incredible amount of attention this story has gotten, not only in the scientific community but on social media and in traditional media as well. Our story has garnered over 60 media hits in over 15 countries and half a dozen languages, including in China, Israel, Australia, the UK, the Netherlands, and Belgium. Our subject might be considered quite technical, so it's wonderful to see that so many people in so many places understand the significance of our discovery and can see the link between our simulations and the development of real-world solutions to pressing problems.





> On behalf of the whole team, thank you once again to all the World Community Grid volunteers who made it possible for us to do this research. As scientists, it's not every day we can say we worked with over 150,000 people around the world to get our results. It's been an inspiring and humbling experience. Each of you has contributed to the research, and we hope you share with us a sense of how groundbreaking this approach truly was, _and how such research has the potential to improve the lives of millions of people._




This is why I Crunch, and well, now, Fold.  We all know how I get about the Daily Numbers, but I really do understand What and Why we do this! I also am extremely Lucky to have landed this job, too! 

The WCG News is like Christmas, to me, every week, or so!! 

Posts like these, showing the work getting REAL World uses that ARE changing things, for the better, are the BEST!!

If I could, I would fly to Geneva and give all these Scientists a Monster sized Chocolate Cookie, for each of them. Well, Probably also a fine Bottle of Red Wine, to go with the Chocolate (oak-y and Italian come to mind!).

 *<I want one of these that says, WCG, also!!*


----------



## Arjai (Aug 18, 2015)

*Help World Community Grid make it onstage at SXSW 2016 *




*17 Aug 2015*



> *Summary*
> World Community Grid is competing for a chance to present at the SXSW Interactive 2016 conference and we need your help to get there! Vote today to help us tell this influential crowd how we’re using crowdsourced computing, donated by you, to take on critical humanitarian challenges, such as improving access to clean water.










> World Community Grid has a chance to present at the South by Southwest (SXSW) Interactive 2016 conference, and *your vote* can help make sure we make it onstage.





> SXSW Interactive is one part of a prominent set of annual festivals and conferences related to music, film and technology. The event is one of the biggest technology conferences in the world and consists of a series of presentations and panels that aim to be “an incubator of cutting-edge technologies and digital creativity.” If World Community Grid is chosen to present, we’ll be able to expose our work and your accomplishments to a huge, tech-savvy and high-profile audience, as well as to the media outlets that cover SXSW. We aim to point to recent successes like the Computing for Clean Water announcement to prove how World Community Grid as an initiative, and volunteer computing as a concept, deliver _real_ results.



*DO IT!!! NOW!!!*

Sign up with an _email,_ confirm the account _from your email._ Come back here and click on the *YOUR VOTE* to go back to the _WCG page and *Thumbs up!!!*_

Easy Peasy and NO CATCH!! *Let's ALL*, *I mean ALL of us vote this thing IN!!* If you're really bold, mentian you are a *TPU'er* and we want _more intelligent computer savvy people on OUR Crunching Team!


Full Story, here_


----------



## Arjai (Aug 27, 2015)

*One step closer to identifying lung cancer biomarkers
	

	
	
		
		

		
		
	


	


*

*19 Aug 2015*



> *Summary*
> Although work continues, enough data has already been processed to let the Mapping Cancer Markers team begin identifying high-scoring signatures and associating them with particular lung cancer biomarkers. The ultimate goal is to find signatures that distinguish many types of cancer, giving physicians and researchers another tool to improve detection, treatment and patient outcomes.






> *A new stage of MCM lung cancer biomarker discovery*
> 
> After a long first stage of exploratory analysis, Mapping Cancer Markers(MCM) began a new, more targeted stage of lung cancer analysis in April 2015. Processing results from the first stage revealed a subset of approximately 1% of the biomarkers that frequently occur in high-scoring signatures. The second stage of the MCM lung cancer study will focus on signatures drawn from this subset of biomarkers.





> Enough second-stage results have been returned to allow us to start the preliminary analysis. One main goal of the second stage is to discover high-performing cancer signatures. We used results from the first stage to narrow the field of potential biomarkers from 22,000+ to a subset of 223. Figure 1 shows how the average cancer-distinguishing ability of the stage-2 gene signatures has improved considerably, compared to signatures discovered in the initial stage.









> *Figure 1. Distribution of signature scores, stage 1 vs. stage 2, by size.*_Signature frequencies are drawn in blue for stage 1, black for stage 2. Note the increase in the quality of scores in both stages between signatures of length 20 vs. length 10, as well as increase in frequency of higher quality scores._





> *A note on run times of research tasks*
> 
> Some of you may have noticed above-average run times of work units in this new stage of MCM. We are working to make run times more consistent and predictable; however, this job is made more difficult as this stage of the research requires changing work unit designs more frequently than before. The design of new work units will also depend in part on results of earlier second-stage results. Consequently, the turnaround time for benchmarking and calibrating work units may limit our success at stabilizing run times. We trust that our wonderful volunteers will be able to continue contributing results no matter what work units we provide, but we wanted to let you know what to expect. Once again, thank you for making our research possible, and please stay tuned for future announcements!





> *Media*
> 
> The Jurisica lab and the MCM1 project scientists were recently interviewed for a Drug Discovery News article about the difficulties of cancer biomarker discovery and validation: Signs of intelligent biomarkers by Randall C Willis, DDNews.
> Igor was also interviewed for the NewsTalk Radio 1010 in June 2015 about the work on discovering prognostic and predictive cancer signatures.
> World Community Grid was also covered by Genevieve Roberts in The Independent on June 10: In 10 years, 'crowdsourced computing' has changed the world; now it's tackling Ebola



The Full Story HERE. There is Plenty more on the linked WCG site. All of this is Great news!! I certainly hope they can help destroy this awful destroyer of lives! 

WCG is the awesome-ist!! Thanks to IBM for have the foresight to start what is becoming the most amazing use of computers, in my world, ever!!


----------



## Arjai (Aug 31, 2015)

*Analyzing crystals to help fight cancer
	

	
	
		
		

		
		
	


	


*
*
28 Aug 2015 
*


> *Summary*
> Behind-the-scenes work continues on the Help Conquer Cancer project - the team is analyzing millions of protein crystallization images processed by World Community Grid volunteers, with the hope of finding patterns that will help researchers build better cancer screening tools.






> Dear World Community Grid volunteers:
> 
> We continue to analyze the millions of protein-crystallization images that you processed as part of Help Conquer Cancer (HCC), with the end goal of gaining insight into the crystallization process. In turn, this will enable us to crystalize cancer and other disease-related proteins, determine their structure, function, and design drugs accordingly. We aim to identify non-trivial, interesting and ultimately useful patterns in this large and valuable data set.





> We have been working on some novel analysis angles with a visiting student from Denmark, and a new student is expected to start working on the project in the Fall 2015. We therefore expect to be able to give you more detailed results in the next HCC update, which we will provide in a few months.





> In the meantime, here are some recent cancer-related publications and media coverage by our group, which all relate to our effort to identify better algorithms for determining prognostic/predictive signatures and work towards finding and validating novel treatment options for cancer patients. Combined, results from these papers feeds into our new work units for the MCM project, and in turn, results from the MCM projects feed into this research.



For the Pubs List and another paragraph, or two, Original report is HERE.

I did not know that MCM and HCC were collaborating and/ or the same team.

I do know, it is awesome-ness that these two projects are feeding each other!


----------



## Arjai (Aug 31, 2015)

*A new version of BOINC is available. (7.6.6)*
*
8/30/2015 

Download it!!

HERE!!

More BOINCNESS!!


*


----------



## Arjai (Sep 3, 2015)

*Summer is a great time to focus on solar energy*





*2 Sep 2015* 



> *Summary*
> A busy summer has led to several advances in the Clean Energy Project: new team members, new database search functionality, new publications and (hopefully) new funding!







_Front: Wendy Woodin, Dr. Ed Pyzer-Knapp, Dipti Jasrasaria
Back: Dr. Steven Lopez _​


> The Clean Energy Project (CEP) team has been working very hard this summer, and have had a number of successes to show for it.
> 
> We are very happy to introduce the latest addition to our team - Dr. Steven Lopez has joined us from UCLA, where he worked for Ken Houk on computational organic chemistry. Steven's knowledge of chemical reactivity, and reaction mechanisms will be invaluable to the team as we strive to deliver libraries of molecules which are synthetically accessible.






> We are also very happy to say that Ed and Kewei have had a manuscript accepted into the journal Advanced Functional Materials. Advanced Functional Materials is one of the most prestigious journals for this area of study so we are very excited to have been accepted! We will share the details of the manuscript once it gets published.





> Finally, we have just submitted a couple of grant proposals for continuing to fund the CEP in the years to come. Grant proposals are incredibly important for keeping our project running, and so we will keep our fingers crossed for a successful response!



And For YOU: 


> As ever, we are very appreciative for the computing time you donate since without it, we would be unable to perform the research which goes on in the CEP. So, thank you again...and keep crunching!



For more, about Wendy and Dipti, or for the original story, go HERE!

This is Great news for the CEP Team! I am hoping to have an opportunity, in my lifetime, to purchase and use a plant based solar panel from this research. I have about 40 years left, if I am Lucky, so, hopefully this can come true!!


----------



## mjkmike (Sep 6, 2015)

thks kid keep up the good work.  I like to tell everyone what I do bye showing one post you did for the team.


----------



## Arjai (Oct 1, 2015)

*Pioneering new techniques in the fight against HIV
	

	
	
		
		

		
			



*

*30 Sep 2015* 

*By: Dr. Arthur Olson *
Professor, The Scripps Research Institute



> *Summary*
> The team behind FightAIDS@Home is launching Phase 2 of the project, putting to use a more accurate simulation tool to help them determine which of the Phase 1 results merit further investigation. Phase 2 will also be applying this analysis technique at an unprecedented scale, which if proven successful, can benefit medical research not only for HIV _but many other diseases as well. _


 emphasis, throughout, is mine.





_Model of a complete HIV Virion with all of the component molecules._​


> There have been some amazing advances in the fight against the human immunodeficiency virus (HIV), including treatments that have improved and extended millions of lives. But the fight continues - HIV is continually mutating, and as it does it evolves resistance to existing treatments. With tens of millions of people currently living with HIV, and millions more infected every year, the search for more effective HIV treatments is as critical as ever. Our team is therefore_ launching a new phase of HIV research_ to build on the success of the first phase and more accurately analyze the most promising drug candidates we've identified so far.





> or almost a decade, FightAIDS@Home has contributed to this fight by exploring different ways of disabling the virus. *World Community Grid members *have provided my team an _unprecedented amount of computing power, _enabling us to investigate a huge number of potential cures. To date, volunteers have performed over *20 billion* comparisons between candidate chemicals and different binding sites on the virus.





> _The massive success of FightAIDS@Home_ has also generated a new challenge: thousands of potential 'hits' (chemicals that might form the basis of effective drugs) - a handful of which we're synthesizing for additional testing. But because there are so many, it is prohibitively expensive and time consuming to synthesize and lab test all of those chemicals. The project now needs a new computational method to double-check the promising Phase 1 results, and ensure that only the most thoroughly vetted and probable candidate compounds proceed for further investigation. Phase 2 of FightAIDS@Home will address both of these goals: refining the Phase 1 results and validating the technology needed to make more accurate simulations.





> ...a new analysis technique called *BEDAM* (Binding Energy Distribution Analysis Method).... BEDAM has proven effective at carrying out more accurate simulations in computational contests, but thanks to *World Community Grid volunteers*, we now have an opportunity to apply it to analyze molecules at an _unprecedented scale_. This is important because if successful, these techniques *can be applied to other drug discovery searches beyond HIV.*







_Collaborating labs for the HIVE Center. Prof. Art Olson directs the Center and collaborators include Prof. Ron Levy, who is partnering with the FightAIDS@Home project._​


> Phase 2 is more radical than its name suggests - *World Community Grid volunteers* have the opportunity to help us validate a new promising research paradigm that can help the search for treatments _for many diseases_, not just HIV. It's only because of the _commitment shown by volunteers_ that FightAIDS@Home has been able to accomplish so much thus far. We hope we can count on your continued support as we continue this important journey.




_Awesome Sauce!!_ Once again the results we crunch are evolving into more than what was being researched. These stories of success, over and over, help me pay my electric bill. I, and the rest of you Crunchers, am changing the World, one WU at a time (or rather 8, or more, at a time. ).

If IBM did nothing else, but WCG, they would be considered a success! When the history books get written, WCG, and IBM, will be there. _So will all of us who helped!_ 

_Folding will be in there, too._ Standford, I believe, was using our GPU's before IBM and WCG. I could be wrong? Anyway, Their work is groundbreaking, also. 

I hope I live long enough to see Ebola gone, HIV/Aids gone, Malaria gone, Cancer considered no worse than the Flu and have a All Natural Solar Panel running my Clean Water cooled Photon Laptop.

*Keep Crunching! Toast those GPU's Folding! Your small sacrifice is changing our lives for the Better!
*​


----------



## Arjai (Oct 9, 2015)

*Finding new avenues to attack Ebola 
	

	
	
		
		

		
		
	


	


*

*6 Oct 2015 *

By: *Dr. Erica Ollmann Saphire, PhD*
_The Scripps Research Institute_



> *Summary*
> Efforts to simulate matches between candidate compounds and one key Ebola virus protein _are largely complete._ Simulations of matches against another, _newly discovered target protein_ are beginning now. Even as simulation work continues, the team is beginning to analyze these results and home in on compounds that could form the basis for effective new drugs against _Ebola and other related diseases._ Thanks to your help, and a new grant, the work is proceeding well.


 Emphasis is mine, throughout.





_Two Protein Data Bank structures for the ribonuclease H domain of HIV reverse transcriptase. We used structural and experimental data for this domain to optimize our analysis protocols for the Lassa NP exonuclease site.
(?)_​


> Thanks to the efforts of thousands of World Community Grid members, my team has continued to make progress on Outsmart Ebola Together, a project whose goal is to find new drugs for curing Ebola and related life-threatening viral hemorrhagic fevers.


 I understand this part! 



> Outsmart Ebola Together began with a study of potential drug attacks against the receptor-binding site of the Ebola surface glycoprotein (GP). We then announced the start of work on a _second drug target:_ the nucleoprotein (NP) of Lassa Fever virus. Specifically, we are looking for drugs that attack the newly discovered "exonuclease site" of Lassa NP. This exonuclease site helps conceal the virus's presence from the infected human cell by destroying the virus's own excess production of double-stranded RNA.
> 
> We have since prepared research tasks for testing the Lassa NP exonuclease site against *millions of potential drugs.* These tasks are now ready for use, and will be _sent out to World Community Grid volunteers over the coming months._


 OK, that makes sense, the picture is starting to focus...



> At this stage in the project, we’ve gathered enough data that we need to begin focusing on analysis procedures for the data already returned by World Community Grid volunteers. We must analyze the data for both the Ebola GP receptor-binding site and the Lassa NP exonuclease site; and our analysis procedures must be sufficient to filter out false positives from the large quantity of results returned.


 As has become the Norm, WCG Volunteers have flooded the Researchers with massive amounts of Data. Now, is when the doors are open and there will be amazing new discoveries flowing through it! 



> We are also happy to announce that a $50,000 grant to support this work has been provided by the Robert Wood Johnson Foundation President’s Grant Fund of the Princeton Area Community Foundation. With this grant and the vast computing resources of World Community Grid, our way to the successful completion of the project is clear.





> As always, we close with a *thank-you to the volunteers* who have run this work for us. As you can see, we’ve already made significant progress but there is much work still to do. _*Make sure you’re signed up to contribute to this project, and spread the word about our lifesaving work!*_



 *Well done WCG,* and to all those,_ like us here at TPU_, that _Crunch Numbers to make the World a Better place!!

 Link to Original Story_


----------



## Silvertigo (Oct 24, 2015)

I just noticed total crunching up-time for TPU has reached 5,200 years!...which got me thinking...
and if I figure things correctly, this is number is calculated overall from the use of one PC crunching?



If correct this means theoretically or broadly speaking that one person has been crunching
on one PC for TPU since the Bronze age!


5,300 years ago: (3300 BC): Bronze Age begins in the Near East Newgrange is built in Ireland. Hakra Phase of the Indus Valley Civilization begins in the Indian Sub-continent.
5,300-5,000 years ago (3300-3000 BC): Saflieni phase in Maltese prehistory
5,200 years ago: (3200 BC): Writing is invented in Sumer, triggering the beginning of history
Pretty amazing I thought!

And this is not including what time the Folding@Home crew do as well!

Source: https://en.wikipedia.org/wiki/Timeline_of_human_prehistory


----------



## Arjai (Feb 11, 2016)

*World Community Grid to Appear at South by Southwest Interactive 2016 
	

	
	
		
		

		
		
	


	


*

*21 Jan 2016 

*


> *Summary*
> Thanks to votes from many World Community Grid volunteers, we were selected to present at South by Southwest on March 13, 2016 in Austin, Texas.


*
Cool!
*


> What do clean water, nanotechnology, volunteer computing, and the world's greatest group of volunteers have in common? They are all part of World Community Grid's presentation at this year's South by Southwest Interactive conference (SXSW).
> 
> Dr. Francois Grey, a researcher on the Computing for Clean Water project, will co-present with Juan Hindo, World Community Grid's project manager. Together, they will talk about how the Computing for Clean Water team used World Community Grid to simulate water flow through carbon nanotubes. This led to a breakthrough understanding of a fundamental physical process which could lead to improved access to clean water for millions of people worldwide


*
*


> SXSW's advisory board and staff received over 4000 submissions from people applying to present at this influential event....
> 
> _Due in large part to the votes and supportive comments from hundreds of World Community Grid volunteers, we were selected, and a new and influential audience will now hear about the power and potential of volunteer computing._


*
Full Story, HERE*


----------



## manofthem (Feb 24, 2016)

Looks like the WCG is looking to get into the Zika issue. Embarrassingly, I wasn't even aware of this Zika til about a week when an online friend brought it up, and then it scared me considering Florida has ridiculous mosquitos 

Anyway, I got this email from *WCG* though dated 2 weeks ago, but I found it interesting 



			
				WCG said:
			
		

> *We're Ready to Help Fight Zika*
> 
> 
> 
> ...


----------



## manofthem (Feb 27, 2016)

Here's a little about Chris Elsass, a musician, science buff, and volunteer, who got involved with the World Community Grid.

"Sometimes you want to help others but you just don't know how," he says. "It is very important to me to 'be green' as much as I can, and I was attracted to the fact that World Community Grid's projects are humanitarian." 



> *Musician, Science Buff, Volunteer*
> *26 Feb 2016 *
> 
> 
> ...


*Link*


----------



## manofthem (Mar 10, 2016)

*Researchers Identify Key Proteins in the Fight Against Leishmaniasis
	

	
	
		
		

		
		
	


	


*



> Leishmaniasis, which is one of the most neglected tropical diseases in the world, infects more than two million people in 97 countries. There are no available vaccines to prevent the disease, and the treatments can cause severe side effects, including death. Furthermore, drug-resistant parasites are causing major problems in many endemic countries. For these reasons, there is an urgent need for new, safe and inexpensive drug compounds.
> 
> Since our last update in July 2015, we have been moving forward in several key areas: 1) we are conducting further research on the findings from Drug Search for Leishmaniasis, which has identified three important proteins, 2) we are publishing and presenting our results, and 3) *we are planning for a second phase of the project, which may also involve World Community Grid. *




Looks like another project will be in bound eventually 

WCG News Article


----------



## hat (Mar 10, 2016)

I still want to see an epilepsy project on WCG. It's a serious, crippling disease which affects a lot more people than you might think.


----------



## manofthem (Mar 23, 2016)

*33.4 Million Virtual Experiments and Counting: An Update on Outsmart Ebola Together
	

	
	
		
		

		
		
	


	


*


> *By: Dr. Erica Ollmann Saphire, PhD*
> The Scripps Research Institute
> 
> *21 Mar 2016 *
> ...















> So far, 33.4 million of these virtual experiments have been conducted by World Community Grid volunteers, the percentage of tasks completed is increasing, and will probably reach 100% soon. We are currently seeking a computational scientist (and funding to support him or her) to filter this tremendous body of work into the most meaningful compounds we can test in a laboratory.



*Full WCG News Article*


----------



## jboydgolfer (Mar 23, 2016)

looks like i should stop sleeping in the yard  after my nightly "blood baths"  

mosquitos around here come @ You like storm troopers...

these insect borne diseases always get me a little too freaked out , srsly . i have to add some humor to it. makes my skin crawl/.


----------



## manofthem (Apr 9, 2016)

*World Community Grid Needs Your Vote to Win a Webby Award*!
	

	
	
		
		

		
		
	


	









> World Community Grid has been selected as one of five nominees for the prestigious Webby Awards in the Corporate Social Responsibility category, which honors corporations with a commitment to help make our world a better place. You can help us win this coveted award by voting today.
> 
> 
> Voting for the Webby's People's Voice Award ends on April 21, so *please vote today and help us spread the word*. Thanks to everyone for your support!




Full WCG News Article


----------



## manofthem (Apr 13, 2016)

*Uncovering Genome Mysteries Hopes to Shed Light on Zika and Other Viruses
	

	
	
		
		

		
		
	


	


*












> *By: Wim Degrave, Ph.D.*
> Laboratório de Genômica Funcional e Bioinformática Instituto Oswaldo Cruz - Fiocruz
> 
> *12 Apr 2016
> ...



WCG News Article


----------



## manofthem (Apr 24, 2016)

*Mapping Cancer Markers Now Examining Ovarian Cancer
	

	
	
		
		

		
		
	


	







By: The Mapping Cancer Markers research team 

21 Apr 2016    *




Summary
The Mapping Cancer Markers project now includes markers for the most common form of ovarian cancer, with a goal to understand the how this disease progresses from early-stage to late-stage.














The Mapping Cancer Markers project, which had been concentrating on lung cancer, now includes work units related to ovarian cancer. The researchers are seeking to identify the genes that are important in differentiating between early-stage and late-stage ovarian cancer.

Full Article Here


----------



## Arjai (May 27, 2016)

*Help an International Research Team Fight the Zika Virus
	

	
	
		
		

		
		
	


	




By: Dr. Carolina Horta Andrade 
Universidade Federal de Goiás, Brazil 

19 May 2016  

Summary*
The Zika virus was relatively unknown _until 2015_, when it made headlines due its rapid spread and its link to severe brain-related deficiencies in newborns born to mothers who contracted the virus while pregnant. Dr. Carolina Horta Andrade, the principal investigator for the new OpenZika project, discusses how she and an international team of researchers are using World Community Grid to accelerate the search for an effective anti-Zika treatment.
*














*


> *Introduction*
> 
> Few people had heard of the Zika virus before 2015, when it began rapidly spreading in the Americas, particularly in Brazil. The virus is mostly spread by _Aedes aegypti_ mosquitoes, although sexual and blood transmission are also possible. A currently unknown percentage of pregnant women who have contracted the Zika virus have given birth to infants with a condition called _microcephaly_, which results in severe brain development issues. In other cases, adults and children who contract the Zika virus have suffered _paralysis and other neurological problems._
> 
> *Currently, there is no treatment for the Zika virus and no vaccine.* Given that Zika has quickly become an international public health concern, my team and I are working with researchers here in Brazil as well as in the United States to look for possible treatments, and _we are using World Community Grid to accelerate our project._


*
*


> ...As a scientist and a citizen of Brazil, which has been greatly affected by Zika, I am committed to the fight against the virus, but _my team and I will need the help of World Community Grid volunteers_ to provide the massive computational power required for our search for a Zika treatment.





> In January of 2016, when the Zika virus outbreak in Brazil became alarming, Sean and I decided to expand our dengue research, and we included the Zika virus in our work, since these two diseases are from the same family of viruses.
> 
> 
> 
> ...



*



			The Open Zika Research Team
		
Click to expand...

*


> After Sean and I began our work on the Zika virus, he introduced me to World Community Grid. Sean has also collaborated with Dr. Alexander Perryman of Rutgers University, New Jersey Medical School, who was previously at The Scripps Research Institute where he played a key role in two World Community Grid projects: Fight AIDS@Home and GO Fight Against Malaria. Sean and Alex are both co-principal investigators with me on the OpenZika project.
> 
> 
> 
> ...





> The research team also includes my colleagues at UFG, Dr. Rodolpho Braga, Dr. Melina Mottin and Dr. Roosevelt Silva; Dr. Jair L. Siqueira-Neto from University of California, San Diego; and *Dr. Wim Degrave* of the Oswaldo Cruz Foundation in Brazil, who is already working with World Community Grid on the Uncovering Genome Mysteries project, among others.
> 
> 
> 
> ...


*



			Our Goals
		
Click to expand...

*


> The Open Zika project on World Community Grid aims to identify drug candidates to treat the Zika virus in people who have been infected.
> 
> ...Our work on World Community Grid is only the first step in the larger project of discovering a new drug to fight the Zika virus. Next, we will analyze the data obtained from World Community Grid’s virtual screening to choose the compounds that show the most promise.
> 
> ...



_I love the Fact that so many previous project people are collaborating with current project people and even using data from other projects to engage in REAL WORLD solutions to problems. It makes me feel so good to read these News Releases, often they are above my understanding, technical terms and all, but, I am good with the context. *Do things that help people.* This is, at the same time, the best thing I do *and* the easiest. *WCG*, constantly amazing, even after all these years! LOL._
*

The whole thing...*


----------



## Arjai (Dec 12, 2016)

Hi guys! It's been awhile, eh? So, my plan is, for the time being, to update this thread on Thursdays. At least until I RE-start school! Then it will be a crap shoot. Hopefully I can settle into a regular weekly post, even while in school. Unsure of my schedules, work and school, so I will have to wait and see. So, look for some updates here on Thursday!!


----------



## Arjai (Dec 15, 2016)

*FightAIDS@Home Team Re-Opens Phase 1





By: The FightAIDS@Home research team 

1 Dec 2016  *

*Summary*
We are happy to announce that we are re-opening Phase 1 of the Fight AIDS@Home project. In collaboration with World Community Grid, and thanks to their affiliated volunteers around the globe, High Throughput Virtual Screening will be performed by targeting the HIV-1 capsid protein with the goal of discovering new chemical compounds to defeat the AIDS virus (HIV). Read more in this update.

*Background*

During the maturation of the HIV virus, the HIV-1 capsid protein (CA) assembles with thousands of copies to forms the capsid core [ref 1] with a characteristic conical shape (see Figure 1C). This core encloses the RNA viral genome. Upon the entry of the HIV in host cells, the capsid core is released into the cytoplasm, and it dissociates in connection with the reverse transcription in a not completely understood process. This leads to the importation of DNA viral genome in the host cell’s nucleus, where it is integrated in the host DNA to finalize the infection.




The critical role of CA protein, in early and late stages of the viral replication life cycle, has led to recent efforts on drug development, targeting the mature form of the protein. Currently, none of these molecules are used in clinic, and some face natural polymorphism and resistant mutations [ref 2]. Therefore, continued development of drugs targeting the CA protein is still needed...

*High Throughput Virtual Screening*

The FightAIDS@Home team is working with _World Community Grid_ to find active compounds which could attach to the CA proteins and mediate the assembly of the capsid core. This computational experiment will be performed using the docking software _AutoDock VINA_ [ref 3].

Thanks to the volunteers, around *2 million molecules will be screened across ~50 conformations of the capsid protein*, and hopefully lead to a reduced selection of molecules. This will be the starting point of a drug discovery process targeting the HIV-1 capsid protein.

*Four pockets of interest*

Based on X-ray structures of CA protein, models of the core, and computational analysis of their flexibility, four pockets of interest have been selected on the surface of the hexamer assembly (see Figure 2).




​More technical stuff, Here!

My interpretation, our work has helped them move forward in Giant Leaps. But, now that they have narrowed down a main culprit, they need us again! Let's give them the stuff they need! Help wave Goodbye to this nasty Virus!!


----------



## Arjai (Dec 15, 2016)

*Meet a World Community Grid Team Member: Keith Uplinger

6 Dec 2016
*
*Summary*
World Community Grid's technical lead not only relishes tackling all sorts of difficult challenges, he enjoys helping others do so as well. Meet Keith Uplinger in this article.

Whether he's coaching his children's sports teams, or helping scientists deploy a new sampling protocol on World Community Grid, Keith Uplinger is always up for a challenge, especially when it means helping others.






_Earlier this year, Keith co-starred in a video of our _
_acceptance speech for the People's Voice Webby Award._
​Keith grew up in a technology-oriented family in Austin, Texas, where his father worked for IBM. Always drawn to math and technology, Keith began programming while still in grade school. Once his family installed a dedicated internet connection, he became even more focused. "I was online almost 24/7, programming and researching 
computer components," he says. 



> He earned a bachelor's degree in computer science at Texas Tech University, and began interning for IBM during his sophomore year. From the beginning, his work focused on grid technology, which involves linking computer resources from multiple locations to reach a common goal. Upon graduation, he was hired full-time to work at World Community Grid, which had recently launched.
> 
> Since then, he has touched nearly all parts of World Community Grid's platform, including developing project screensavers, server management, running the testing environment, website development, and working closely with the BOINC group to help with the open source platform on which World Community Grid runs. "I've stayed with World Community Grid for the challenges," Keith says. "Many people work on a single product, but our scope is broader. Every few months we have a new project that needs to go out to large groups of people all over the world."



Keith is currently World Community Grid's technical lead. His latest work-related challenge is leading World Community Grid's work on asynchronous replica exchange, a new sampling protocol being developed by the research team for FightAIDS@Home - Phase 2. He explains, "When World Community Grid receives completed work units (research tasks) back from volunteers' devices, we don't send the results back to the researchers until the entire batch of work units is complete. This isn't always ideal for researchers like the Fight AIDS@Home team, who need to process their results more quickly. With asynchronous replica exchange, these researchers will get their data back more quickly, which will help them analyze their data more quickly."







To the many volunteers that he has served over the years, Keith says, "Thanks for your ongoing efforts to help find answers to science's toughest questions. I hope we can grow to millions of volunteers, and someday I'd like to see us cure cancer."
​I am sure we have the same, *'Thanks'*, and respect for _Keith_ and all the _IBM staffers_ that make *WCG* work so well. 

_No?_

      rest of article, Here!


----------



## Arjai (Dec 15, 2016)

​*Release Notes for BOINC 7.6*

*



*





*Get it NOW!!!

Can you smell the freshness? ***​


----------



## Arjai (Dec 15, 2016)

*Big Data and Big Plans: Next Steps for Uncovering Genome Mysteries*
*
By: Wim Degrave, Ph.D. 
Laboratório de Genômica Funcional e Bioinformática Instituto Oswaldo Cruz - Fiocruz 

15 Dec 2016  
*
*Summary*
World Community Grid’s role in the Uncovering Genome Mysteries project has ended, but the research team’s work continues as they analyze the results of the calculations and prepare to apply the data to medical, agricultural, and other real-world applications.










​*Background*

The Uncovering Genome Mysteries project began on _World Community Grid in November 2014_, with the aim of analyzing protein sequences to help understand how organisms function and interact with each other and the environment. The project began with *120 million* predicted protein sequences from close to *150,000 organisms*. These protein sequences and organisms represent a wide variety of known or uncharacterised life forms in our biosphere. They came from organisms in samples taken from a range of environments, including water and soil, as well as on and inside plants and animals. Additionally, *70 million sequences*, derived from prospective analysis of genetic information from microbial marine ecosystems from Australia were added, with the objective to add to the identification of possible functionalities of these sequences. In July 2015, we added yet another *20 million newly predicted sequences of proteins.*

_Thanks to the enthusiastic contributions of more than 76,000 World Community Grid volunteers, all of these protein sequences were analyzed in approximately 24 months. (!!!!!)(Yea Baby!)

*Results to Date and Plans for the Future*

So, what is next? The research team at Fiocruz has spent the last year designing and testing new algorithms to transform the output of the comparisons with distance calculations between the genomes of the organisms included. Scientific literature cites many different ways to do this, depending on the purpose of the analysis and the views on evolutionary biology.

The results of the Uncovering Genome Mysteries can be summarized as follows:





*More complete and precise information is now available on the structure and function of proteins encoded by living organisms in our biosphere.* More proteins are being studied and experimented with each day in the thousands of laboratories around the world, and by using results from the comparison performed through the project, functional parallels can be drawn for proteins that show structural similarity between organisms. This is particularly valuable when predicted protein fragments are compared from uncharacterised organisms, for example in environmental and ecology studies, such as those originated from the laboratory of co-investigator Dr. Torsten Thomas, and his team from the Centre for Marine Bio-Innovation & the School of Biological, Earth and Environmental Sciences at the University of New South Wales, Sydney, Australia. The resulting database with these functional annotations will be made publicly available as the next version of our protein comparison database, ProteinWorldDB, in the coming months.


Click to expand...

_


> *Through comparison, new protein functions are discovered that can have medical, agricultural, technological or industrial applications.* These can be as new biopharmaceuticals, bioinsecticides, biodegradation of waste, or enzymes for production of chemicals, but especially when part of new biochemical pathways in cells, that help laboratories to develop new green chemistry or energy production, or biosynthesis and transformation of new drugs. This also adds to the growing knowledge of biotechnology and synthetic biology.





> *The group at Fiocruz has developed new ways to compare genomes from different organisms. *Traditionally, such analyses consider what is conserved between genomes, resulting in distance calculations that are used for phylogenetic studies and the estimation of evolutionary relationships between organisms. However, we feel that this is only part of the picture, and the Fiocruz team designed a new algorithm that also takes differences into account. This was coupled to a new visualization method for such comparisons, resulting in a markedly faster way to add new data to the picture. We hope that this method will enable us to keep track of data from new organisms that becomes available, adding results to the growing ProteinWorld DBdatabase.



_That's a lot of 1's!! Seriously though, something in the page formatting did that when I copy/paste-ed it...?
_
*Thank you to all World Community Grid volunteers who supported this project, and we plan to keep in touch as we have further news about our ongoing research.*
*
Interesting Stuffs, Here!!
*


----------



## Arjai (Dec 29, 2016)

*Community Achievements in 2016*





*27 Dec 2016*

*Summary*
We're grateful for the volunteers and scientists who worked with us this year to launch two new research efforts, make progress on existing projects, and spread the word about volunteer computing to new audiences. Here are some of the highlights of 2016, which wouldn't be possible without each of you.

Two new research projects, two awards, several conferences...and volunteers around the globe whose support made all of this progress possible. Because of you, 2016 was a great year for World Community Grid! Below are a few of this year's highlights.

_*I essentially Copy and Pasted the whole article here! I couldn't decide where to edit anything out! So, here it is, 2016 WGC view!*_

*Helping Stop a Global Killer *
Tuberculosis is one of the world's deadliest disease, killing approximately 1.5 million people every year. In March, researchers at The University of Nottingham launched Help Stop TB on World Community Grid to study the molecular structure of the bacterium that causes tuberculosis, so that scientists can learn how to overcome it.

*Not sure where this Project is. I have not had any work from them since I restarted, a few weeks ago. In fact this is ALL I have ever had..."
Help Stop TB 6,281 3 0:002:01:15:56 *









*Reaching a New Audience*
Thanks to votes from volunteers and supporters, an influential audience at South by Southwest (SXSW) learned how World Community Grid volunteers have supported humanitarian research projects since 2004, and heard how these volunteers helped scientists make a breakthrough that could bring clean water to millions. Listen to audio of our full presentation, which was given in March, or read about our experience.





_Researcher Francois Grey, 
who was part of the Computing for Clean Water project, 
and program manager Juan Hindo presented the results 
of the project at South by Southwest 2016. _​*One day, I will get down to Austin, WHEN THIS is there, also!! SXSW, sounds like a blast! Austin is a great city, also!!
*
*Searching for Potential Treatments for Zika*
The Zika virus began spreading rapidly through the Americas in 2015. In 2016, it continued moving north and was also reported in Asia. There is no effective treatment for Zika, no vaccine, and the virus as been linked to serious complications, including lifelong brain-related issues for infants whose mothers contract Zika while pregnant. In response to volunteer requests, we looked for a project to fight the virus, and in May, an international team of researchers launched the OpenZika project on World Community Grid to search through millions of chemical compounds for those that may become treatments.

*OK, so, I love this woman's voice. *










*Getting Inspired by Changemakers*
Program manager Juan Hindo was invited to attend South by South Lawn 2016 at the White House in October. This first-time event brought together leaders in art, technology, innovation, and social change who are helping to improve the world. Read about Juan's experience and how it inspired us to re-ssue our call for research projects that address climate change.

*I wonder if THIS will ever happen, again.* 




​
*Winning Awards*
We appreciate awards because they recognize and raise awareness for the important work made possible by World Community Grid volunteers.

Thanks to votes from volunteers and supporters, we were honored to receive a People's Voice Webby Award in the Corporate and Social Responsiblity category. This award recognized our new online experience to help people learn about and join World Community Grid, which helped improve our sign-up rate. The Webby statuette traveled around the U.S. this summer and fall to spend time with each team member, as shown in the video below.

*Funny? Cute? It is a fun video, though.*









We also received a D&AD Wood Pencil Impact Award, which was created by the advertising industry to recognize programs that have a societal impact that helps change the status quo.

*THIS AWARD is a good thing, however, the linkable site, sucks. Doesn't even give a short paragraph about WCG.* 

*Thank You*
_Twelve years_, _27 projects_, and (as of November) _3 billion research results_ later, we are very grateful to the volunteers all over the world who are supporting basic science by donating unused computing time. Thanks for making 2016 a year of new beginnings and continued progress. Stay tuned for exciting news in early 2017!

*Keep Crunching!!
*


----------



## Arjai (Jan 16, 2017)

Nearly 3 weeks, tomorrow, and no new News. I will keep scanning the site, every couple days but it has been slow going recently. Apparently, I like to think, we have overwhelmed the researchers with data and they have their heads down working overtime to disseminate it!

Either way, Go Team TPU!

Keep Crunching!!


----------



## Arjai (Jan 19, 2017)

*Meet a World Community Grid Team Member: Jonathan Armstrong



*

*19 Jan 2017*

*Summary*
This Texan's role with World Community Grid focuses on helping the researchers' work run smoothly, and he's just as focused outside of work. Meet Jonathan!

*Hi Jon!!  
*



> Originally hailing from the San Antonio area, Jonathan Armstrong is a lifelong Texan. He received a bachelor's degree in computer engineering from Texas Tech University, and interned at IBM during his senior year. Immediately after graduation, he was hired to work at IBM's Austin office in the services division.







_Jonathan in IBM's Austin, Texas office_​


> "Our focus was on disruptive technologies," he says. "In 2001, when I started working at IBM, these technologies included virtualization, automation, and grid computing." For several years, Jonathan was involved in proof of concept and customer engagement work on these technologies, helping to determine how they might have the best real-world applications for IBM's various markets. He also mentored a college student named *Keith Uplinger* (scroll up to see Keith!) who later became one of his World Community Grid teammates.







_Jonathon checking out his new quadcopter drone._​




A Drone's view of Jonathon!​


> Jonathan and his wife have been married for 19 years. They have three young children who are the primary focus of their time and energy outside of work. When he finds time he enjoys listening to live music around Austin. Jonathan also loves the outdoors, and spends time flying his new quadcopter drone.
> 
> Like all World Community Grid team members, Jonathan is grateful for the people who help make the work possible. He says, “A big thanks to the volunteers. Without you and the resources you contribute, we couldn’t do what we do.”



*More about Jonathon, HERE!

Thanks Jonathon*


----------



## Arjai (Jan 27, 2017)

*Outsmart Ebola Together Approaches Completion of Initial Phase*

By: Dr. Hal Wasserman

The Scripps Research Institute

*26 Jan 2017  *

*Summary*
The Outsmart Ebola Together research team has conducted an enormous number of virtual docking experiments, and they are now ready to embark on a new stage of their research.




​


> The Ebola virus killed many thousands of people in 2014 during the largest outbreak of the disease since it was first discovered in 1976. Significantly, research has shown that the virus's long incubation period and our highly connected modern world could allow the virus to spread to new geographies and across oceans._ Currently, there are no approved treatments or vaccines for this deadly disease, and the search for an effective antiviral drug to treat the disease is a high priority. _
> 
> Outsmart Ebola Together is now *approaching completion of its first phase,* having conducted hundreds of thousands of docking computations. In this phase, we have simulated the binding of potential small-molecule drugs against atomic structures of proteins of the filovirus family. We have in particular targeted the receptor binding site (RBS) of the Ebola virus glycoprotein (GP), which plays a key role in viral entry into human cells.





> *Our study now expands to consider multiple stages in the dynamic molecular transformations of GP and other Ebola proteins. These transformations are essential to the viral life cycle, and therefore represent an ideal target for the design of effective antiviral drugs.*
> 
> _*Thank you to all volunteers who have supported this project.*_



More Info HERE!

*I am sure we all want to Thank YOU for doing this research and God-Speed to finding the cure, i.e. antiviral, to this devastating VIRUS!!*

_*Crunch ON!!*_


----------



## Arjai (Feb 10, 2017)

OK guy and Gals, I will be back on Sunday to update this thread with the New and Exciting News from WCG.

I was having issues with my lappytop this evening. Apparently the Kingston SSD card, used as a cache, by Windows, has died or, is well on it's way. It causes major hiccups and before I, finally, waited it out I had rebooted from a frozen screen 3 separate times! 

Upshot is, now I have no time to post anything but this, coffee shop is closing! So, Sunday it is!!

Then, sometime next week it is time to pay the local comp shop, I can do it...Don't wanna spend the time...school and work leave little time for sleep. Doing this swap, is my sleep time deprived even more.  I will just pony up and support the local shop!

See you Sunday!!


----------



## Arjai (Feb 20, 2017)

Well, some dismaying news. One of my favorite bosses, laidback, friendly and of an even demeaner with a good sense of humor, was fired. Of course, the guy who fired him did not have a plan in place. He's a dweeb. 

Upshot? I am attending school, leave at 6:28 am, then work until close, 7pm, if lucky, and get home after eight, often 8:30. Since the firing of my boss, I lost my Thursday off. I now only get Sundays. A lot to do in one day a week, including resting! So, my post's will be a little erratic for a few weeks as they find and replace my boss and then have to deal with the inevitable new Sheriff rules and scheduling! There are so few obvious changes that could make this job worth doing happily. I won't get into it, rather I will use the little time I now have, on Holiday from School, not work, to update the News!! Stay tuned...


----------



## Arjai (Feb 20, 2017)

*The Importance of Protein Social Behavior




*

*13 Feb 2017*



> *Summary*
> 
> Which proteins are most likely to interact with other proteins, and how might these interactions affect disease, and life itself? Results from data computed by World Community Grid are being used to help create a protein sociability index, which could help future advances in biology and medicine.
> 
> ...



_I have never met *Dr. Carbone.* I am sure, I would fall deeply in love with her. I should probably *avoid meeting her.* _




​

> How different proteins interact with each other is important to understanding life and disease processes. The first steps of identifying protein interactions include computationally searching for complementary surfaces among the collection of proteins, because those are more likely to interact, as was done using World Community Grid for the Help Cure Muscular Dystrophy project.
> 
> However, some proteins tend to evaluate as sticking to many proteins, hiding their true interactions. Dr. Carbone and her co-investigators found an algorithm to improve the accuracy of identifying true protein interactions using a sociability factor to compensate for the apparent "stickiness" of some proteins.


​


> ...Sociability is proved to be more discriminative than geometrical shape of interacting surfaces. This work brings to light new avenues of investigation on protein interaction principles which could become fundamental to solving this difficult computational problem of high interest for biology and medicine.
> 
> Thank you to all World Community Grid volunteers who contributed to the Help Cure Muscular Dystrophy project!



_"Sociability is proved to be more discriminative than geometrical shape of interacting surfaces." Imagine THAT! Even Proteins are Social!!_



> Technical abstract:
> 
> Cells are interactive living systems where proteins movements, interactions and regulation are substantially free from centralized management. How protein physico-chemical and geometrical properties determine who interact with whom remains far from fully understood.




More article and tech abstract and perhaps more "physico-chemical," talk! ...HERE!


​


----------



## twilyth (Feb 20, 2017)

Just as an aside to this, many proteins are intrinsically disordered.  IOW, they don't have a fixed 3 dimensional structure.  They change shape depending on the environment and the molecules they encounter.  Other proteins are partially disordered so that they have certain regions with a fixed structure but other regions that are fluid.  This is something that has only been realized in recent years (since about 2001) and researchers are only beginning to get a handle on.

https://en.wikipedia.org/wiki/Intrinsically_disordered_proteins


----------



## Arjai (Feb 26, 2017)

Well, imagine my surprise! One, our fearless leader has returned! Hip, Hip, Hooray! @Norton is back to guide us!! 

The second big Surprise? No alerts from WCG in the BOINC Mgr. Me has a sad. One of the things I look forward to, on my single day off (soon to change back to two days, essentially I am getting my Thu. night's back!), is to hit up my favorite coffee shop and post up to update this thread.

Also, @twilyth , Thanks! I always enjoy your pearls of knowledge! I am unsure where you find this stuff but, 9 out 10, you amaze me and make me think! I believe one of the benefits of IQ is admiring different types and flavors of knowledge.

Anyway, I hope everyone is doing well. I am going to enjoy my late breakfast and cruise around here for a bit.

See you all, next time I have time!


----------



## twilyth (Feb 26, 2017)

Thanks for the kind words.  I try to read as much as I can about science and technology and have a particular interest in molecular biology.  The exact mechanisms behind how we function as living machines has always been fascinating to me.  I'm glad you find these things interesting too.  It's nice to be involved with a group of people who are contributing to the advancement of knowledge in these sorts of areas.


----------



## Arjai (Mar 5, 2017)

Hmmm, 2 weeks of silence from WCG...I wonder what is in the works! If it is taking this long to produce, could be a doozy! Or, could be they are just stuck in the doldrums of working hard on the new project and have no time to set aside informing us of all the greatness we do!!

That's fine. We need their work as they need ours. I am content with that, although it does make this thread a bit of a bore. 

I will continue to keep my eyes open, at least once a week, to any new postings on WCG. Thanks everyone for the Thanks and the visits to this thread. Makes me feel good. 

Take Care everyone!


----------



## Arjai (Mar 19, 2017)

Well, still nothing from WCG. So, just a "Hello!" and I hope everyone is doing well!

On a personal note, I should hit 1.8 Million BOINC points, soon! Despite not having anything but my Lappy-Top Crunching! The little i5 that could! 

Take Care Team TPU!!


----------



## Arjai (Mar 19, 2017)

Well, Looky here! WCG must have heard my moaning!!

*Meet a World Community Grid Team Member: Al Seippel
	

	
	
		
		

		
		
	


	


*

*14 Mar 2017 *

*Summary*
This team member was an experienced coder by the time he was in his teens, and began working for IBM while still in college. Meet _Al Seippel_ in this article.









> Al Seippel may have been destined for a career in computer science from a very young age. He was born and raised in Austin, Texas, where his father worked for IBM. "I definitely grew up around computers and always found them interesting," says Al." We had an original IBM PC, with the 8088 processor. And I began to learn how to get around in DOS in order to get early video games running."





> During high school, Al worked at a movie theater, where one of his co-workers was a fellow high school student who later became his wife. Two years into college, Al began working at IBM's AIX Support Center where he solved customer problems related to IBM's AIX operating system. (AIX is an open operating system similar to UNIX that was created by IBM.) Just as he had done as a child while learning about basic programming, Al studied as much as he could at night to learn more about the technology he was supporting at IBM.





> Al completed a computer science degree at Baker College, and eventually transferred to IBM's Electronic Tools Support Team, where he helped manage the Software Service Request tool which was used to report software issues. While there, he helped to consolidate the suite of software problem reporting tools into one tool, to simplify the customer experience.





> During this time, he heard about *World Community Grid* and became a volunteer. He also met Jonathan Armstrong, Viktors Berstis, and Keith Uplinger, who were already part of the *World Community Grid* development team. When a development position opened up within *World Community Grid*, he applied and became the newest team member in 2010. Currently, Al is responsible for managing the work unit build processes, creating project screen savers, and modifying science applications to run on *World Community Grid*. He also helps handle eblasts and website updates.



_Thanks, Al!!
_
_




Al with one of his children, passing his computer skills along 
to the next generation.
_​


> As a husband and father of two young children, Al's life outside of work revolves around his family. He is deeply involved in helping revamp the technology at his son’s school. He's also passionate about the work of





> *World Community Grid*. “Since I’ve joined the team, I’ve lost two family members to breast cancer," Al says. _"Like many volunteers, this is very personal for me. It's very important to me that my work is connected to something that helps others, and promotes progress that can benefit everyone in the future."_




*Thanks, AGAIN, Al!!
*
The Full Article, HERE!


----------



## Arjai (Mar 19, 2017)

*Findings from Nutritious Rice for the World Project Made Public*

*By: Dr. Ling-Hong Hung *
University of Washington

*8 Mar 2017  *

*Summary*
The data from the Nutritious Rice for the World project is now available on a web server built by the researchers, and they recently published a short paper about their findings.



> The findings of the Nutritious Rice for the World project were recently published in an open access paper, making them available to the public and any researchers who wish to use the information for their own work.





> We have described our work in a short paper that has been posted to Cold Spring Harbor Laboratory's BiorXiv pre-print server. Researchers can now read about how the Nutritious Rice for the World project’s rice structures were generated and the best models chosen. The paper also describes the web server which allows scientists to find a particular protein of interest and download the structures. The formats and query procedure are described in detail to facilitate the use of the server and the protein structures. The entire dataset can also be downloaded upon request.





> Depending on the usage and response, we may submit the paper for publication in a more formal journal. _However, publishing this paper officially concludes the project. *We thank the members of World Community Grid* for donating their time to the *Nutritious Rice for the World project.* It has been an honor to participate in this project and have support from so many volunteers._



More, HERE!

_Awesome work!! I love how our work is always made public for others to use and hopefully benefit from!

_


----------



## Arjai (Mar 19, 2017)

*Help Stop TB Team Selects Data Analysis Tools



*

*By: The Help Stop TB Team *
University of Nottingham

*28 Feb 2017  
*


Spoiler



"_*Hello everyone, and thank you for contributing your computer time to Help Stop TB! We would have never completed so many simulations if it wasn’t for you!*_" 



*Summary*
The Help Stop TB team is hard at work analyzing the data they’ve received so far from *World Community Grid.* They recently chose two new data analysis tools, which will help them better understand the behavior of the bacterium which causes tuberculosis.



> *Background*
> 
> Help Stop TB was created to examine a particular aspect of the highly resistant and adaptable bacterium that causes tuberculosis. The bacterium has an unusual coat which protects it from many drugs and the patient's immune system. Among the fats, sugars and proteins in this coat, the TB bacterium contains a type of fatty molecules called mycolic acids. Our project simulates the behavior of these molecules in their many configurations to better understand how they offer protection to the TB bacteria. With the resulting information, scientists may be able to design better ways to attack this protective layer and therefore develop better treatments for this deadly disease.





> *Choosing Data Analysis Tools and Methods*
> 
> Since our previous mini update in November, Athina has been focusing on analysing our simulation data, and at the same time she is writing up her PhD thesis. As a team, we have now achieved our main goal, which was to come up with a robust and efficient analytical strategy. This will enable us to efficiently process the heaps of data we’re receiving from the simulations conducted by *World Community Grid volunteers*, and will answer our questions about mycolic acids’ conformational behaviour and its biological implications.



_I left a lot out of this section. If this interests YOU, the full article is linked at the bottom of this post._



> *Figures 1 and 2* below are examples of how we are looking at the shapes of mycolic acids. These structures are important as we are looking at all the possible conformations that mycolic acids can assume in order to try to understand how those molecules work, how their conformations dictate any biological implications and/or affect the disease itself, in the hope to find any links and discover more for prevention methods.






​


> Additionally, the length of time that the molecules choose to remain in a certain adopted conformational pattern may also elucidate further biological implications. Each molecule assumes different shapes throughout its folding pathway and these shapes can be very dependent to each other. From the PCA clustering tool data, we have extracted important information regarding the dependency *(Figure 1)* between the different shapes the molecules assume.
> 
> Another analytical approach that we employed was the distance matrix analysis. We created and analysed matrices *(Figure 2)* of the distances of all the carbon atoms along the mycolic acid chain. This method can provide further insight into the frequency of the folding events and can also help us understand more about the flexibility of each structure.






​


> That was all our news for now! Thank you again for your contributions, and let’s all wish good luck to Athina with her writing! Until the next time, happy crunching!



Wow, I must be a bit Brain Dead!! I couldn't muster the concentration to take all that in. So, These are some excerpts, from the article, that I had some understanding. The rest, HERE!  And there is a lot more to take in!!

BTW, Good Luck Athina with the paper!!

Thanks to all of you for the Crunching Powerhouse TPU is!! Crunch ON!!


----------



## Arjai (Mar 19, 2017)

*OK, something to report!!* Looks like they were sitting on these for a bit!! Good fortune was, I was about to pack it up, leave the Coffee Shop, and go home for a bit. I decided to do some updates on my software, every week there is something, especially the malware and antivirus, and such.

_Let's hope Al keeps on his toes and doesn't throw updates out in bundles like this!! _Keep them steady Bud!! 

Take Care and Crunch ON!! TPU is King!!


----------



## Arjai (Mar 24, 2017)

*OpenZika Researchers Continue Calculations and Prepare for Next Stage
	

	
	
		
		

		
		
	


	


*

By: The OpenZika research team 

21 Mar 2017  

*Summary*
The OpenZika researchers are continuing to screen millions of chemical compounds as they look for potential treatments for the Zika virus. In this update, they report on the status of their calculations and their continuing work to spread the word about the project.







> *Project Background*
> 
> While the Zika virus may not be getting the continuous press coverage that it received in 2015 and 2016, it is still a threat to the health of people across the globe. New infections continue to be reported in both South America and North America, and medical workers are just beginning to assess the effects of the virus on young children whose mothers were infected while pregnant.
> 
> ...








> *Progress on choosing compounds for lab testing
> *
> We began the analysis phase of the project by focusing on the results against the apo NS3 helicase crystal structure (apo means that the protein was not bound to anything else, such as a cofactor, inhibitor, or nucleic acid) to select our first set of candidates, which are currently being assayed by our collaborator at University of California San Diego, Dr. Jair L. Siqueira-Neto, using cell-based assays. The NS3 helicase is a component of the Zika virus that is required for it to replicate itself.
> 
> In the second set of screening results that we recently examined, we used the new crystal structure of NS3 helicase bound to RNA as the target (see the images / animation above). Similar to the first set of candidates, we docked approximately 7,600 compounds in a composite library composed of the US Food and Drug Administration-approved drugs, the drugs approved in the European Union, and the US National Institutes of Health clinical collection library against the new RNA-bound structure of the helicase. Below are the results of this second screening:





> 232 compounds passed the larger collection of different energetic and interaction-based docking filters, and their predicted binding modes were inspected and measured in detail.
> Of the compounds that were inspected in detail, 19 unique compounds passed this visual inspection stage of their docked modes.
> From the compounds that passed the visual inspection, 9 passed subsequent medicinal chemistry-based inspection and will be ordered soon.



Um, Awesome! No?



> *Status of the calculations*
> 
> In total, we have submitted 2.56 billion docking jobs, which involved the virtual screening of 6 million compounds versus 427 different target sites. We have already received approximately 1.9 billion of these results on our server. (There is some lag time between when the calculations are performed on your volunteered machines and when we get the results, since all of the results per “package” of approximately 10,000 different docking jobs need to be returned to World Community Grid, re-organized, and then compressed before sending them to our server.)
> 
> Except for a few stragglers, we have received all of the results for our experiments that involve docking 6 million compounds versus the proteins NS1, NS3 helicase (both the RNA binding site and the ATP site), and NS5 (both the RNA polymerase and the methyltransferase domains).  We are currently receiving the results from our most recent experiments against the NS2B / NS3 protease.



*A new stage of the project

Publications* *and Collaborations

Additional News

Fundraising
*
*



*​_You can get Open Zika Merch, like that shirt and more (mousepads, anyone?) at their store page, HERE._
_https://www.zazzle.com/openzika+gifts_
*Outreach*

_All those Headings, and more info, is available at the WCG Site, HERE._

_Also, a link to the Video (of the NS3 Helicase), HERE._
_https://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=518_


> We are very grateful for all of the volunteers who are donating their unused computing time to this project!  Thank you very much!!



_*THANK YOU!!!! Awesome work Team TPU AND Open Zika!*_

_**_


----------



## Arjai (Apr 14, 2017)

*Clean Energy Project Researchers Sharing Results and 
Planning for the Future
	

	
	
		
		

		
		
	


	


*


*By: The Clean Energy Project team *
Harvard University

*28 Mar 2017  *



> *Summary*
> The Clean Energy Project team is working on publicizing their results to-date. They have wrapped up the second phase of the project, and are also making decisions about their future work with _World Community Grid._





> The Clean Energy Project research team at Harvard would like to thank the volunteers who supported us through two phases of the project! Currently, we are getting ready to share our findings in at least one publication and a conference. We are also weighing different options for further work with _World Community Grid,_ which might include new types of calculations on solar cells or perhaps a study with a much larger scope.





> *Publishing Our Results*
> We have completed our screening of non-fullerene acceptor materials for new organic photovoltaic devices. The findings were quite interesting and have kept us very busy! We describe our results in a manuscript that was submitted to the high-impact journal Energy & Environmental Science.
> 
> Steven Lopez will travel to San Francisco to present this work at the American Chemical Society national meeting in April 2017. Alán has presented the results of the Clean Energy Project in several forums and they have helped inform the screening for other materials, such as organic flow batteries, in his research group.





> *Future Work with World Community Grid*
> We have not been able to submit work units for volunteer calculation because we had been working to expand the number of molecules we will test by using a low-cost computational method to evaluate the properties of potential photovoltaic materials. With our efficient calibration scheme, this would allow us to screen 10-100 times as many candidates in the same amount of time. If this process can be fully optimized, we could begin generating these work units for volunteers. Benjamin Sanchez-Lengeling has pushed this aspect of the project forward; keep an eye on this rising star!
> 
> However, it is also possible that we may go in a different direction altogether. Another idea we are considering is to use these efficient computational methods to catalog the properties of molecules that benefit humanity and have applications beyond clean energy. _Molecular Space is vast and full of useful molecules for the world._





> _We appreciate everyone’s patience while we take stock of the resources and personnel available in our lab, and make decisions about the best scientific use of the generous donations of computing time provided by World Community Grid volunteers.
> 
> Thanks again to everyone for your support of this project over the years,
> 
> ...



*More about this News Item, HERE!*


----------



## Arjai (Apr 14, 2017)

*Mapping Cancer Markers Team Analyzes Lung Cancer Data*

*By: The Mapping Cancer Markers research team 

6 Apr 2017  *



> *Summary*
> In this project update, the Mapping Cancer Markers team describes how they are analyzing 45 million of the most promising lung cancer data results, and how they have begun to disseminate their early findings.





> The Mapping Cancer Markers (MCM) project continues to process work units for the Ovarian Cancer dataset. As we accumulate these results, we continue to analyze MCM results from the previous Lung Cancer dataset. Below, we discuss one direction in which we are pursuing the analysis.





> *Patterns of gene-family signatures in lung cancer*
> In cancer, and human biology in general, multiple biomarkers (genes, proteins, microRNAs, etc.) can have similar patterns of activity. This may be because the genes serve redundant roles, or because the genes (or other molecules) participate together in a group to serve a biological function. A cancer signature composed of a set of specific genes may appear different than another signature composed of different, specific genes, and yet perform equivalently because the genes in each are functionally related. With this problem in mind, post-doctorate fellow Anne-Christin Hauschild is leading a study of frequently-occurring patterns (or motifs) of genes present in high-performing lung cancer gene signatures.





> This project looked at the first phase results from the Lung Cancer MCM analysis, which was a systematic exploration of the entire space of potential fixed-length signatures. We began by selecting 45 million high-performing signatures derived from World-Community-Grid-computed MCM results. These are the signatures evaluated to carry the most information for lung cancer diagnosis.





> Next, we divided all genes in the lung cancer dataset into 180 clusters (gene families), where genes in each family show similar activity in the lung cancer dataset.





> To help understand the gene-families themselves, we can visualize each one with word clouds that describe the functions of the genes they contain, or the biological pathways they represent. We draw this information from databases such as Gene Ontology, pathDIP, or other sources.





> From there, we looked for patterns in these gene-family signatures: which families appear unusually frequently (or rarely) in high-performing signatures, or families that tend to appear multiple times in the same signature.





> *Early project results presented at Personalizing Cancer Medicine 2017*
> We presented the preliminary results of this project to Canadian and international cancer researchers this February, in a poster at the _Personalizing Cancer Medicine Conference 2017_ in Toronto, Ontario. We gained many insights and ideas from discussing this early work, and we continue developing them further.





> *Thank you to members*
> _This work would not be possible without the participation of World Community Grid Members. Thank you for generously contributing CPU cycles, and for your interest in this and other World Community Grid projects._



_If this interests you, there is a BUNCH more in this article. I truncated it due to not wanting a two page post!!

Find more, HERE!_


----------



## Arjai (Apr 28, 2017)

World Community Grid Moves to IBM Cloud
	

	
	
		
		

		
		
	


	








24 Apr 2017  




Summary
On May 15, World Community Grid will begin migrating to IBM Cloud, as part of an effort to modernize and enhance our infrastructure capabilities. Our system will be unavailable for approximately 48 hours while the migration takes place, but otherwise the move will not affect most volunteers.











We're happy to announce that World Community Grid is moving to IBM Cloud. Through this migration, we are leveraging more scalable and powerful hosting capabilities, as well as IBM and open source automation tools that make our development and deployment processes more efficient. This allows us to identify, diagnose and address major technical issues more quickly. Most significantly, IBM Cloud's global footprint of more than 50 data centers across 19 countries allows us to expand more easily and prepares us for years of growth.

*The migration will begin on May 15 and is expected to last approximately 48 hours, during which World Community Grid will be unavailable. This means that volunteers will not be able to access the website, fetch new research or return completed work during that time. *

No action is required by most volunteers, as our systems will resume sending and receiving research tasks once the migration is complete. However, for individuals or organizations who have restricted firewall rules, you may need to update those rules in order to continue contributing, by allowing connections to our new IP address (169.47.63.74).

Anyone with questions about this migration can post in this forum thread. We appreciate everyone's support during this migration, which will provide a modern hosting environment for volunteers and researchers for years to come.


_I certainly hope this did not cause any problems!!  


_


----------



## Arjai (Apr 28, 2017)

*“It’s not just big data. It’s for the good of humanity.”



*






*27 Apr 2017* 




*Summary*
Three co-workers wanted their company to support World Community Grid, but they knew they’d need to convince many people to make their vision a reality. Here’s how they did it.




This, folks, is a great story!

It is all right HERE.



Spoiler: The best part!



*Plans for the Future*

The team is working on internal marketing efforts to continue to spread the word within SILCA, such as working with their communications team to put a World Community Grid widget on SILCA’s intranet site.

The team would like to extend the project to other groups within Crédit Agricole. “SILCA is just one subsidiary of Crédit Agricole,” says David. “We are presenting the results of our project to other groups, and it would be a great victory if others would join.”


----------



## Arjai (Jun 17, 2017)

*FightAIDS@Home Targeting a Key HIV Protein*





*By: The FightAIDS@Home research team 

15 Jun 2017  *




> *Summary*
> FightAIDS@Home researchers restarted the first phase of the project at the end of 2016, _and in just a few months, they have completed approximately 46 percent of their projected work on World Community Grid._ Read about their progress on finding compounds that could stop HIV from replicating.



*Background*




> FightAIDS@Home is searching for possible compounds to target the protein shell of HIV (called a capsid), which protects the virus. Currently, there are no approved drugs that target this protein shell.





> The virtual docking techniques used in Phase 1 are an approximation of the potential effectiveness of promising compounds. Phase 2 of FightAIDS@Home uses a different simulation method to double-check and further refine the virtual screening results that are generated in Phase 1.





> _The research team is examining a library of approximately 1.6 million commercially available compounds to find promising treatment prospects._ The team estimates that _they will need to carry out roughly 621 million docking computations on World Community Grid _to thoroughly test each potential compound. With the help of many volunteers who are supporting this project, _they’ve already completed 46 percent of their goal._





> You can keep up with the research team’s progress on their website, which includes frequent updates on their experiments and progress.
> 
> Please read below for a detailed look at the technical aspects of their recent work.



*Insilico search for novel drugs targeting the HIV-1 mature capsid protein*

*The importance of the capsid protein*




> The capsid protein (CA) plays crucial roles in the HIV replication cycle1. After viral and host cell membrane fusion, the capsid core is released into the cytoplasm. This core, which corresponds to the assembly of ~1200 capsid proteins, contains and protects viral RNA and proteins from degradation. (edited)






> *To date, no drugs targeting CA are approved for clinical use.* With the goal of identifying novel active molecules which destabilize the capsid core, we set up a high throughput virtual screening (VS) campaign in collaboration with World Community Grid as part of the FightAIDS@Home (FA@H) project.








Figure 1: PDB 4xfx, the hexamer structure of the native HIV-1 mature capsid protein. (Credit: Pierrick Craveur)
​


> Targeted structures
> 
> The main target of the docking calculations was the recently solved structure of the CA hexameric assembly2. Four pockets of interest were selected at the surface of the hexamer in order to perform focused dockings, mainly at the CA-CA dimer interfaces.






> Structural variability surrounding these pockets was analyzed by comparing this X-ray structure from the PDB (4xfx, see Figure 1), and the two full capsid core models assembled by Schulten's lab3(3j3q and 3j3y, see Figure 2).







Figure 2: The 2 models of the capsid core assembly. (Credit: Pierrick Craveur)​


> Based on that, 36 different conformations were selected as targets for the VS, including the X-ray structure and structures from the models. Each target was set as full rigid and also with a specific combination of residue side chains defined as flexible.





> An extended library of ~1.6 million commercially available compounds was used for the screening. Replicate computations were performed for each docking experiment in order to assess the consistency of the results. In total ~621 million docking computations will be performed on World Community Grid.





> For the time being, ~46% of the computation is completed, with an ending date estimated at the end of 2017 if the computation does not increase in speed.






> *However, in one month we will be able to propose to our collaborators from the HIVE Center a selection of compounds (focusing one of the four pockets) for experimental binding and infectivity assays.*




_Progress being made! Because of what YOU do every day and many of you do more than their share! It is things like this that make me Proud to be a Cruncher! It was this site that got me going, with a Socket A computer! Time flies but, it can be marked by the innovation and discovery that our power bills provide! LOL!_



OK! For more, go HERE!


----------



## Arjai (Jun 26, 2017)

https://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=527

Unplanned outage effecting their storage servers. The IT team is working on it. Link is to the WCG site and on that page is a link to the forum thread about it. There is currently 8 pages of people bitching, go ahead and add to it!


----------



## Arjai (Jun 30, 2017)

*Help Cure Muscular Dystrophy Lead Researcher Releases Two New Open Data Tools
	

	
	
		
		

		
		
	


	


*


*29 Jun 2017  *



> *Summary*
> In this letter to volunteers, Dr. Alessandra Carbone, the principal investigator for the Help Cure Muscular Dystrophy project, announces the release of two new open access tools which can accelerate the work of researchers who investigate protein interactions.



_Alessandra Carbone_...I love that name, and this woman. She has done it again, Sharing and creating awesomeness!




​


> *Dear volunteers for the Help Cure Muscular Dystrophy (Phase 2) project,*
> 
> I am writing to update you on the analysis of the dataset of docking conformations produced by the Help Cure Muscular Dystrophy (HCMD2) project. The project’s goal was to investigate protein-protein interactions for more than 2,200 proteins whose structures are known, with a particular focus on those proteins that play a role in neuromuscular diseases.
> 
> The complete cross-docking dataset containing these protein-protein interactions is under analysis. For this, we are using the various computational tools that we developed in parallel with the calculations run on World Community Grid.





> *JET2 Viewer: A Repository of Protein Interfaces*
> 
> We have built a database of protein interfaces for the scientific community. This database, called JET2, is a milestone for the identification of protein partners.





> We are now concentrating on extracting useful information relating to muscular dystrophy from the JET2 dataset that your support helped to construct.





> *BIS2Analyzer: A Server to Help Our Data Analysis*
> 
> We have released a server, called BIS2Analyzer, to help identify signals of interaction based on coevolution analysis within proteins or between protein partners. This server, which is also openly accessible to the scientific community, is important because it can help to identify signals of protein interaction. It was useful to reconstruct the first protein-protein interaction network for viruses (see the reference below on the reconstruction of the network for the Hepatitis C Virus).





> Thanking you again strongly for your contributions. I shall keep you updated on our results. Be assured that we are making progress, thanks to your support!
> 
> Best regards,
> 
> Alessandra



_Thank *YOU* (!!) Alessandra! _



P.S. Dr. Alessandra Carbone named "Woman Scientist of the Year"
	


P.P.S I found a picture, and a recording of her at a 2014 lecture on HCMD. 















Her web page, listing all her Awards.

I have finally found her online. I did some searching, some time ago, and had some difficulty locating the Dr. This time, I found it.  She is a remarkable woman in Science, a Mathematician and Italian. Um, Yea, just woke up from a wonderful fantasy. I think those three things add up to what I consider a Perfect woman, or some semblance of one! (in my mind)

Hearing her speak is mesmerizing, I need to turn it off. It is a well done speech, about WCG and HCMD.

*Oh, The rest of the article on the WCG site...Much more good stuff there.


*
https://www.researchitaly.it/en/news/legion-of-honour-to-the-italian-alessandra-carbone/

This is a VERY good Beer, BTW. 

**** post those pics in the thread manofthem linked ****

​


----------



## manofthem (Jun 30, 2017)

Arjai said:


> Her web page, listing all her Awards.



I listened to the whole thing, but man I didn't understand 99% of it   But thanks for sharing! 


Arjai said:


> This is a VERY good Beer, BTW.



I'd recommend posting these goodies over in this thread so as to enhance the discussion


----------



## Silvertigo (Jul 10, 2017)

Smoking in Oz eh.

http://www.abc.net.au/news/2017-07-...ter-punching-out-data-for-researchers/8687104


----------



## Arjai (Jul 12, 2017)

*Supercharging Environmental and Climate Change Research
	

	
	
		
		

		
		
	


	


*


*10 Jul 2017  *



> *Summary*
> IBM invites scientists to apply for grants of supercomputing power through World Community Grid, meteorological data from The Weather Company, and IBM Cloud storage to support their environmental and climate change research projects.












*more here...*https://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=529


----------



## Arjai (Jul 18, 2017)

*Short Planned Outage for Tuesday, July 18



*

*17 Jul 2017*

*Summary*
We will be performing some maintenance which will result in volunteers being temporarily unable to access the website or download new work at _14:00 UTC on Tuesday, July 18._

We will be temporarily disabling the ability for World Community Grid volunteers to access the website and download/upload results at 14:00 UTC on Tuesday, July 18. _The window for this outage is 6 hours_; however, we estimate that the interruption to _volunteer-related functions will last for approximately 30 minutes._

The Whole Story...

Hope this isn't an inconvenience!! LOL. Thanks WCG for announcing something that most of us won't notice. I suppose transparency, is to blame.


----------



## Arjai (Jul 30, 2017)

*Planned Update to World Community Grid's Security Certificates
	

	
	
		
		

		
		
	


	


*

*24 Jul 2017* 

*Summary*
We will be updating our security certificates on Tuesday, July 25 at 19:00 UTC.



> Update: Our security certificates have now been updated.





> Date of outage:  Tuesday, July 25, 2017
> 
> Reason for outage: Secure Sockets Layer (SSL) certificates are used to encrypt communications between volunteers' web browsers and our servers, and between the software client and our servers. SSL certificates must be renewed periodically, and we are therefore updating our current certificates.



I was out of town, on Holiday, this past week. I am sure this went well, as I had no problems while I was gone.


----------



## Arjai (Jul 30, 2017)

*New Lab at Tsinghua University Created to Work on Computing for Clean Water Project Findings*





_By: The Computing for Clean Water team 
Tsinghua University _

*25 Jul 2017  *

*Summary*
Dr. Ming Ma, one of the original members of the Computing for Clean Water research team, has created his own lab at Tsinghua University. Dr. Ma and his team continue to analyze the data generated by the project. Learn more about their current work and plans for the future in this update.






> *Background*
> 
> The Computing for Clean Water project was created to provide deeper insight on the molecular scale flow of water through a novel class of filter materials. Thanks to the millions of virtual experiments that the team was able to run on _World Community Grid,_ they discovered conditions under which water can pass through tiny carbon nanotubes much more efficiently. This groundbreaking understanding of a fundamental physical process could help improve access to clean water for millions of people through more efficient water filtration and desalination, and also may have applications in clean energy and medicine.








> *A Growing Team*
> 
> It has been one year since the main team member, Dr. Ming Ma, returned to Tsinghua University, China, after doing research at University College London and Tel Aviv University. During the past year, as an Associate Professor in the Department of Mechanical Engineering, Dr. Ma recruited four new researchers as members of the team with the help from Prof. Quanshui Zheng, the leader of the Computing for Clean Water team. The new team members include one postdoc, Dr. Wei Cao; and three PhD students: Jin Wang, Kunqi Wang, and Yao Cheng.





> *Next Steps*
> 
> The team is now working on two main tasks. The first task is to improve the algorithm used in the previous study (see the reference below) by incorporating new techniques developed during the last three years, and to implement them into LAMMPS, a molecular dynamics software. The second task is to investigate new systems with the algorithm being developed. With these tasks finished, the team wishes to bring new, interesting information into the volunteer computing community.
> 
> _We thank everyone who supported Computing for Clean Water, and hope to work with you again in the near future._



More HERE.


----------



## Arjai (Jul 30, 2017)

*Help Cure Muscular Dystrophy Lead Researcher Releases Two New Open Data Tools*


*29 Jun 2017  *

*Summary*
In this letter to volunteers, Dr. Alessandra Carbone, the principal investigator for the Help Cure Muscular Dystrophy project, announces the release of two new open access tools which can accelerate the work of researchers who investigate protein interactions.





​


> Dear volunteers for the Help Cure Muscular Dystrophy (Phase 2) project,
> 
> I am writing to update you on the analysis of the dataset of docking conformations produced by the Help Cure Muscular Dystrophy (HCMD2) project. The project’s goal was to investigate protein-protein interactions for more than 2,200 proteins whose structures are known, with a particular focus on those proteins that play a role in neuromuscular diseases.
> 
> The complete cross-docking dataset containing these protein-protein interactions is under analysis. For this, we are using the various computational tools that we developed in parallel with the calculations run on World Community Grid.





> *JET2 Viewer: A Repository of Protein Interfaces*
> 
> We have built a database of protein interfaces for the scientific community. This database, called JET2, is a milestone for the identification of protein partners. Why is this important? The analysis of the HCMD1 and HCMD2 data highlights that a precise description of protein interfaces is crucial in discriminating protein partners, and the database produces a highly accurate set of such predictions. Improvement is still necessary, but the results are already very accurate.
> 
> We are now concentrating on extracting useful information relating to muscular dystrophy from the JET2 dataset that your support helped to construct. As you know, progress in research is slow, but we are making definite advances and expect that the methodological approach used in HCMD2 will be very successful in the large-scale identification of protein partners at protein-residue-level resolution! (A protein-residue is a portion of a protein.*)





> *BIS2Analyzer: A Server to Help Our Data Analysis*
> 
> We have released a server, called BIS2Analyzer, to help identify signals of interaction based on coevolution analysis within proteins or between protein partners. This server, which is also openly accessible to the scientific community, is important because it can help to identify signals of protein interaction. It was useful to reconstruct the first protein-protein interaction network for viruses (see the reference below on the reconstruction of the network for the Hepatitis C Virus).
> 
> _Thanking you again strongly for your contributions. I shall keep you updated on our results. Be assured that we are making progress, thanks to your support!_





> _Best regards,
> 
> Alessandra_



*Best Regards to YOU, Alessandra!  *


----------



## Arjai (Aug 3, 2017)

*Potential New Treatments for Leishmaniasis Tested in Lab
	

	
	
		
		

		
		
	


	


*


_By: Dr. Carlos Muskus López 
Coordinator, Molecular Biology and Computational Unit, PECET University of Antioquia _

*1 Aug 2017  *

*Summary*
The Drug Search for Leishmaniasis team has begun lab testing potential treatments for this serious—yet neglected—tropical disease. In this update, Dr. Carlos Muskus discusses the results of topical (on the skin) testing of four compounds.






> *Background*
> 
> Leishmaniasis is one of the most neglected tropical diseases in the world, infecting more than two million people in 98 countries. One form of the disease, caused by _Leishmania infantum_ in America, mainly affects children, who can die if adequate treatment is not provided promptly. The classical treatments for all forms of Leishmaniasis can cause severe side effects, including death. Furthermore, drug resistant parasites are causing major problems in many endemic countries. For these reasons, there is an urgent need for new, safe, and inexpensive drug compounds.





> *Identifying Potential Compounds*
> 
> _After analyzing many compounds with the best docking score based on the data from the project on World Community Grid_ and our further testing, 10 compounds were finally selected to test in vitro. The in vitro evaluation involved cytotoxicity analysis against human-derived cell lines. (As part of the process of drug discovery, we do testing to ensure that the promising compounds do not affect human cells, thus decreasing the chance of side effects.) In addition, we evaluate the effectiveness of each compound against _Leishmania,_ the parasites that cause leishmaniasis. The best compounds are those that kill the parasites at a low dose and do not affect the human cells even at higher doses.










> *Lab Testing of Potential Compounds*
> 
> *Next Steps*
> 
> ...



_We also Thank You! For all your hard work in curing this disease! _

More info/Technical stuffs about the Lab Testing is HERE


----------



## Arjai (Aug 24, 2017)

*Help Stop TB Uncovers New Data on Mycolic Acids*





*By: The Help Stop TB Team 

 University of Nottingham 

*
*17 Aug 2017 *

*Summary*
The Help Stop TB project is turning out to be the most comprehensive study of mycolic acids_ ever_ undertaken, which will be of enormous value to all researchers who are interested in how these molecules protect bacteria. In this update, the researchers describe mycolic acid folds that have_ never been detailed before_, and explain how they plan to continue their exploration of this new territory as the project continues.



> _Hello everyone, and thank you for contributing your computer time to Help Stop TB!_





> *Background*
> 
> 
> 
> ...





> *Studying Mycolic Acids*
> 
> Since our last update in February, the team has been focusing on analysing the simulation data that we’ve received from *World Community Grid*, and coming up with meaningful conclusions about how the different configurations of mycolic acids can offer protection to the TB bacteria. _The mycolic acid folds that we will talk about in this section have not been described before_, and there has_ never been such an in-depth study of mycolic acid folds and their relations to one another._
> 
> ... utilizing a tool developed at the School of Pharmacy at the University of Nottingham, and distance matrix calculations. An example of the different information we can extract from distance matrix calculations can be found below.








> This figure is an illustration of the distance matrix for two folds; a “knot” fold and a five-chain fold. _ These mycolic acid folds have not been described before._ This figure shows that these different folds (left) are in fact connected and have dependencies with one another, as can be shown from their average distance matrices (right) that are quite similar visually. This similarity is further confirmed by root-mean-square deviation (RMSD) calculations.
> 
> These different folding patterns are currently in the process of being analyzed for the whole data set retrieved from *World Community Grid. *
> 
> The remaining challenge for the analysis of the *World Community Grid *data is to condense the vast amount of information into the important key features we are aiming for and the key question: *why do distinct mycolic acids play such different biological and immunological roles?* Stay tuned, we are working on it.





> *Future Plans*
> 
> Future plans include letting our results “run dry” in a few months’ time. ... Additionally, new simulations will be added to the workflow based on the information we have already gathered.
> 
> ...



Edited slightly for size, the WHOLE thing is, HERE

"*mycolic acids"*, eh? Could be the beginning of an end, to TB. _This is Exciting_, for me. A_s highlighted, we have, again, allowed researchers to discover something unknown._ WORLD COMMUNITY GRID, the best thing I do, each day, _*by far.*_ And by "do?" I leave my computer on and pay my electric bill. That's it! _Changing the world has never been easier_, or more fulfilling, than doing this. The discoveries by these teams, using the results we flood them with, is changing our world.
*
Thank You IBM and WCG! *


----------



## Arjai (Aug 24, 2017)

*The Bacteria Inside Us: Gaining a New Understanding of Human Disease*





*By: The Microbiome Immunity Project research team *



* 23 Aug 2017    *

*Summary*
What if you could help researchers learn more about how the bacteria in and on our bodies play a role in diseases such as Type 1 diabetes? We're proud to announce our latest project, which will be the first of its kind, large-scale, comprehensive study of the human microbiome.












> *What's the microbiome, and why is it important?*
> 
> The human microbiome is a collection of all of the bacteria that live inside our bodies and all of the genes that they have. Scientists have found that we each have as many as 30 trillion bacteria in our own microbiome, and most of them live in our gut.
> 
> The bacteria in the microbiome are usually beneficial to humans. They can even be essential to our health. However, some are linked to diseases such as Type 1 diabetes, Crohn's disease, and ulcerative colitis. These diseases are becoming more common all over the world.





> *What's the microbiome's role in various diseases?*
> 
> The short answer: scientists don't know exactly how the microbiome influences the beginning and development of disease, but they know that it plays an important role. That's why our group–consisting of researchers from the Broad Institute of MIT and Harvard, Massachusetts General Hospital, University of California San Diego, and the Simons Foundation's Flatiron Institute–is partnering with* World Community Grid* on the _Microbiome Immunity Project. _The project's goal is to study all the proteins (the building blocks of organisms) of the human microbiome, so that we and other researchers have a strong foundation to address these diseases.
> 
> ...





> *You can help!*
> 
> We're enlisting the help of volunteers like you from all over the world to support the Microbiome Immunity Project. Together, _World Community Grid volunteers_ provide researchers like us with the enormous computing power we need to carry out studies that would not otherwise be possible.








> Here's how it works: ....
> _To contribute to the Microbiome Immunity Project, join World Community Grid, or if you are already a volunteer, make sure the project is selected on your__ My Projects__ page._



*Fresh Project!! Get 'em while they're HOT!!* 

I have one, on each machine, so far. The earliest one I have is from Tuesday morning. They look to be small in size, so far. Could be good, if they stay that way, been looking to add another easy one for my Android phone to crunch!

So, yea. *Here it is, the NEW Project!!* Let's bury 'em with results!! Ready, Set, _*GO!!!*_


----------



## Arjai (Aug 24, 2017)

Well, um, after doing a slight bit of research on this NEW Project. No Android. 

I guess I cannot expect everything from the NEW guys! It's OK.


Oh, HERE, are the requirements, for this and all the projects...


----------



## Arjai (Sep 11, 2017)

*NEW BOINC!!

http://boinc.berkeley.edu/download.php

7.8.2
No notes on it, that I could find. But, I am going for it now. I will update tomorrow, how it goes. Then maybe Tuesday, switch the Linux boxes over.*​


----------



## Arjai (Sep 23, 2017)

*Plans for Future Development Discussed at BOINC Workshop 2017 
	

	
	
		
		

		
		
	


	


*

*22 Sep 2017 *



> *Summary*
> A group of BOINC developers, project managers, researchers, and volunteers recently participated in a workshop where they exchanged information and ideas that will help set the direction for the future development of the BOINC open source project.
> 
> 
> ...






​_Does anyone else feel that Mr. Reed looks a little ghostly?_
​


> The workshop's primary purposes were to connect members of the BOINC community, share information about the various projects that use BOINC, and discuss future plans for the continued development of the platform. Some of the items discussed were:
> 
> 
> Demonstration of a proof-of-concept that enables communication between a user's browser and the BOINC client, which could potentially be used to simplify how volunteers register and attach to World Community Grid
> ...





> _World Community Grid's Keith Uplinger gave the group an update about how World Community Grid uses DevOps (a software development method that helps communication and collaboration between software developers and IT personnel). _Kevin Reed, who serves as Chair of the BOINC Working Committee, gave a report on the committee's current tasks and goals, which include increasing the number of volunteer developers who contribute regularly to the development of BOINC.
> 
> Other presentations included an update on BOINC project climateprediction.net, which is the world's largest climate modelling experiment; and a talk about the_ BOINC Pentathlon, a 14-day online event which brings in new volunteers_ from all over the world.





> For more information about the BOINC Workshop 2017, visit the event website.



From the event website...



​*Participant List *

* 35 participants *
Andrey Voronkov Digital BioPharm ltd.
Andy Bowery Oxford University
Bernd Machenschalk Albert-Einstein-Institute
Bruce Allen Albert Einstein Institut Hannover
Carl Christensen
Christian Beer Einstein@Home (Albert-Einstein-Institute)
Christian Köckritz
David Anderson UC Berkeley
David O'Connor Team Gridcoin
David Wallom Unviersity of Oxford
Eamonn O'Connor Team Gridcoin
fayssal sarghini
Frederick McIntosh CERN
George Emsden BOINC volunteer since 1999 and OU Science student
Ivan Reid Brunel University London (GB)
Joachim Becker-Bergemann User / Foerderverein der Carl-Schurz-Schule in Frankfurt am Main
Joël Duet Gridcoin community
*Keith Uplinger World Community Grid *
* Kevin Reed IBM/World Community Grid *
Krzysztof Piszczek DrugDiscovery@Home, Universe@Home
Laurence Field CERN
Laurent Domisse IAP
Marius Millea Institut Lagrange de Paris
Matt Blumberg GridRepublic + Charity Engine
moussaoui moussa
Nils Hoimyr CERN
Oliver Bock Einstein@Home
Olivier Fehr Olivier Fehr Media
Patrick Schoefer SETI.Germany
Richard Csabai
Richard Haselgrove
Richard Main
Romain Pouzol
Steven Clark Purdue University
Valera Rozuvan









​2 things, I hadn't heard about this and I want to go to Paris. _TPU should have sent me, the WCG reporter,to Paris to cover this! _

__
__


----------



## Arjai (Sep 23, 2017)

No worries, those were corrupted links that I effed up and then figured out. Why they are un-edit-able, IDK. But, you have all the content, Plus a few corrupted, x-ed out mistakes.


----------



## Arjai (Sep 27, 2017)

*The Road Ahead for Help Fight Childhood Cancer*





By: Dr. Akira Nakagawara, MD, PhD CEO of the Saga Medical Center KOSEIKAN and President Emeritus, Chiba Cancer Center

*26 Sep 2017*

*Summary*
The Help Fight Childhood Cancer researchers discuss how they’re moving forward with data analysis and continuing their search for pharmaceutical partners.




​
*Background*

The Help Fight Childhood Cancer (HFCC) project was created to look for better treatments for neuroblastoma, which is refractory among childhood cancers (meaning that it is resistant to treatment). The project’s goal was to target certain cell proteins regulating cancer cell growth—such as TrkB tyrosine kinase receptor, ALK tyrosine kinase receptor, N - CYM protein and others—with the help of _World Community Grid’s enormous computing power, which is donated by an international community of volunteers._

Looks as though they found something interesting...



> Our research team conducted in-silico (computer simulation-based) drug discovery screening using _World Community Grid_ to search through a library of three million small molecular compounds. We discovered a small molecule compound which competitively binds to the TrkB protein pocket to which BDNF (a specific growth factor) binds. The discovered molecule can thus prevent BDNF from binding to the TrkB protein and diminish cancer cell growth. *This could lead to a new and improved treatment for neuroblastoma.*
> 
> Subsequently, the anti-tumor effect of the compound was examined using cultured cancer cells, or human neuroblastoma transplanted into mice, and this laboratory research confirmed that this small molecular compound and possibly some others could be candidates for anticancer drugs targeting TrkB. We announced this breakthrough and published our findings in the peer-reviewed, English language journal, Cancer Medicine, in 2014.





> *Current Research*
> 
> Currently, we are conducting research to develop even more potent inhibitors by synthesizing small molecular compounds similar in structure to the compounds found using the screening. The road to developing commercial, approved new drugs is a tough task. We must find a pharmaceutical company that will conduct joint research and development and create a patentable compound so that this expensive effort is profitable._ If any of you have contacts with a pharmaceutical company that may be interested in pursuing this venture, please introduce us._



Anybody got contacts to the big Pharm's?



> Additionally, using _World Community Grid _to screen drug candidates, we found other small molecular compounds showing the ability to inhibit the ligand BDNF. These results were presented it in another English language journal (Neurochem International, 2016, abstract here). These compounds also look promising *as a remedy for depression and dementia*, and similarly, we are seeking a pharmaceutical company to cooperate in research and development of these.



Yet again, something I love, a focused project we flood with data, finds answers to things they weren't looking for!



> The N-CYM is a new protein we discovered which is implicated in neuroblastoma. A published paper about this can be found here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879166/. Before we can screen for drug candidates, we must determine this protein's three-dimensional structure. Therefore, we are currently working on the difficult task of crystallizing the N-CYM protein so that we can perform X-ray analysis to determine the protein’s three-dimensional structure. Once the three-dimensional structure of the protein is determined, we will screen to find inhibiting compounds in the Smash Childhood Cancer project, which is building on the work from this project.



_"We thank all volunteers who supported this project, and look forward to keeping you updated on the progress of this project as well as the Smash Childhood Cancer project."_

More here, enjoy!


----------



## Arjai (Oct 1, 2017)

*A Volunteer in France on Why He Joined World Community Grid*





By: Gil Rivet _Crunchers Sans Frontieres_

*29 Sep 2017 *


*Summary*
Meet Gil Rivet, a volunteer from France who is an administrator for the _Crunchers Sans Frontieres_ team. Here's his story in his own words.




​....



> My participation in the World Community Grid project can be summarized as follows: Use my computer to process data, which cannot be done by my brain. As long as World Community Grid has humanitarian projects, I will continue to be motivated to participate.



Not quite sure how this became a post on WCG. But, it is.

For more of this AMAZING STORY confused, Click HERE


----------



## Arjai (Oct 4, 2017)

*Open Zika Researchers Continue Calculations, Share the Wealth, and Spread the Word
	

	
	
		
		

		
		
	


	


*

By: The OpenZika research team

*3 Oct 2017*

*Summary*
The OpenZika researchers are continuing to screen millions of chemical compounds as they look for potential treatments for the Zika virus. In this update, they report on the second stage of the project, using a newly prepared, massive library of 30.2 million compounds that are being screened against the Zika virus proteins. They also continue to spread the word about the project.



> *Project Background*
> 
> The Zika virus has “evolved” from a global health emergency to a long-term threat. Scientists throughout the world continue to study the virus and search for ways to stem its spread, including potential vaccines and means of controlling the mosquito population, as well as looking for treatments. As of this update, there is still no vaccine for the Zika virus, and no cure.
> 
> We remain convinced that the search for effective treatments is crucial to stemming the tide of the virus. In addition to the OpenZika project, several other labs are doing cell-based screens with drugs already approved by the U.S. Food and Drug Administration (FDA). Still, few to none of the compounds that have been identified thus far are both potent enough against Zika virus and also safe for pregnant women.





> *Continuing progress on choosing compounds for lab testing*
> 
> We are continuing the analysis phase of the project, focusing on the results against the new target structures solved for NS3 helicase, NS5 polymerase, NS2B-NS3 protease, and NS1 glycoprotein.
> 
> ...





> *Status of the calculations
> 
> ...
> Thus far, the > 80,000 volunteers who have donated their spare computing power to OpenZika have given us > 34,000 CPU years worth of docking calculations, at a current average of 73 CPU years per day! Thank you all very much for your help!!*





> *A new stage of the project, and sharing the wealth*
> 
> As described above, instead of docking 6 million compounds, we are now screening a new library of 30.2 million compounds against all the ZIKV targets. This new, massive library was originally obtained in a different type of format from the ZINC15 server. It represents almost all of “commercially available chemical space” (that is, almost all of the “small molecule” drug-like and hit-like compounds that can be purchased from reputable chemical vendors).
> 
> The ZINC15 server provided these files as “multi-molecule mol2” files (that is, up to 100,000 different compounds were contained in each “mol2” formatted file). These files had to be re-formatted (we used the Raccoon program from Dr. Stefano Forli, who is part of the FightAIDS@Home team) by splitting them into individual mol2 files (1 compound per file) and then converting them into the “pdbqt” docking input format.





> By splitting, reformatting, and testing hundreds of thousands of compounds per day, day after day, after approximately 6 months this massive new library of compounds was prepared and ready to be used in our OpenZika calculations. Without the tremendous resources that _*World Community Grid volunteers provide for this project, we would not even dream of trying to dock over 30 million compounds against many different targets from the Zika virus. Thank you all very much!!!*_
> 
> Soon after we started using this new massive library for our virtual screens in OpenZika, Viktors Berstis at IBM/World Community Grid put us in contact with Dr. Akira Nakagawara, the principal investigator of the Smash Childhood Cancer project. To help expand the scope of their experiments that search for new cancer drugs, we gave them a copy of our new library of 30.2 million compounds.
> 
> For more information about these experiments, please visit our website.





> *Publications* *and Collaborations*
> 
> OpenZika project results were presented on July 7-14 at an International Conference, the 46th World Chemistry Congress, in Sao Paulo, Brazil, which had almost 3,000 attendees.












The slides from her presentation are available on SlideShare.​


> We will be presenting a poster at *Cell Symposia: Emerging and Re-emerging Viruses*, on *October 1-3, 2017, in Arlington, VA, U.S.A:*
> 
> *Title:*
> 
> ...





> We have also recently published another research paper entitled “Molecular Dynamics simulations of Zika Virus NS3 helicase: Insights into RNA binding site activity” in a special issue on Flaviviruses for the journal _Biochemical and Biophysical Research Communications_. This study of the NS3 helicase system helped us learn more about this promising target for blocking Zika replication. The results will help guide how we analyze the virtual screens that we performed against NS3 helicase, and the Molecular Dynamics simulations generated new conformations of this system that we will use as targets in new virtual screens that we perform as part of OpenZika.





> *Additional News*
> 
> Dr. Sean Ekins has hired a postdoctoral scientist and a master’s level scientist who will get involved with the OpenZika project. We have also started to collate literature inhibitors from Zika papers.
> 
> Also, Drs. Sean Ekins and Carolina Andrade have bought some of the candidate compounds that we identified in the virtual screens from OpenZika, so that they can be assayed in the next round of tests.



*Fundraising
*
*



*​


> Thank you to anyone who has visited our store on Zazzle to check out OpenZika merchandise, such as T-shirts, polo shirts, mugs, buttons, mouse pads, tote bags, hats, ties, pillows, key rings, and phone cases that have the OpenZika logo! All profits that we receive from the sale of this merchandise will go toward buying compounds for lab testing.





> The OpenZika team is working on grants from the National Institutes of Health (NIH), CNPq and FAPESP (Brazilian funding agencies), and other organizations to try raise funds for purchasing and testing compounds. In May 2017, Rutgers University gave Dr. Perryman “Principal Investigator” status for NIH grant purposes. Consequently, in June he submitted his first grant application, which focuses on the OpenZika results against the NS2B-NS3 protease.  In August, Dr. Perryman and Dr. Ekins submitted an NIH grant together, which also focuses on the results of docking 30 million compounds against the NS2B-NS3 protease.





> *Outreach*
> 
> We have been working hard to promote the project, and we continue to look for additional opportunities. Below is a list of our most recent outreach efforts.
> 
> ...








> Dr. Carolina Horta Andrade gave an invited lecture at the National Health Conference – CONMSAÚDE regarding drug design and discovery for Neglected Tropical Diseases (May 26, 2017).
> Dr. Melina Mottin, one of the OpenZika team members, gave an invited oral presentation, titled “OpenZika: Opening the discovery of new antiviral candidates against Zika virus and insights into dynamic behavior of NS3 Helicase,” at the 46th World Chemistry Congress, in Sao Paulo, Brazil, on July 7-14.
> Dr. Carolina Horta Andrade gave an invited lecture at the Brazilian Young Medicinal Chemistry Scientists Workshop, at the University of Sao Paulo, Brazil, regarding “Experimental and computational approaches integrated for the discovery of new drug candidates,” for the general public, as well as to pharmacy and chemistry students (June 12, 2017).
> OpenZika project update has been released on some Brazilian news channels and websites:
> ...



_*We are very grateful for all the volunteers who are donating their unused computing time to this project!  Thank you very much!!*_

WOW! Lot's of progress and a big News Report!!
For all of it, Click HERE

Keep up the Good Work, and buy something from their store!!


----------



## Arjai (Oct 11, 2017)

https://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=540
Thursday maintaince, they say an hour. We hope they are correct.


----------



## Arjai (Oct 22, 2017)

*Discovering Dengue Drugs - Together Takes a New Approach to Data Analysis*

*By: Dr. Stan Watowich, PhD 

 University of Texas Medical Branch (UTMB) in Galveston, Texas 



 18 Oct 2017  *



> *Summary*
> In this update, Dr. Stan Watowich, principal investigator for the Discovering Dengue Drugs - Together project, explains how the research team is shifting their approach to data analysis. The research team has also released their best-scoring results in order to help other scientists conducting similar studies.














> _We wish to thank the World Community Grid volunteers for their support over these past years_.





> *The World Community Grid* phase of our "Discovering Dengue Drugs – Together project completed its computations a while ago. The mission of the project is to identify promising drug candidates to combat dengue, hepatitis C, West Nile, yellow fever, and other related viruses.
> 
> As noted in a previous update, we have been analyzing the results, retesting some of the calculations, modifying the underlying assumptions for the calculations, and testing compounds in the laboratory using in vitro (test tube/culture dish) and in vivo (in living organisms) systems. We have worked with our medicinal chemists to synthesize variants of several initial inhibitor "hits" with the goal of improving their activity for planned pre-clinical trials. Our current designs, unfortunately, have not yet produced a highly potent dengue protease inhibitor suitable for in vivo testing. Thus,_ we are shifting our approach for this project and are now screening combinatorial chemistry libraries for protease inhibitor "hits" to use as starting points for "hit-to-lead" improvement. _Free energy perturbation calculations and 3-D structure-guided design will be used to improve the potency and physiochemical properties of these hits.





> The links below contain the ~1000 lowest (best) scoring small molecules predicted to bind to the catalytic site of NS2B-NS3 proteases from dengue and West Nile viruses that were used in this virtual screening project. _We hope this information may be of use to other investigators in their development of computational chemistry tools and/or dengue antivirals._
> 
> Dengue virus protease (PDB 2FOM)
> 
> ...



*Let's hope the new testing works!*

**


----------



## Arjai (Oct 25, 2017)

*Planned Maintenance on Wednesday, October 25*

That is today. Right Now! I only noticed due to a WU sitting and waiting to upload.

More HERE.


----------



## Arjai (Oct 25, 2017)

*Release Notes for BOINC 7.8*

New BOINC out there!

*Changes in 7.8.3*



*

client: extensions, fixes to account manager functionality

client: eliminate possible buffer overflow in reporting result errors

lib: fix boinc_file_exists() on Windows

Mac: Changes to Xcode project to support screensaver changes for Mac OS 10.13.

Screensaver: Changes for screensaver to support Mac OS 10.13

api: BOINC graphics library changes to support Mac OS 10.13

client library: inconsistent terminology for intel_gpu

update project list

Locale: Update french localization files

update installshield files
*
 



I am SOOOO glad they fixed those French localization files!! Man has that been a pain! 

Get it!! Get it HERE!


----------



## Arjai (Nov 1, 2017)

*The Whats and Whys of Basic Research*

*31 Oct 2017*

*Summary*
What is basic research and how is it applicable to the work done on World Community Grid? In this article, we'll address some of the fundamental questions about basic research, which is the foundation of scientific discovery.

_“Basic research is performed without thought of practical ends. It results in general knowledge and understanding of nature and its laws. The general knowledge provides the means of answering a large number of important practical problems, though it may not give a complete specific answer to any one of them.”_

_Vannevar Bush,
"Science, the Endless Frontier"_






> *What is basic research?*
> 
> When scientists study a phenomenon, a particular subject, or a natural law, with the primary intention of understanding what they’re studying, they’re conducting *basic research*. This type of research, which can be conducted in any branch of science, is meant to add to and strengthen the very core of scientific knowledge.





> On the other hand, *applied research*, which involves testing possible applications of theories and methods, often gets more attention than basic research because it can more directly result in new discoveries. But applied research depends on the accumulation of knowledge that is only possible from many basic research studies, some of which are branded as “failures” before they turn out to have applications that the original researchers never may have guessed.





> In the scientific world, there’s often not a clear division between basic and applied research. Many *World Community Grid* projects could be considered a combination of both. For example, the Mapping Cancer Markers project, which is looking for biomarkers for various types of cancer, can be considered basic research in that it involves sifting through massive amounts of raw data in a new way, but is also applied research because its goals—such as helping find personalized treatments for cancer—are concrete.











_The researchers for the Computing for Clean Water project (described in the video above) discovered a phenomenon that could improve water filtration technology and desalination.
_​


> *Why is it crucial for continued scientific discovery?*
> 
> Future discoveries depend on the basic research of yesterday and today. And basic research projects often uncover knowledge no one expected, and lead to paths that were previously unknown.
> 
> One recent example for* World Community Grid* researchers occurred in 2016, when the Help Fight Childhood Cancer researchers discovered that two of the chemical compounds they were studying for their effectiveness against neuroblastoma might be useful in developing a treatment for depression and dementia.




*Why is public involvement in this type of research so important? *

_“Basic research is often misunderstood, because it often seems to have no immediate payoff.”_

_Massachusetts Institute of Technology, _
"The Future Postponed"



> Public funding for all types of science has been declining in many countries for a number of years. For example, researchers in Argentina and Brazil have experienced steep decreases in federal funds, and in 2016 scientists in Italy launched an online petition for greater funding that received more than 77,000 signatures. When scientific funding is cut, the sparse remaining monies are often allocated to projects that are viewed as having a quicker “payoff,” such as the proposed 2018 budget for the USA’s National Science Foundation that cuts funding to certain graduate fellowships while prioritizing other programs.



_“Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world.”_


_Louis Pasteur
_
More of this Story, HERE

_Interesting quotes from the Science World and some definitions of terms, some non-scientist's may find enlightening. 

_


----------



## Arjai (Nov 25, 2017)

*Analysis Underway on 30 Terabytes of Data from the Uncovering Genome Mysteries Project*





*24 Nov 2017 *

*Summary*
The Uncovering Genome Mysteries data (all 30 terabytes) was transferred to the research teams in Brazil and Australia this year. Now, the researchers are analyzing this vast amount of data, and looking for ways to make it easy for other scientists and the public to understand.









_In this video, Dr. Torsten Thomas explains the primary goals of the Uncovering Genome Mysteries project._
I found this video to be a little hard to understand, first time through. The sound has a bit of contrast, making it hard to hear. I closed my eyes and listened to it a couple of times before I could make it out.​


> *Background*
> 
> Last year, World Community Grid volunteers completed the calculations for the Uncovering Genome Mysteries project, which examined approximately 200 million genes from a wide variety of life forms to help discover new protein functions. The project’s main goals include:
> 
> ...





> *Transferring 30 Terabytes of Data*
> 
> The data generated by _World Community Grid volunteers_ has been regrouped on the new bioinformatics server at the Oswaldo Cruz Foundation (Fiocruz), under the direction of Dr. Wim Degrave. Additionally, a full copy of all data has been sent to co-investigator Dr. Torsten Thomas and his team from the Centre for Marine Bio-Innovation & the School of Biological, Earth and Environmental Sciences at the University of New South Wales in Sydney, Australia. At the University of New South Wales, the results from protein comparisons will help to interpret the analyses of marine bacterial ecosystems, where micro-organisms, coral reef, sponges and many other intriguing creatures interact and form their life communities. The dataset, more than 30 terabytes under highly compressed form, _took a few months to be transferred_ from Brazil to Australia.





> *Data Processing and Analysis at Fiocruz
> *
> Some of the data are currently being used in projects such as vaccine and drug design against arboviruses such as Zika, dengue, and yellow fever viruses, but also for understanding of the interaction of bacteria with their environment and how this reflects in their metabolic pathways, when free living bacteria are compared with their close relatives that are human pathogens, such as Mycobacterium tuberculosis versus environmental mycobacteria.





> *Searching for Partnerships*
> 
> Fiocruz is looking for partnerships that would add extra data analytics and artificial intelligence to the project. The researchers would like to include visualizations of functional connections between organisms as well as particularities from a wide variety of organisms, including deep sea thermal vent archaeal bacteria; bacteria and protists (any one-celled organism that is not an animal, plant or fungus) from soil, water, land, and sea or important for human, animal, or plant health; and highly complex plant, animal, and human genomes.



*We thank everyone who participated in the World Community Grid portion of this project, and look forward to sharing more updates as we continue to analyze the data.
*
Some info was not copied to this post. For the Whole article, Click HERE.


----------



## Arjai (Dec 3, 2017)

*New Facility and Expanded Plans for the Mapping Cancer Markers Research Team*





By:* Dr. Igor Jurisica*
Krembil Research Institute, University Health Network, Toronto

*30 Nov 2017 *

*Summary*
The Mapping Cancer Markers researchers recently moved to a new institute, but continues analyzing results, planning for expanded research, and creating new work units throughout the transition. Learn about their plans in this article.



> *Background*
> 
> The Mapping Cancer Markers (MCM) project continues to process data to identify biomarkers for ovarian cancer. We are also in the process of analyzing MCM results from the lung cancer dataset, and we are finalizing preparation of the new work units for sarcoma, a type of malignant tumor. We will devote more space in the next project update to this work. Below we provide details about an exciting new development in the team.





> *The Move*
> 
> After more than 17 years at Ontario Cancer Institute (now Princess Margaret Cancer Centre), we got an opportunity to join Krembil Research Institute (KRI) to work on a more complex approach to chronic diseases, where we moved in mid-November. ..the physical move was smooth, and our severs stayed in the original server rooms, reducing the risk of any hiccup for World Community Grid work units and results. We will not only continue, but will expand on our research..





> *New Computational Biology Platform*
> 
> Importantly, we are in the finalizing stages of paperwork to embark on a newly-funded research by the Ontario Government: _The Next Generation Signalling Biology Platform_. This will provide us funds to create a software infrastructure for the comprehensive, integrative computational biology analyses workflows, in collaboration with translational research and clinical trials groups.




*Thank you to everyone for your support, and we look forward to providing additional updates as our work progresses.*

Edited for size, the Whole Story, HERE.


----------



## Arjai (Dec 9, 2017)

*Planned Maintenance on Saturday, December 9 (Completed)
	

	
	
		
		

		
		
	


	


*

*Summary*
We are upgrading the software on multiple parts of the system on Saturday, December 9, beginning at 2:00 UTC. 

Update:  This work has been completed.  It finished at 3:55 UTC.  Thanks for participating!

Um, it is Friday and their done already?


----------



## Arjai (Dec 15, 2017)

*Sustainable Water Data Available to Interested Scientists*

*By: Gerard P. Learmonth Sr.*, _*M.B.A.*_, *M.S.*, *Ph.D.*
University of Virginia

*14 Dec 2017*

*Summary*
Dr. Gerry Learmonth, the principal investigator for the Computing for Sustainable Water project, gives an update on the primary findings of the project as well as how other scientists can access the data.




​


> *Project Background*
> The Computing for Sustainable Water project was created to study the effects of potential management practices on the Chesapeake Bay Watershed, a large watershed in the southeastern United States, and to gain deeper insights into what actions can lead to restoration, health, and sustainability of watersheds around the world.





> *Our Results*
> The project is now finished. _For all the contributors on the World Community Grid – a sincere thank you!_ The project started when then President Obama issued an Executive Order to restore and sustain the quality of the Chesapeake Bay Watershed. This project involved a very detailed simulation of the Bay with the goal of better understanding the impact of a set of practices—in fact, best management practices—on achieving that goal.





> *Further Reading and Data*
> Please check out the Computing for Sustainable Water website. There you will find a new, as yet unpublished paper about the project, entitled “Impact of Best Management Practices on Water Quality.”
> For other scientists and others interested in doing a deep dive into the data, we’ve also created a document describing how the results of the experiments are formatted, and how to request data from particular experiments. We invite anyone doing research in this area to make use of the data.



*"To all the World Community Grid volunteers who donated to this project – thank you!"*

More of the Story, HERE.


----------



## Arjai (Jan 5, 2018)

*Planned Maintenance on Saturday, January 6
	

	
	
		
		

		
		
	


	


*

*4 Jan 2018*

*Summary*
We are updating the operating system on our servers on Saturday, January 6, beginning at 2:00 UTC. 
	

	
	
		
		

		
		
	


	




We will be applying an important operating system update to our servers on Saturday, January 6, beginning at 2:00 UTC. We anticipate that the work will take approximately four hours.
During this time, volunteers will not be able to upload or download new work. The website will not be accessible during this time. No action is required by volunteers, as devices will automatically retry their connections after the maintenance work is completed.

We appreciate your patience and participation.

_Plan accordingly! _

__


----------



## Arjai (Jan 25, 2018)

*Computing for Clean Water Results Inspire Further Study*

*By: The Computing for Clean Water team 
22 Jan 2018 *

*Summary*
An international team of researchers was inspired by the *Computing for Clean Water* project to do a series of further simulations, using a slightly different model and studying the diffusion of oxygen molecules as well as water molecules. Learn about their results, which validated the work done on *World Community Grid*, in this article.












> *Background*
> The Computing for Clean Water project was created to provide deeper insight on the molecular scale flow of water through a novel class of filter materials. Thanks to the millions of virtual experiments that the team was able to run on *World Community Grid*, they discovered conditions under which water can pass through tiny carbon nanotubes much more efficiently. This groundbreaking understanding of a fundamental physical process could help improve access to clean water for millions of people through more efficient water filtration and desalination, and also may have applications in clean energy and medicine.





> *The Value of Independent Verification*
> ...
> The story behind these articles illustrates an important point in science: the value of independently verifying new results. In this case, an international team with lead author Eduardo Cruz-Chú at ETH Zurich was inspired by our results to do a series of complementary simulations. The team used a somewhat different model of the water flow, and also focused on the diffusion of oxygen atoms in the water.
> ...
> These authors did, however, obtain a smaller diffusion enhancement using their model than what we had reported in our study. In the field of molecular dynamics simulations, it is quite common to see some variations depending on the details of the models used. So, we did a series of further simulations to test the robustness of our original results. What we found is that the effect of phonons on the water diffusion is always large compared with a phonon-free calculation, even allowing for considerable variation in some of the parameters used in our model.





> *Differences between Studies *
> A significant difference between the two studies concerns the type of diffusion that is being monitored – we only considered water molecules, whereas our colleagues studied also the diffusion of oxygen atoms. Their results suggest that the diffusion of other molecules or ions will be different. This difference is something that we hope to study in future, since it has implications for how effective nanotubes can be in filtering out unwanted molecules and ions, for example salt ions from seawater.
> ...
> In the end, the ultimate arbiter of the importance of simulated results like ours will be hard experimental data. You can read our detailed response to the new article here.





> *In the meantime, we thank all World Community Grid participants in Computing for Clean Water for helping to obtain the original results, which are clearly getting the attention of the scientific community.*



_Excellent news. More stuffs than planned, from the initial work, is always good news! _

_Read the entire post, this has been edited, click this link to the __WCG Page._


----------



## Arjai (Jan 28, 2018)

Hmmm, it has gotten a little quiet in here. Are my posts getting too boring?  Do I need to change the format? I know that the text palette has changed and the colors are more muted...

*Is this Color even readable?*
* Is this Color even readable?
Is this Color even readable?
 Is this Color even readable?
Is this Color even readable?
 Is this Color even readable?
Is this Color even readable?*
* Is this Color even readable?*
*Is this Color even readable?*
* Is this Color even readable?*
*Is this Color even readable?*
*Is this Color even readable?*
*None of these colors have any POP
The blue, from the last palette, was a bit bolder.*

*Case in Point... **Old Blue*
*and the **New Blue*

Old Blue
*



*
New Blue





Another New Blue




No POP!!

It's like sleepy time around here!

I WANT MY BLUE BACK!!!!!​@W1zzard ?


----------



## Arjai (Feb 9, 2018)

*Planned Maintenance on Monday, February 12
	

	
	
		
		

		
		
	


	


*

*8 Feb 2018 * 

*Summary*

We are updating the operating system on our servers on Monday, February 12 beginning at 15:00 UTC.

We will be applying an important operating system update to our servers on Monday, February 12, beginning at 15:00 UTC. We anticipate that the work will take approximately four hours. 

During this time, volunteers will not be able to upload or download new work, and the website will not be accessible. No action is required by you, as your devices will automatically retry their connections after the maintenance work is completed.
We appreciate your patience and participation.

_Hope it goes smoothly!_


----------



## Arjai (Mar 2, 2018)

*Planned Maintenance on Monday, March 5*





*1 Mar 2018 *

*Summary*
We are performing database updates on our servers on Monday, March 5 beginning at 18:00 UTC.



> We will be performing a database update to our servers on Monday, March 5, beginning at 18:00 UTC. _We anticipate that the work will take approximately one hour. _
> During this time, volunteers will not be able to download new work. No action is required by you, as your devices will automatically retry their connections after the maintenance work is completed.
> We appreciate your patience and participation.


----------



## Arjai (Mar 9, 2018)

*Microbiome Immunity Project Already Extending the Known Universe of Protein Structures*






*By: Tomasz Kosciolek, PhD
 UC San Diego Center for Microbiome Innovation                        

7 Mar 2018 *

*Summary*
The Microbiome Immunity Project is off to a great start on predicting the structures of hundreds of thousands of bacterial proteins within the human gut. Read about their progress and their plans in their first project update.










*Background*
The Microbiome Immunity Project was created to better understand the role of the microbiome in intestinal immune response and diseases such as Type 1 Diabetes (T1D) and Inflammatory Bowel Disease (IBD). In this project, we predict structures of bacterial proteins and use this information to annotate their functions and to understand host-microbiome interactions which are responsible for the pathology of IBD and T1D. This is a massive undertaking, as the human gut microbiome has more than 2 million unique proteins, with hundreds of thousands of proteins potentially interacting with human cells. A project of this scale is only possible thanks to the power of _World Community Grid._

*Our Progress So Far*



> With your help, we have already predicted the structures of over 50,000 prioritized proteins! In the grand scheme of the 2 million unique bacterial proteins in our gut, this may not seem like a lot, but keep in mind that the experimental work to date covers only approximately 125,000 proteins. In only 6 months we have made tremendous progress by extending our universe of known protein structures by almost 28 percent!






> You may have already realized that at this pace, predicting all bacterial protein structures would take years to complete. Fortunately, we don’t have to predict every single structure, because proteins can be grouped into families. These families consist of proteins with similar structures and functions, enabling a comprehensive understanding of the family’s function with only one representative member per family. Once we identify protein families of interest, we will investigate them in more detail.






> In the meantime, we have adjusted our strategy on how to prioritize the predictions. Instead of looking only at bacterial genomes (genes of an individual bacterial species), we are investigating bacterial pangenomes (genes of all bacterial strains belonging to the same species)...





> We are now extracting information from your predictions, and during the course of the project we plan to make the data available to the public for other exciting research. We are also working on methods to improve predictions of protein functions, enabling us to find the important protein families involved in T1D and IBD among thousands of predictions we have made so far.




_All this progress has been made possible thanks to your generous contributions! There is still a lot to discover about the microbiome, but with each computation that you support we are getting a step closer to having a more detailed picture of this important ecosystem inside each of our bodies and understanding IBD and T1D. So, thank you and let’s continue working together on unraveling the mysteries of microbiome!_


----------



## Arjai (Mar 21, 2018)

Drug Search for Leishmaniasis Project Continues Quest for Better Treatments





By: *Dr. Carlos Muskus López* 
Coordinator, Molecular Biology and Computational Unit, PECET University of Antioquia                        

*20 Mar 2018 *

*Summary*
The Drug Search for Leishmaniasis researchers recently conducted lab testing on 10 compounds. The testing showed that none of the compounds were good potential treatments, and the researchers will turn their attention to additional compounds.  



*Short description of the team’s latest findings*



> Leishmaniasis is one of the most neglected tropical diseases in the world, infecting more than two million people in 98 countries. The current treatments for all forms of leishmaniasis can cause severe side effects, including death. Furthermore, drug resistant parasites are causing major problems in many countries. For these reasons, there is an urgent need for new, safe, and inexpensive drug compounds.





> The Drug Search for Leishmaniasis team has continued their lab testing since their last update. The most recent round of testing involved 10 compounds that had been identified as having potential to be safer, more effective treatments.
> 
> The compounds were tested first for toxicity, then for effectiveness against two common parasites that can cause leishmaniasis. Based on the testing, _none of the compounds tested would be effective treatments for the disease._





> Once the team has obtained additional funding, they will test additional compounds that may be useful in treating leishmaniasis.



Anyone interested in a full scientific description of this latest round of testing can read below. Thanks to everyone who supported this project.
*In vitro evaluation of the anti-leishmanial activity of predicted molecules by docking*



> *Conclusion*
> 
> _None of the 10 molecules evaluated showed promising anti-leishmanial results based on the in vitro cytotoxicity inhibition assays._



_Well, if nothing else, they have narrowed the field some! _

_I hope they can secure the funding needed to continue the research. Of all the good thing we hear, about these projects, it is refreshing to see that not everything is all rosy. However, it is this type of basic research that is needed and can, often, lead to new discoveries that were not expected. _

_I want to congratulate them on all the hard work and wish them the best in securing funding for more research._

There is more, mostly scientific stuff, on the WCG site.

__
​


----------



## manofthem (Mar 21, 2018)

Arjai said:


> Drug Search for Leishmaniasis Project Continues Quest for Better Treatments
> 
> 
> 
> ...



Just saw that notice and took a quick gander.  does this mean a new project is on the brink? Certainly wouldn't mind that


----------



## Arjai (Mar 30, 2018)

*Help Stop TB Researchers Seek New Team Members*

*By: Dr. Anna Croft
University of Nottingham, UK*

*29 Mar 2018*

*Summary*
The Help Stop TB researchers are looking to expand their team as they analyze the large amount of data generated by World Community Grid. Read about their plans in this update.






> *Background*
> Tuberculosis remains one the world’s major killers from infectious disease. The World Health Organization announced in a recent report that 6.3 million new cases of TB were reported in 2016, up from 6.1 million in 2015.
> Tuberculosis can be difficult to treat because the bacterium which causes the disease has an unusual coating which protects it from many drugs and from a person’s immune system. Among the fats, sugars and proteins in this coat, the TB bacterium contains a type of fatty molecules called mycolic acids. The Help Stop TB (HSTB) project simulates the behavior of these molecules to better understand how they offer protection to the TB bacteria. With the resulting information, scientists may be able to design better ways to attack this protective layer and therefore develop better treatments for this deadly disease.





> *Congratulations and Changes*
> Since our last update, we’ve been undergoing further changes to the project team.
> Athina Meletiou is now Dr. Athina Meletiou, having successfully passed her PhD viva (oral examination). She has taken up an EU-funded postdoctoral fellowship working on another large data project of one of our colleagues at University of Nottingham, Professor Charles Laughton, “Advanced multiscale simulation of DNA.”
> Athina will still be touching base, as we will be preparing publications from her work in the near future. In the meantime, we wish her well with her next step in her career, with many thanks for the hard work she has put into the HSTB project to grow it into the success it has been so far.





> *The Search for New Team Members*
> As a result of Athina’s move, we are now actively looking for new team members, especially those with a strong interest in data science, as we now have a significant quantity of data to mine, for which we would love to apply new approaches. We also want to tackle the development of accurate membrane models, now that we have sufficient atomistic data. Applications from suitably qualified chemists, biochemists, mathematicians, engineers, and computer scientists are welcomed, both for PhD-level and postdoctoral posts.



_Best of luck to Athina, and to the HSTB team. It is good to see that these projects not onlyhelp us, the public, but also provide meaningful, and gainful, employment for these highly skilled, and learned, people. What concerns me though, is that the pool of potential candidates, for this position, is not getting bigger._

*The WHOLE Story, HERE*






STEM Education Data and Trends 2014



The share of grade 8 students at or above the proficient level rose by 10 percentage points, to 36%, from 2000 to 2013 (Figure  1-2). Changes between 2000 and 2013 for most groups were in the range of 8–13 percentage points; however, Asians or Pacific Islanders gained 19 percentage points, and 60% of them performed at or above the proficient level in 2013. English language learners gained just 3 percentage points, with only 5% reaching the proficient level in 2013 (Appendix Table  1-2).

The percentage of all students in grade 12 who were at or above the proficient level in 2013 stood at 26%, below that of eighth graders (36%) and fourth graders (42%) (Figure  1-2). Changes between 2005 and 2013 were generally in the range of 2–4 percentage points, and only Asians or Pacific Islanders were moderately near the 50% mark (Appendix Table  1-2).

Chapter 1. Elementary and Secondary Mathematics and Science Education Open/close all chapter tables and charts. Chapter downloads. Print Elementary and Secondary Mathematics and Science Education PDF. Share chapter.

National Science Board
Science & Engineering Indicators 2016
Table 1-4 Mean mathematics literacy assessment scores of 15-year-old students in developed countries, by country: 2012

Score higher than United States' score of 481
Singapore                574
South Korea            554
Japan                        536
Switzerland             531
Netherlands            523
Estonia                     521
Finland                     519
Canada                     518
Poland                      518
Belgium                    515
Germany                  514
Austria                      506
Australia                   504
Ireland                      502
Slovenia                    501
Denmark                  500
New Zealand           500
Czech Republic       499
France                      495
United Kingdom    494
Iceland                    493
Latvia                      491
Luxembourg          490


_My point in all of this is, there are smart people left in this world. But the number of them that are able and willing to Study the Sciences, is falling. Especially, in the United States. The NSF has been doing what they can to amend that but, they probably need more money to actually be effective._

_I am no expert, on these trends but, I read these charts and see what I see._

__


----------



## Arjai (Apr 21, 2018)

*W**hat's tech got to do with it? We went to SXSW to talk about how volunteer computing can help save the planet**.*

*20 Apr 2018  *

*Summary*
World Community was invited to give two presentations on the power of crowd-sourced computing power at SXSW 2018 in Austin, Texas. See the full presentations, as well as a short video with excerpts from both, in this article.



> In this short video, two scientists talk about the crucial issues they're researching: climate change and clean energy. World Community Grid project manager Juan Hindo and software developer Jonathan Armstrong explain the important role of volunteers in accelerating research.













> Last year, IBM issued a call for proposals to climate change and environmental researchers, offering them not only World Community Grid supercomputing power, but also data from The Weather Company and storage on IBM Cloud Object Storage. In this video, IBM Distinguished Engineer and Chief Scientist Lloyd Treinish joins Juan and Jonathan to talk about the most pressing issues in climate change, the extent of the climate change science community's technical needs, and the opportunity for the tech community to help.













> Dr. Alan Aspuru-Guzik was the lead researcher for the Clean Energy Project, which uncovered a large number of potential new and improved solar cells. In this presentation, Alan gave an overview of the work so far, and talked about his plans for further extending his collaboration with World Community Grid and other organizations.


----------



## Arjai (Apr 27, 2018)

*Announcing Three Winning Climate Change Projects*


*26 Apr 2018 * 




*Summary*
After a rigorous review of dozens of applications from all over the world, we're excited to announce the research groups who will receive super-computing power, weather data, and cloud storage from IBM to accelerate climate change science.






> As our planet faces the mounting impacts of climate change, scientists are on the front lines of understanding complex consequences and developing solutions.
> 
> We've heard from climate change scientists that common bottlenecks they face include limited access to weather data, and insufficient computing power and data storage capacity to accurately simulate the impacts of climate change.





> As a result of this call for proposals, we received more than 70 responses from researchers all over the world. We're thrilled to announce the winners of these resources:





> *Impact of climate change on public health (Emory University, USA)*
> 
> *Impact of atmospheric aerosols on climate change (Far Eastern Federal University, Russia)*
> 
> *Rainfall modeling in Africa (Delft University of Technology, Netherlands)*





> These proposals were evaluated by IBM scientists and an outside team of experts for scientific merit, potential to contribute to the global community's understanding of specific climate and environmental challenges, and the capacity of the research team to manage a sustained research project. Researchers also agreed, if they received these resources, to abide by our open data policy by publicly releasing the data from their collaboration with us.





> _In the coming months, we'll be updating everyone as we get ready to launch these projects. _In the meantime, current World Community Grid volunteers who want to support these projects as soon as they start can go to the My Projects page to opt in to new projects as they become available.



*Fresh Meat, umm,err, I mean, New Projects!!  *

*The Whole article, with more, is **HERE.*

_The resources IBM is providing for these projects:_



> *Supercharged by IBM Resources*
> 
> Each of these three winning projects will use one or more of these resources:
> 
> ...



_*More about these resources, *__*HERE*_

_**_


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## Boatvan (Apr 27, 2018)

Arjai said:


> *Fresh Meat, umm,err, I mean, New Projects!! *


My takeaway from this post


----------



## Arjai (May 23, 2018)

*FightAIDS@Home – Phase 2 Prepares for A New Stage*


*By: The FightAIDS@Home research team*

*22 May 2018*

*Summary*
       The FightAIDS@Home – Phase 2 researchers are making plans to write a paper and to test new compounds as part of the continuing search for new and better treatments.




*Background* 


> ...UNAIDS estimates that 36.7 million people were living with HIV in 2016. And while AIDS-related deaths have decreased significantly since their peak in 2005, approximately 1 million people died of causes related to AIDS in 2016. (See the UNAIDS website for more statistics.)





> HIV continues to be a challenge because it quickly mutates in ways that make existing drug treatments ineffective. FightAIDS@Home joined World Community Grid more than a decade ago with the simple but challenging goal of finding new treatments for HIV. During Phase 1 of the project, the team identified thousands of potentially promising candidates to be confirmed experimentally in the lab. However, because it’s cost and time prohibitive to lab test all the potential candidates, Phase 2 was created to prioritize the candidate compounds by evaluating them with more accurate methods.



*Current Work* 


> Our team is processing the current type of work units through World Community Grid as quickly as possible. Once these work units are completed, we plan to write a paper about the process, including its strengths, limitations, and lessons learned.





> We are also planning to use *World Community Grid’s* computing power to *analyze new compounds* that are important to our work with the HIVE Center at the Scripps Research Institute. *This work will begin after we run a sample of these new compounds on our own grid computing network.*



_Another new Project, on it's way!_

*Thank You*
We appreciate everyone who continues to donate their computing power to the search for better anti-HIV treatments. _We also encourage everyone to opt in to Phase 2 of the project—*the more quickly we can run through the current work units, the sooner we can move ahead to new compounds.*

Always good news to see progress and the opportunity to help with new project discoveries!_

_A little more info, __HERE_

*Release Notes for BOINC 7.8*

*Changes in 7.8.5*
(Mac only release) 
Mac screensaver: under OS 10.13+ if the BOINC screensaver cannot display a graphics app with hardware acceleration using the IOSurface APIs because the app has not been linked with the current graphics libraries, then display it using the much slower CGWindowListCreateImage API. 

If you are crunching on a Macintosh, this is for YOU! Otherwise, us PC user's are fine!


----------



## Arjai (May 26, 2018)

*Updates to World Community Grid Policies and Options for Data Protection*


*25 May 2018*

*Summary* 

We have updated our Online Privacy Statement and Terms of Use, and are introducing new features to give World Community Grid volunteers more control over their data.

A few of the major changes are listed below. You can read our updated Online Privacy Statement and Terms of Use for more details. 

The changes go into effect as of May 25, 2018. Thanks to all volunteers for your continued support and participation.

_More details in the links above and HERE on the WCG post_


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## Arjai (Jun 1, 2018)

*Planned Maintenance on Monday, June 4*

*31 May 2018 *

*Summary*
       We are updating the operating system on our servers on *Monday, June 4, beginning at 15:00 UTC.*

We will be applying an important operating system update to our servers on Monday, June 4, beginning at 15:00 UTC. We anticipate that the work will take approximately four hours.

During this time, volunteers will not be able to upload or download new work, and the website will not be accessible. No action is required by you, as your devices will automatically retry their connections after the maintenance work is completed.

We appreciate your patience and participation.


----------



## Arjai (Jun 6, 2018)

*Smash Childhood Cancer Researchers Choose New Target Molecules*


By: *Dr. Akira Nakagawara, MD,* *PhD* 
CEO of the Saga Medical Center KOSEIKAN and President Emeritus, Chiba Cancer Center

*5 Jun 2018*

*Summary*
       The Smash Childhood Cancer research team recently chose several new target molecules as the focus of their current work. Learn more about the significance of these molecules in this update.














Almost a year and a half has passed since we kicked off the Smash Childhood Cancer project. On behalf of all the team members, _I really appreciate volunteers' contributions to this project. _



> By adding new members to the original group from the Help Fight Childhood Cancer project, our research team for Smash Childhood Cancer has become quite international, with pediatricians from Japan, Hong Kong, and the United States involved in this big, new drug development project.
> 
> While the Help Fight Childhood Cancer project's goal was to search for new and better treatments for *neuroblastoma*, Smash Childhood Cancer addresses not only neuroblastoma, but other childhood cancers such as* brain tumors, osteosarcoma (bone cancer), germ cell tumors, hepatoblastoma (liver cancer), and others.*





> Several proteins--beta-catenin, *LIN28B* , *N-CYM* and others--have been newly chosen as target molecules....





> The *N-CYM *protein, which was discovered by my team and myself, is the novel driving gene product of neuroblastoma. The protein is only found in humans and chimpanzees, and is created through de novo evolution (meaning it is part of the evolution of the cancer). The protein is quite difficult to crystallize for some reason and we are still working on determining its exact structure so that drug discovery against it could begin.





> Recently, we received a grant from Japanese government to support our drug discovery against the *LIN28B *protein, which may help accelerate our progress on Smash Childhood Cancer.



_Once again, I would like to express our gratitude for volunteers all over the world who have been supporting the project. For children who are fighting childhood cancer, we would like to discover a new drug as soon as possible and develop a treatment without subsequent side effects. 

 A little more, __HERE_


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## Arjai (Jun 11, 2018)

*Release Notes for BOINC 7.10*

*Changes in 7.10.3*

(Mac only release)


Patch wxWidgets 3.1.0 to fix BOINC Manager crash on OS 10.6

*Changes in 7.10.2*


MGR: don't crash if GUI RPC returns empty reply
MGR: use "client" instead of "daemon"
MGR: Rename OK button to Save button
MGR: remove excess blank lines in notices
client: fix bug where client does tight loop if no_gui_rpc set
client, MGR: add auto-login
MGR: don't show Attach Wizard at startup if autologin in progress
client: make autologin work for account managers as well as projects
Mac client: Fix bug which caused BOINC client built with SDK OS 10.11 or later to fail to get correct system RAM size when running on older versions of OS X
Mac client: fix a bug which caused the BOINC client to crash immediately on launch under OS X versions OS 10.11 and earlier
client: update ca-bundle.crt to latest copy of certificates
boinccmd: show CPU/GPU resources in --get_task
Update all_projects_list.xml file.
Linux: Default working directory changed to /var/lib/boinc
Show build not OS platform in messages

*BOINC 7.10 now compatible with Domain Controllers*

Since BOINC 7.6.1 the test whether BOINC is being installed on a domain controller no longer returns an error. In the past the installer would make BOINC limited user accounts for the client to run with whether you installed as a user installation or as a service installation.
Since some time now these limited user accounts only get installed when BOINC is installed as a service, no longer on user installations. Because these limited user accounts were a problem for DCs that run with a global user account, you can install the new client and see that it now works. Do make sure to install as the user install, not as a service. (It may be that the service install is disabled, we'd like to get feedback on that.)
*Note*: do know that when you only allow BOINC to do work when no one is logged on, that this only works with the service installation. Using the user installation will only allow BOINC to do work when someone is logged in.
For all changes, fixes and additions, see the BOINC Version History.
*Known Issues*

The following issues are already known to the developers:
*Windows*

*Service Installation, GPU detection and Windows XP*: Due to problems with up-to-date GPU drivers causing BOINC to crash or hang, it was decided that for all versions of Windows the GPU detection will no longer work when BOINC is installed as a service. This may change in a future version, but only after the GPU manufacturers have adjusted their driver code. So even in Windows 2000 and XP you can now no longer install BOINC as a service yet still have it detect your GPU(s) and run work on it. This change is present since 6.12.38

_In it's entirety. Sure don't know the difference between user install and a service install. I guess I don't really care, at this point. Since, I also don't know what a Domain Controller is, I am probably immune from the update. 

It also mentions something about moving directories in Linux. Not sure this would benefit my Linux boxes, or not, since they seem to be running just fine. _

Download it HERE


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## Arjai (Jun 21, 2018)

*Microbiome Immunity Project Researchers Create Ambitious Plans for Data*


By: *Dr. Tomasz Kościółek* and *Bryn Taylor*
University of California San Diego

*19 Jun 2018*

*Summary*
       The Microbiome Immunity Project researchers—from Boston, New York, and San Diego—met in person a few weeks ago to make plans that include a 3D map of the protein universe and other far-ranging uses for the data from the project.









_The research team members pictured above are (from left to right): Vladimir Gligorijevic (Simons Foundation’s Flatiron Institute), Tommi Vatanen (Broad Institute of MIT and Harvard), Tomasz Kosciolek (University of California San Diego), Rob Knight (University of California San Diego), Rich Bonneau (Simons Foundation’s Flatiron Institute), Doug Renfrew (Simons Foundation’s Flatiron Institute), Bryn Taylor (University of California San Diego), Julia Koehler Leman (Simons Foundation’s Flatiron Institute). Visit the project's Research Participants page for additional team members._​


> During the week of May 28, researchers from all Microbiome Immunity Project (MIP) institutions (University of California San Diego, Broad Institute of MIT and Harvard, and the Simons Foundation’s Flatiron Institute) met in San Diego to discuss updates on the project and plan future work.
> Our technical discussions included a complete overview of the practical aspects of the project, including data preparation, pre-processing, grid computations, and post-processing on our machines.





> We were excited to notice that if we keep the current momentum of producing new structures for the project, we will _double_ the universe of known protein structures (compared to the Protein Data Bank) by mid-2019! We also planned how to extract the most useful information from our data, store it effectively for future use, and extend our exploration strategies.





> We outlined three major areas we want to focus on over the next six months.



*Structure-Aided Function Predictions *



> We can use the structures of proteins to gain insight into protein function—or what the proteins actually do. Building on research from MIP co-principal investigator Richard Bonneau’s lab, we will extend their state-of-the-art algorithms to predict protein function using structural models generated through MIP. Using this new methodology based on deep learning, akin to the artificial intelligence algorithms of IBM, we hope to see improvements over more simplistic methods and provide interesting examples from the microbiome (e.g., discover new genes creating antibiotic resistance).



*Map of the Protein Universe *



> Together we produce hundreds of high-quality protein models every month! To help researchers navigate this ever-growing space, we need to put them into perspective of what we already know about protein structures and create a 3D map of the “protein universe.” This map will illustrate how the MIP has eliminated the “dark matter” from this space one structure at a time. It will also be made available as a resource for other researchers to explore interactively.



*Structural and Functional Landscape of the Human Gut Microbiome *



> We want to show what is currently known about the gut microbiome in terms of functional annotations and how our function prediction methods can help us bridge the gap in understanding of gene functions. Specifically, we want to follow up with examples from early childhood microbiome cohorts (relevant to Type-1 diabetes, or T1D) and discuss how our methodology can help us to better understand T1D and inflammatory bowel disease.


_The future of the Microbiome Immunity Project is really exciting, thanks to everyone who makes our research possible. Together we are making meaningful contributions to not one, but many scientific problems! _

_Exciting! I hope to see more from this team! Wouldn't it be nice to rid ourselves of Diabetes!!!_

__

_It is all here in this post. The original WCG post is __HERE__._

__


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## Arjai (Jun 26, 2018)

*Planned Maintenance on Tuesday, June 26*


*25 Jun 2018   * 




*Summary*
       We are updating the operating system on our servers on Tuesday, June 26, beginning at 18:00 UTC.                                                      


We will be applying an important operating system update to our servers on Tuesday, June 26, beginning at 18:00 UTC. We anticipate that the work will take approximately four hours.

During this time, volunteers will not be able to upload or download new work, and the World Community Grid website will not be accessible. No action is required by you, as your devices will automatically retry their connections after the maintenance work is completed.

We appreciate your patience and participation.


----------



## Arjai (Jun 27, 2018)

*Data from Help Cure Muscular Dystrophy Project Helps Shed Light on the Mysteries of Protein Interactions*


By: *Dr. Alessandra Carbone*
Sorbonne  Université

*26 Jun 2018 *

*Summary*

       Protein-protein interactions are the basis of cellular structure and function, and understanding these interactions is key to understanding cell life itself. Dr. Alessandra Carbone and her team continue to analyze data on these interactions from the Help Cure Muscular Dystrophy project, and they recently published a new paper to contribute to the body of knowledge in this field. 









 _In the video above, Dr. Alessandra Carbone gave an overview of the Help Cure Muscular Dystrophy project and its work as of 2014. Since that time, she and her team have published several papers using the project data, including the paper described in this update._ ​Dr. Alessandra Carbone (principal investigator of the Help Cure Muscular Dystrophy project) and team have published a paper entitled "Hidden partners:  Using cross-docking calculations to predict binding sites for proteins with multiple interactions" in the journal _Proteins_. 



> Protein interactions are the basis for most biological functions. How they interact with each other and other compounds (such as DNA, RNA, and ligands) in the cell is key to understanding life and disease functions. Complicating things, proteins often interact with more than one other kind of protein. To better understand protein functions, tools are required to uncover these potential interactions.
> 
> Different parts (surfaces) of the protein can be binding sites that attract another protein. This paper describes a methodology the research team developed to better predict these alternative binding sites. A subset of the Help Cure Muscular Dystrophy project data was used to validate their technique, which will be subsequently applied to the whole dataset computed via *World Community Grid.*





> RESEARCH ARTICLE
> *Hidden partners: Using cross‐docking calculations to predict binding sites for proteins with multiple interactions*
> 
> Nathalie Lagarde
> ...





> *Abstract*
> 
> Protein‐protein interactions control a large range of biological processes and their identification is essential to understand the underlying biological mechanisms. To complement experimental approaches, in silico methods are available to investigate protein‐protein interactions. Cross‐docking methods, in particular, can be used to predict protein binding sites. However, proteins can eract with numerous partners and can present multiple binding sites on their surface, which may alter the binding site prediction quality





> For the large majority of these proteins, we show that the predicted alternate binding sites correspond to interaction sites with hidden partners, that is, partners not included in the original cross‐docking dataset. Among those new partners, we find proteins, but also nucleic acid molecules. Finally, for proteins with multiple binding sites on their surface, we investigated the structural determinants associated with the binding sites the most targeted by the docking partners.



Full Published Paper, available for rent or purchase, HERE

Full WCG story, copied here, can be found HERE

_This is a lot to wrap my head around but, I must confess, I listened to all 29 minutes of the video. I am sure I could eventually glean more from this video, but I found myself distracted by Alessandra's voice. As I've mentioned before, I have a bit of a crush on Dr. Carbone. She actually has such a great grasp on this subject, she can colloquially explain it, in English, beautifully._

_Of course, aside from my musings, this is a VERY important step in Biological study. I can't possibly explain this importance but, I do know that what Dr. Carbone, and her team, are doing will have a great effect on the future of Genetic Disease's._


----------



## Arjai (Jul 5, 2018)

*The Expanding Frontiers of Carbon Nanotube Technology*

*3 Jul 2018*

*Summary*
       The Clean Water Project made an exciting discovery about the possible applications of carbon nanostructures to water purification, biomedical research, and energy research. Dr. Ming Ma, one of the scientists on the project, recently published a paper that summarizes the current status of work in this field. 




​


> Dr. Ming Ma (of the Computing for Clean Water project) at Tsinghua University recently published a paper in the Journal of Micromechanics and Microengineering entitled "Carbon nanostructure based mechano-nanofluidics." The paper is a thorough survey of all the recent research work on fluid flow in carbon nanostructures, such as carbon nanotubes and graphene sheets.





> Carbon atoms can form single-atom thick sheets known as graphene. When these are rolled into tube shape, they are called carbon nanotubes....By using _World Community Grid_ to simulate water flow through carbon nanotubes at an unprecedented level of detail, the project's research team discovered that under specific conditions, certain kinds of natural vibrations of atoms inside the nanotubes can lead to a 300% increased rate of diffusion (a kind of flow) of water through the nanotubes.





> There is much research being conducted to understand how this happens and ultimately how to make best use of this property to potentially purify water, desalinate water, and meet other goals in biomedical and energy research.



You can read the paper at http://iopscience.iop.org/article/10.1088/1361-6439/aaa782.

Thanks to everyone who supported this project.

_More of the story, HERE._


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## Arjai (Jul 6, 2018)

*Planned Maintenance on Tuesday, July 10*

*5 Jul 2018*

*Summary*
       We are updating the operating system on our servers on _Tuesday, July 10, beginning at 14:00 UTC_.







We will be applying an important operating system update to our servers on Tuesday, July 10, beginning at 14:00 UTC. We anticipate that the work will take approximately four hours.

During this time, volunteers will not be able to upload or download new work, and the World Community Grid website will not be accessible. No action is required by you, as your devices will automatically retry their connections after the maintenance work is completed.

We appreciate your patience and participation.


----------



## phill (Jul 18, 2018)

I'll remember to look here in future if I have connection issues!!  

Thanks for the post @Arjai   Thanks to @Norton for pointing it out!!


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## phill (Jul 23, 2018)

It appears that Free-DC is down for the moment, not sure what is happening but can't seem to get any stats for the day at the moment


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## Arjai (Aug 2, 2018)

*Farewell and Hello to OpenZika Team Members*


*By: The OpenZika research team
1 Aug 2018*

*Summary*
        The data analysis continues while the OpenZika team bids farewell to one of the project co-investigators and brings on new team members.

*Project Background* 

*A change in roles* 


> Dr. Alexander Perryman will be leaving the OpenZika team. In mid-August, Dr. Perryman will become a Senior Scientist II at Repare Therapeutics, a start-up pharmaceutical company in Montreal, Quebec, Canada, that focuses on drug discovery for cancer.



*A fond farewell from Dr. Perryman* 


> “I have been working with the IBM team on different_ World Community Grid _projects for almost a decade. Starting with FightAIDS@Home, followed by GO Fight Against Malaria, and for the last two years with OpenZika, it has been a pleasure and a profound privilege to work with the IBM team, the project scientists, and the volunteers who donate their computer power to advance these projects that combat infectious diseases. Although I will be switching from academia to industry, and from infectious diseases to cancer, I will keep focusing on advancing the discovery of drugs that can make a significant impact by reducing suffering and improving human health. The OpenZika team will keep on fighting this good fight without me, and I am confident that progress against the Zika virus will continue to be made. I wish them well, and I thank all of you for your tremendous support during this last decade.”





> *How job creation and data analysis will be handled going forward*
> Dr. Melina Mottin, a research associate on the OpenZika team, has been trained by Dr. Perryman, and she will be in charge of the data analysis. She is also going to handle the file preparation to “feed the beast” (that is, to keep creating the docking jobs that you all crunch for us).



*Plans for Melina to visit Sean's lab* 

*New candidate inhibitors were recently discovered* 





In the figure above (created by Dr. Perryman), H-bond signifies hydrogen bonds (a key type of interaction that drives both the strength of binding and the specificity of binding to only the target that you want it to hit). In the image on the bottom right-hand corner, the spheres depict the results of AutoLigand calculations, which detect binding sites and characterize the “hot spots” that give the tightest binding. Green spheres represent hydrophobic interactions in the allosteric site, red spheres depict hydrogen bond acceptors, and blue spheres signify hydrogen bond donors. ​
*Upcoming publications* 


> One is a keynote review paper, “The A-Z of Zika drug discovery”, to be published in the journal _Drug Discovery Today_. The online version of this paper is now available here.





> The other paper, “Computational drug discovery for the Zika virus”, will be published soon in a special issue of the _Brazilian Journal of Pharmaceutical Sciences_. In this paper, we summarize current computational drug discovery efforts and their applicability to the discovery of anti-ZIKV drugs.





> In addition, Dr. Perryman, Dr. Ekins, and Dr. Joel Freundlich recently published the paper “Naïve Bayesian Models for Vero Cell Cytotoxicity” in the journal _Pharmaceutical Research_. (Read the paper here.)





> Moreover, the OpenZika project results will be presented at the 256th ACS National Meeting, on August 19-23, 2018, in Boston, MA, USA. Dr. Melina Mottin will be giving an oral presentation and presenting a poster titled “*OpenZika: Discovery of new antiviral candidates against Zika virus*”, in the session Chemoinformatics Approaches to Enhance Drug Discovery Based on Natural Products.



*Past publications and outreach* 

*New collaborations* 



> *New students*
> Dr. Andrade has hired a new graduate student, Bruna Souza, to work in the OpenZika project. She started working on Dr. Andrade’s lab in March 2018, and she is very enthusiastic about learning and collaborating with the project.





> *Status of the calculations*
> In total, we have submitted almost 5 billion docking jobs, which involved 427 different target sites. Our initial screens used an older library of 6 million commercially available compounds, and our current experiments use a newer library of 30.2 million compounds. We have already received approximately *4.6 billion *of these results on our server.





> Thus far, the more than 80,000 volunteers who have donated their spare computing power to OpenZika have given us more than *51,471 CPU*_* years’ *_worth of docking calculations, at a current *average of 64.5 CPU years per day! * Thank you all very much for your help!



*Fundraising* 

_"We are very grateful for all the volunteers who are donating their unused computing time to this project!  Thank you very much!"_

More of this Post, much more, can be found HERE.


----------



## Arjai (Aug 16, 2018)

*Planned Maintenance on Tuesday, August 21*


*15 Aug 2018                   *
*



*
*        Summary*
        We are updating the operating system on our servers on Tuesday, August 21, beginning at 14:00 UTC.







We will be applying an important operating system update to our servers on Tuesday, August 21, beginning at 14:00 UTC. We anticipate that the work will take approximately four hours.
During this time, volunteers will not be able to upload or download new work, and the website will not be accessible.
Volunteers will not need to take any particular action, as your devices will automatically retry their connections after the maintenance work is completed.
We appreciate your patience and participation.


----------



## phill (Aug 16, 2018)

I wonder if it's Windows 10 I mean... Server 2016


----------



## Arjai (Aug 17, 2018)

*Sarcoma Dataset Coming Soon to Mapping Cancer Markers Project*


*By: Dr. Igor Jurisica*
Krembil Research Institute, University Health Network, Toronto
*8 Aug 2018*

*Summary*
        In this comprehensive update, the Mapping Cancer Markers team explains how they are determining which genes and gene signatures carry the greatest promise for lung cancer diagnosis. They also introduce the next type of cancer--sarcoma--to be added soon to the project.



> The Mapping Cancer Markers (MCM) project continues to process work units for the ovarian cancer dataset. As we accumulate these outcomes, we continue to analyze MCM results from the lung cancer dataset. In this update, we discuss preliminary findings from this analysis. In addition, we introduce the sarcoma dataset that will be our focus in the next stage.





> *Patterns of gene-family biomarkers in lung cancer*
> In cancer, and human biology in general, multiple groups of biomarkers (genes, protein, microRNAs, etc.) can have similar patterns of activity and thus clinical utility, helping diagnosis, prognosis or predicting treatment outcome. For each cancer subtype, one could find large number of such groups of biomarkers, each having similar predictive power; yet current statistical and AI-based methods identify only one from a given data set.
> We have two primary goals in MCM: 1) to find good groups of biomarkers for the cancers we study, and 2) to identify how and why these biomarkers form useful groups, so we can build a heuristic approach that will find such groups for any disease without needing months of computation on World Community Grid. The first goal will give us not only information that after validation may be useful in clinical practice, but importantly, it will generate data that we will use to validate our heuristics.








> Multiple groups of biomarkers exist primarily due to the redundancy and complex wiring of the biological system. For example, the highly interconnected human protein-protein interaction network enables us to see how individual proteins perform diverse molecular functions and together contribute to a specific biological process, as shown above in Illustration 1. Many of these interactions change between healthy and disease states, which in turn affects the functions these proteins carry. Through these analyses, we aim to build models of these processes that in turn could be used to design new therapeutic approaches.





> ...However, using these groups of biomarkers for patient stratification may not be straightforward. Groups of biomarkers often do not validate in new patient cohorts or when measured by different biological assays, and there are thousands of possible combinations to consider....





> At the present time, there is no effective approach to find all good groups of biomarkers necessary to achieve the defined goal, such as accurately predicting patient risk or response to treatment.





> The first goal of the Mapping Cancer Markers project is to gain a deeper understanding of the “rules” of why and how proteins interact and can be combined to form a group of biomarkers, which is essential to understanding their role and applicability. Therefore, we are using the unique computational resource of *World Community Grid * to systematically survey the landscape of useful groups of biomarkers for multiple cancers and purposes (diagnosis and prognosis).





> The combination of this clustering and the *World Community Grid *patterns enables us to identify generalized gene clusters that provide deeper insights to the molecular background of cancers, and give rise to more reliable groups of gene biomarkers for cancer detection and prognosis.
> Currently, we are focusing on the first-phase results from the lung cancer dataset, which focused on a systematic exploration of the entire space of potential fixed-length groups of biomarkers.








> As depicted above in Illustration 2, *World Community Grid* computed about 10 billion randomly selected groups of biomarkers, to help us understand the distribution of which group sizes and biomarker combinations perform well, which in turn we will use to validate heuristic approaches. Analysis showed that about 45 million groups of biomarkers had a high predictive power and passed the quality threshold. This evaluation gives us a detailed and systematic picture of which genes and gene groups carry the most valuable information for lung cancer diagnosis.








> To find the appropriate clustering algorithms and the right number of gene groups (clusters) we use different measures to evaluate the quality of each of the individual clustering. For instance, Illustration 3 (above) shows the results of the evaluation of the hierarchical clustering for different numbers of clusters. To evaluate clustering quality, we used silhouette value (method for assessing consistency within clusters of data, i.e., measure of how well each object relates to its own cluster compared to other clusters). A high silhouette value indicates good clustering configuration, and the figure shows a large increase in the silhouette value at 700 gene groups. Since this indicates a significant increase in quality, we subsequently select this clustering for further analysis.





> ...Since some gene-pattern-families are likely to occur even at random, we use enrichment analysis to ensure the selection only contains families that occur significantly more often than random.
> In the subsequent step we validated the selected generalized gene-pattern-families using an independent set of 28 lung cancer data sets. Each of these studies report one or several groups of biomarkers of up- or down-regulated genes that are indicative for lung cancer.






​


> Illustration 4 depicts a selection of the most prevalent pattern families and the studies that support them. Each circle in the figure indicates the strength of the support: The size of the circle represents the number of clusters in the family that where found significantly more often in the biomarker of this study. The color of the circle indicates the average significance calculated for all clusters in the pattern-family.






​


> Finally, we annotated the most effective gene-pattern-families and their gene clusters with molecular functions and pathways that the genes or corresponding proteins are involved in. Illustration 5 shows an example for such a gene-pattern-family that comprises gene-clusters 7, 1 and 21.



_This next quote is the business!_



> The word cloud visualization indicates that cluster 7 is involved in pathways related to GPCRs (G protein–coupled receptor) and NHRs (nuclear hormone receptors). In contrast, the genes in cluster 1 are highly enriched in EGFR1 (epidermal growth factor receptor) as well as translational regulation pathways. Mutations affecting the expression of EGFR1, a transmembrane protein, have shown to result in different types of cancer, and in particular lung cancer (as we have shown earlier, e.g., (Petschnigg et al., _J Mol Biol_ 2017; Petschnigg et al., _Nat Methods_ 2014)). The aberrations increase the kinase activity of EGFR1, leading to hyperactivation of downstream pro-survival signaling pathways and a subsequent uncontrolled cell division. The discovery of EGFR1 initiated the development of therapeutic approaches against various cancer types including lung cancer. The third group of genes are common targets of microRNAs. Cluster 21 indicates strong involvement with microRNAs, as we and others have shown before (Tokar et al., _Oncotarget _2018; Becker-Santos et al., _J Pathology_, 2016; Cinegaglia et al., _Oncotarget_ 2016).







​


> The final illustration evaluates the 20 most significantly enriched pathways for cluster 1. The size of the pathway nodes corresponds to the number of involved genes, and the width of the edges corresponds the number genes of overlapping between pathways. One can see that all pathways involved in translation are highly overlapping. mRNA-related pathways form another highly connected component in the graph. The EGFR1 pathway is strongly overlapping with many of the other pathways, indicating that genes that are affected by those pathways are involved in a similar molecular mechanism.





> *Sarcoma*
> After lung and ovarian cancers, next we will focus on sarcoma. Sarcomas are a heterogeneous group of malignant tumors that are relatively rare. They are typically categorized according to the morphology and type of connective tissues that they arise in, including fat, muscle, blood vessels, deep skin tissues, nerves, bones and cartilage, which comprises less than 10% of all malignancies (Jain 2010). Sarcomas can occur anywhere in the human body, from head to foot, can develop in patients of any age including children, and often vary in aggressiveness, even within the same organ or tissue subtype (Honore 2015). This suggests that a histological description by organ and tissue type is neither sufficient for categorization of the disease nor does it help in selecting the most optimal treatment.





> Diagnosing sarcomas poses a particular dilemma, not only due to their rarity, but also due to their diversity, with more than 70 histological subtypes, and our insufficient understanding of the molecular characteristics of these subtypes (Jain 2010).
> Therefore, recent research studies focused on molecular classifications of sarcomas based on genetic alterations, such as fusion genes or oncogenic mutations. While research achieved major developments in local control/limb salvage, the survival rate for “high-risk” soft tissue sarcomas (STSs) has not improved significantly, especially in patients with a large, deep, high-grade sarcoma (stage III) (Kane III 2018).






> For these reasons, in the next phase of *World Community Grid *analysis, we will focus on the evaluation of the genomic background of sarcoma. We will utilize different sequencing information and technologies to gain a broader knowledge between the different levels of genetic aberrations and the regulational implications.





> _We will provide a more detailed description of the data and the incentives in the next update._



*MORE detailed description? Really?*



> *Other news*
> We have secured a major funding from Ontario Government for our research: _The Next Generation Signalling Biology Platform_. The main goal of the project is developing novel integrated analytical platform and workflow for precision medicine. This project will create an internationally accessible resource that unifies different types of biological data, including personal health information—unlocking its full potential and making it more usable for research across the health continuum: from genes and proteins to pathways, drugs and humans.



"*Thank you*
This work would not be possible without the participation of *World Community Grid Members.* Thank you for generously contributing CPU cycles, and for your interest in this and other World Community Grid projects."

More of the DETAILS and bib. sheet are HERE

_The upshot of it all? Progress is being made, step by step, with the help of US cruncher's crunching the figures, that are saturating them with the info to use their knowledge to untangle this killer and it's many forms._

_I love what we can do, working together!  WCG is 'da BOMB, Yo!!!
_


----------



## Arjai (Sep 6, 2018)

*BOINC Developers and Leaders Gather in the UK*

*30 Aug 2018*

*Summary*
        This year's annual BOINC Workshop was held at University of Oxford and focused on the BOINC platform's future development. 




​
The Oxford e-Research Centre at University of Oxford recently hosted the BOINC Workshop 2018. 

BOINC, which stands for Berkeley Open Infrastructure for Network Computing, is an open-source software platform that supports volunteer computing. You can learn more about how BOINC is structured here.

World Community Grid project manager Juan Hindo, and technical team members Kevin Reed and Keith Uplinger, represented World Community Grid at the event.

This year's workshop included topics such as:    

How the new GDPR regulations may affect BOINC projects    


BOINC's technical development over the past year
 
Discussion of BOINC review, testing, and release processes
 
Overview of current BOINC projects
 
An open discussion on working together for the betterment of BOINC
Kevin Reed, who serves as Chairman of the BOINC Project Management Committee (PMC), gave a presentation on the development of the BOINC community. 

Keith Uplinger, Secretary of the BOINC PMC, discussed Google Test (a unit testing library for C++). 

Juan Hindo gave the group an overview of World Community Grid to the group.

You can see all of the presentations from the workshop here, and listen to audio from the conference here.

Original Story, HERE


----------



## Arjai (Sep 18, 2018)

*THOR Challenge Aims for New Heights in 2018*

*17 Sep 2018*

*Summary*
        CRUNCHERS SANS FRONTIERES, one of World Community Grid's most dedicated teams, issues the THOR Challenge each fall. Find out how you and your team can join this year's challenge and beat last year's results.




​
Every fall, the CRUNCHERS SANS FRONTIERES team begins a new school year by issuing the THOR Challenge (between September 24 and November 11 for 2018). The first week of this team challenge is open to every World Community Grid team, between September 24 and September 30. You can learn more about how the THOR Challenge is structured in this post by Thomas H.V. Dupont, Captain of the CRUNCHERS SANS FRONTIERES team.

Last year, 58 teams with 16,000 volunteers from 19 countries donated 1,172 hours of computing time during the THOR Challenge (second edition). Can we beat last year's statistics? If you are a team captain, register your team today. And if you're a team member, tell your captain that you'd like the team to be part of a challenge that aims to donate a record amount of computing time to seven worthy projects.

Thank you to everyone who supports the THOR Challenge, and who donates their computing power to World Community Grid.

*@Norton ? Starts in a WEEK!*

News Article HERE. Although this is all of it


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## phill (Sep 18, 2018)

I think we should have a go


----------



## Arjai (Sep 29, 2018)

*A Graduation, a Paper, and a Continuing Search for the Help Stop TB Researchers*


*By: Dr. Anna Croft*
University of Nottingham, UK

*28 Sep 2018*

*Summary*
        In this update, principal investigator Dr. Anna Croft shares two recent milestones for the Help Stop TB research team, and discusses their continuing search for additional researchers.            
	

	
	
		
		

		
			







The Help Stop TB (HSTB) project uses the massive computing power of _*World Community Grid*_ to examine part of the coating of _Mycobacterium tuberculosis_, the bacterium that causes tuberculosis. We hope that by learning more about the mycolic acids that are part of this coating, we can contribute to the search for better treatments for tuberculosis, which is one of the world's deadliest diseases.

*Graduation Ceremony for Dr. Athina Meletiou*
In recent news for the HSTB project, Dr. Athina Meletiou has now officially graduated. It was a lovely day, finished off with some Pimms and Lemonade in the British tradition.










​


> *Search for New Team Members Continues*
> We are still looking for suitably qualified chemists, biochemists, mathematicians, engineers and computer scientists to join our team, especially to develop the new analytical approaches (including machine-learning approaches) to understand the substantial data generated by the *World Community Grid* volunteers.
> 
> We will be talking to students from our BBSRC-funded doctoral training scheme in the next few days and encouraging them to join the project. Click here for more details.





> *Paper Published*
> Dr. Wilma Groenwald, one of the founding researchers for the HSTB project, recently published a paper describing some of the precursor work to the project. The paper, which discusses the folding behavior of mycolic acids, is now freely available on ChemRXiv.
> 
> We hope to have Athina’s first papers with *World Community Grid* data available later in the year, and will keep you updated.



Thank you to all volunteers for your support. 

*Congratulations Athina!! Great job, Dr. !!*

*This is the full article, from **HERE.*


----------



## Arjai (Oct 4, 2018)

*Outsmart Ebola Together Ends Current Phase of Work to Process Data, Look for Additional Collaborators*


*By: Dr. Erica Ollmann Saphire, PhD*
The Scripps Research Institute
*3 Oct 2018*

*Summary*
        The Outsmart Ebola Together research team is moving on to the data analysis phase of the project. Read more in this message from principal investigator Dr. Erica Ollmann Saphire. 



> Dear Volunteers,





> Your response to Outsmart Ebola Together has been terrific, and you have returned more than 350 million results to help find new drug targets against Ebola virus. Thank you!





> We now have more than enough data to analyze to find new directions for antiviral drugs. So, we are ending this phase of the project to finish processing the suggestions your computers, phones, and tablets have sent us.





> We will be stopping work on World Community Grid in the next three or four weeks.
> 
> We will be in touch with more information and results!
> 
> ...



Rest of the info, HERE.


----------



## Arjai (Oct 10, 2018)

*Planned Maintenance on Thursday, October 11* 


*8 Oct 2018   * 




*Summary*

        We are updating the operating system on our servers on Thursday, October 11, beginning at 14:00 UTC.

We will be applying an important operating system update to our servers on Thursday, October 11, beginning at 14:00 UTC.  We anticipate that the work will take approximately four hours.

_During some of this time, volunteers will not be able to upload or download new work, and the website will not be accessible._

Volunteers will not need to take any particular action, as your devices will automatically retry their connections after the maintenance work is completed.

Attached in full. Original message, HERE.


----------



## Arjai (Oct 23, 2018)

*New Version of World Community Grid for Mac and Windows Now Available for Download*






*22 Oct 2018                   *

*Summary*
Volunteers can now upgrade to version 7.14.2 of the software that runs World Community Grid. 
We're happy to announce an updated version of the software which runs World Community Grid. You can begin to install the upgrade          here. 



> *Background*
> World Community Grid uses the BOINC open source project as the underlying software for running our research projects. The BOINC project periodically releases new versions of the software to add features and fix bugs.
> Every few years, World Community Grid conducts a security review and performs our own additional testing on top of the existing BOINC community testing of the software. Once we have completed these steps, we then adopt that new version as the version that we recommend and provide as a download to our volunteers. The previous version of the software that we recommended was version 7.2, which was released in 2014.





> *What's the difference between the new and old versions?*
> We're adopting this new version because it's easier for new users get the software installed and running on their systems. Previously, users would have to come to our website, register, download the software, install it, and then enter their user name and password into the software in order to complete the process. The new version eliminates the last step in the process; once the software is installed, it should automatically connect with the user's account on our website.
> We are also providing a World Community Grid-branded version of the BOINC client for both Windows and Mac. (Previously, we only provided this for Windows).





> *For more information*
> If you are curious about other changes in the software, you can read the release notes on the BOINC website.
> We encourage all volunteers to upgrade to the latest version. If you have any questions about this upgrade, please free to ask questions on our website in the forum thread we've created for this release on our website.





> *Release Notes for BOINC 7.14*
> 
> 
> 
> ...



Copied in its entirety, from HERE


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## phill (Oct 23, 2018)

Does anyone notice any performance increases/decreases with any updates to Boinc?   What version does everyone run now? 

Just done a quick test for my laptop I crunch with at work..  Here's my results 





After a few runs the scores went higher for me, on the integer MIPS, around 8200..  Would be interesting to know if anyone else has had a increase or decrease


----------



## Arjai (Nov 14, 2018)

*Shining a Beacon for Science*

*13 Nov 2018 *

*Summary*
        Scientists, and science itself, are facing increasing challenges in many parts of the world. To mark _World Community Grid's 14th anniversary_, we're asking you to publicly show your support for science on social media, in our forum, and on your own website or blog. 




​


> Science and scientists are under attack all over the world. Fields such as climate research, drug discovery, and environmental protection are increasingly politicized. Once-certain sources of research funding are shrinking or disappearing.





> But _World Community Grid_ has been a beacon for science to people who understand the need for continuing research since it was created in 2004. What started out as a relatively small,short-term proof of concept initiative has grown into a major source of computing power for 29 (and counting) humanitarian scientific research projects. So far, this has led to breakthrough discoveries for childhood cancer, water filtration, and renewable energy, as well as many smaller discoveries that may one day lead to future breakthroughs.





> This is only possible because of generous people around the globe who donate their unused computing power to research, and scientists who have the patience and skill to tackle thorny problems that have no obvious answers.



We're inviting everyone involved with _World Community Grid to shine a beacon for science on November 16, which is our 14th anniversary. _*You can do this by:*

 
Creating your own social media posts on your favorite platform (tag us on Twitter or Facebook so we can say thanks, and use the hashtag #Beacon4Science) 
 
Posting your thoughts about being involved in World Community Grid in our forum 
 
Sharing our Facebook post and/or retweeting our tweets on November 16
 
Sending us an email with your thoughts at beacon@worldcommunitygrid.org



> Feel free to include pictures or videos, especially if they're science or World Community Grid-related.
> We'd like to share the thoughts and stories of those who give us permission, to let the scientists we work with–and any other supporters of humanitarian scientific research–know that they have friends around the world.
> 
> *Thanks for helping us shine a beacon for science since 2004.*


----------



## Arjai (Dec 12, 2018)

*Let Your Computer Daydream Protein Structures: The Microbiome Immunity Project's 1st Full Year*

By: Dr. Tomasz Kosciolek, Dr. Doug Renfrew, and Dr. Tommi VatanenUC San Diego, 
Flatiron Institute, Broad Institute of MIT and Harvard

*11 Dec 2018 *

*Summary*
Researchers from three leading scientific institutions are collaborating to explore the proteins in the human microbiome. Learn more about how they work together, and what they've accomplished at the end of the project's first full year, in this update. 

*Background*

Trillions of bacteria live inside and on our bodies. The Microbiome Immunity Project is using the computational power of World Community Grid to study the proteins produced by these bacteria, which are encoded in their genomes.



> Our first step is to determine the physical structures (shapes) of the protein molecules coded by each bacteria’s genes. This is important because the physical structure of a protein determines its function.
> 
> Once the protein functions are determined, we can explore how the bacterial proteins react with each other, and determine which proteins may play a role in autoimmune diseases such as Type 1 diabetes, ulcerative colitis, and Crohn’s disease.
> 
> We’ve created three short videos, one from each institution working on the project, to give you more information about how the project works, what we’ve done so far, and what we hope to accomplish with the help of your donated computing power.



*Our Progress So Far*

In this video, Dr. Tomasz Kosciolek of the University of San Diego gives an update on the project’s progress to-date. Look for a summary slide at 0:34, and don’t miss the bison! (Please note that the number of proteins listed on the summary slide is as of October; the project has predicted the structures of additional proteins since then.)









*Predicting the 3D Structures of Proteins*

Below, Dr. Doug Renfrew of the Flatiron Institute explains how your computing power is helping the research team predict the 3D structure of proteins, and summarizes why this is important. (And he does it all in about 90 seconds.)









*The Human Microbiome’s Role in Disease*

The Broad Institute of MIT and Harvard is where microbiome protein research and medical research intersect. In this video, Dr. Tommi Vatanen outlines what we do and don’t know right now about the human microbiome’s role in certain diseases…and what we hope to find out, with your help.









*Thank You*

Everyone who donates their unused computing power is an important part of the Microbiome Immunity Project. We couldn’t do it without you!



​


----------



## Arjai (Dec 27, 2018)

OpenZika Team Adds New Resources to Continue Massive Data Analysis
	

	
	
		
		

		
		
	


	




I will edit this post tomorrow...just noticed it and I need sleep


----------



## Arjai (Dec 30, 2018)

*OpenZika Team Adds New Resources to Continue Massive Data Analysis*

*By: The OpenZika research team*

*20 Dec 2018*

*Summary*
New research models, a new student, new publications, new collaborations, and continuing data analysis are all detailed in this comprehensive update from the OpenZika research team.




*Current Lab Work*


> *Dr. Carolina Andrade’s* research team, LabMol, is working on analyzing the data generated by OpenZika project. *Dr. Melina Mottin* is leading this task.
> 
> We are analyzing the virtual screen from OpenZika against the ZIKV NS5 protein, a key viral enzyme that is required for the virus to mature and form infectious viral particles. The full-length NS5 protein contains two domains, representing two distinct targets: the NS5 methyltransferase and NS5 polymerase. NS5 methyltransferase domain methylates, or attaches methyl (CH3) radicals to, the RNA cap structure; and NS5 polymerase domain synthesizes the viral RNA, and is thus essential to ZIKV survival and establishment of the infection in host cells.





> We are being assisted by other Brazilian researchers, who are helping to analyze the big data generated by the docking calculations from _World Community Grid_. *Professor Roosevelt Alves da Silva* (Federal University of Goias), *Dr. Joao H. Martins Sena* (Oswaldo Cruz Foundation, FIOCRUZ), and *Dr. Pedro Torres* (University of Cambridge) are helping *Dr. Mottin* and the LabMol team to handle the massive amount of data we have been generating. Also, our new Master’s student, *Bruna Souza*, is being trained by *Dr. Mottin*. _She is already analyzing the data and preparing reports._






​


> *Dr. Mottin* spent almost a month as a visiting researcher at *Dr. Sean Ekins’* lab in North Carolina. She worked on Bayesian and Random Forest models for Zika, dengue and Ebola using publicly available data. The main goal of this work was to develop and implement these models to help increase the efficiency of the final selection of the compounds to test against the viruses. (For example, we can build a machine learning model for Zika and related flaviviruses that could help predict which compounds are more likely to have whole-cell activity, which will complement our target-based docking in OpenZika.) Models are now being optimized with new datasets obtained from the literature and databases such as ChEMBL and PubChem, to build new and more robust machine learning models for predicting activity for Zika and dengue viruses.



*New Candidate Inhibitors Recently Discovered*



> We recently finished analyzing a virtual screen from OpenZika against the ZIKV NS2B/NS3 protease, a key viral enzyme that is required for the virus to mature and form infectious viral particles. Approximately *6 million compounds *were docked against the ZIKV protease, followed by interaction-based docking filters to find compounds that were predicted to dock well to the allosteric site. We then used machine learning models as filters (our suite of Bayesian models that predict mouse liver microsomal stability, lack of cytotoxicity, and solubility). We ultimately visually inspected the binding modes of the *top 318 compounds*, and we narrowed it down to *27 candidates*. These candidates will be purchased and then assayed by our collaborators, to discern their potency at inhibiting the protease, as well as their efficacy in cell-based assays.





> We also analyzed the docking results regarding the Chembridge database (*~1 million compounds*) against NS5 polymerase (RNA and NTP sites) and NS5 methyltransferase (active, SAM and GTP sites), as well as the NS3 helicase (ATP and RNA sites). We filtered the best ranked compounds through the developed ZIKV QSAR models and performed a medicinal chemistry inspection of the filtered compounds, selecting *33 compounds in total*. The next steps will be to order these compounds and experimentally test them (Figure 1).






​*Upcoming and Recent Publications*



> We recently published a review paper entitled “Computational drug discovery for the Zika virus.” This paper was published in a special issue of the _Brazilian Journal of Pharmaceutical Sciences_. In this paper, we summarize current computational drug discovery efforts and their application to the discovery of anti-ZIKV drugs. We also present successful examples of the use of computational approaches to ZIKV drug discovery, including our OpenZika project.





> In November, we published a keynote review entitled “The A–Z of Zika drug discovery” in the journal _Drug Discovery Today_. This is a comprehensive review of the recent advances in ZIKV drug discovery efforts, highlighting drug repositioning and computationally guided compounds, including recently discovered viral and host cell inhibitors. Promising ZIKV molecular targets are also described and discussed, as well as targets belonging to the host cell, as new opportunities for ZIKV drug discovery. All this knowledge is not only crucial to advancing the fight against the Zika virus and other flaviviruses, but it will also help the scientific community prepare for the next emerging virus outbreak to which we will have to respond.





> *Dr. Ekins*, *Dr. Andrade*, and *Dr. Mottin*, along with other researchers, recently had a review paper “High Throughput and Computational Repurposing for Neglected Diseases” accepted in the journal _Pharmaceutical Research_*. *This paper describes the many drug repurposing efforts that have been going on in different labs around the world to try to find treatments for many tropical diseases.











​*Past Publications and Outreach*

*New Collaborations*

*New Student Team Member*



> As mentioned above, *Dr. Andrade* has hired a new graduate student, *Bruna Sousa*, to work on the OpenZika project. She started working in Dr. Andrade’s lab in March 2018, and she is very enthusiastic about learning and collaborating on the project. She is a volunteer for the OpenZika project with an Android device, and has invited students and professors of the graduate program, during classes and through her personal social media, to participate in the project. _She is joining in the OpenZika calls with World Community Grid._











​*Status of the Calculations*



> In total, we have submitted almost *6.8 billion docking jobs*, which involved *427 different target sites*. Our initial screens used an older library of *6 million commercially available compounds*, and our current experiments utilize the new ZINC15 library of *30.2 million compounds*. We have already received approximately *6.3 billion of these results on our server*. (As a reminder, there is some lag time between when the calculations are performed on our volunteer’s machines and when we get the results, since all of the results per “package” of approximately 10,000 – 50,000 different docking jobs need to be returned to World Community Grid, re-organized, and then compressed before they are sent to our server.)





> So far, the > 80,000 volunteers who have donated their spare computing power to OpenZika *have given us > 63,023 CPU years*’ worth of docking calculations, at a current average of *66.3 CPU years per day*!  Thank you all very much for your help!





> Except for a few stragglers, we have received all of the results for our experiments that involve docking 6 million compounds versus NS1, NS3 helicase (both the RNA binding site and the ATP site), NS5 (both the RNA polymerase and the methyltransferase domains), NS2B/NS3 protease and capsid (binding pockets 1 and 2).



*Thank you to all the volunteers who are donating their unused computing time to this project!  We appreciate your help! *

It is good to see a lot of work getting done and the scientist's doing their best to promote the work, for all to use!

All of the Story, HERE.
Bruna is a beautiful addition to the Zika project!!


----------



## Arjai (Jan 5, 2019)

*Planned Maintenance on Tuesday, January 8*





*Summary*
We are updating the storage system on our servers on *Tuesday, January 8, beginning at 15:00 UTC. *

We will be applying an important storage system update to our servers on Tuesday, January 8, beginning at 15:00 UTC. We anticipate that _the work will take approximately four hours._

During this time, *volunteers will not be able to upload or download new work.* No action is required by you, as your devices will automatically retry their connections after the maintenance work is completed.

We appreciate your patience and participation.


----------



## hat (Jan 5, 2019)

That seems like it should affect almost nobody. Doesn't BOINC already queue up a larger buffer than that by default?


----------



## phill (Jan 5, 2019)

Only if you leave it at default, I think it buffers about a day or two's work


----------



## Arjai (Jan 6, 2019)

I cache 3.1 days of work. So, They (WCG servers)  could have a *big* issue, and I would still have work.


Or, alternately, I could have an issue with my ISP, or the ISP might have an issue. Both scenarios I have lived through. I ran out of jobs, ONCE!! That taught me to cache jobs.


----------



## phill (Jan 6, 2019)

Arjai said:


> I cache 3.1 days of work. So, They (WCG servers)  could have a *big* issue, and I would still have work.
> 
> 
> Or, alternately, I could have an issue with my ISP, or the ISP might have an issue. Both scenarios I have lived through. I ran out of jobs, ONCE!! That taught me to cache jobs.



I've stopped caching so many just in case I never get to finish them in time and they just get taken away anyways, but I'll add two days onto the ones I'm running now just in case   But loving the thread for the updates, thank you!!


----------



## Arjai (Feb 20, 2019)

*Meet Your Fellow Volunteer Computing Enthusiasts at the BOINC Workshop 2019 *

*19 Feb 2019  *




*Summary*
We're excited host this year's BOINC Workshop in Chicago, Illinois, USA. If you're reading this, you're part of the BOINC community and we'd like to meet you.






> It's almost that time of year again...the 13th annual BOINC Workshop is happening from _July 9 to July 12_, and registration is now open. This year, the workshop is being hosted by World Community Grid in IBM's Chicago offices.
> 
> Attendees to the 2019 workshop are invited to give a 15-30 minute presentation about the work they are doing with BOINC.





> All scientists, project administrators, developers, volunteers, and anyone with an interest in volunteer computing will be welcome to attend. Past BOINC Workshops have covered topics such as presentations on the science supported by BOINC projects, ideas for future development, how GDPR may affect the ways that BOINC projects handle data, and suggestions for simplifying volunteer registration. You can see all of the presentations from last year's workshop here, and listen to audio from the workshop here.





> Registration is free. We'll update the BOINC Workshop 2019 page as more information becomes available, but in the meantime feel free to ask any question in the workshop forum thread.
> 
> See you in Chicago!



Entire post is HERE.

_I am, sincerely, considering this as I have some Holiday pay to use!_


----------



## phill (Feb 20, 2019)

If only it was a little closer to me


----------



## Arjai (Mar 1, 2019)

*New Type of Work Unit and New Team Members for FightAIDS@Home - Phase 2*

*By: The FightAIDS@Home research team*

*28 Feb 2019*

*Summary*
FightAIDS@Home - Phase 2 has released a new, more efficient type of work unit. They've also added four new members to their research team.






> *New Work Units*
> For the past year and a half, the research team at Temple University has worked closely with the World Community Grid software developers (particularly Keith Uplinger and Jonathan Armstrong) to create and implement a simulation scheme that more closely mimics the simulations run on non-grid computing resources. This new sampling protocol is called asynchronous replica exchange.





> *How Asynchronous Replica Exchange Work**s*
> 
> *Previous Process:*
> Multiple copies of a protein-ligand complex (the structure consisting of a drug candidate compound docked with a protein receptor) were sent out to many volunteers and are simulated with no interaction with one another. The collective information from all those simulations are combined during analysis at the very end.





> *New Process:*
> Asynchronous replica exchange drastically increases the efficiency of the computations. This means that, in addition to being more valuable in terms of analysis, the number of batches running simultaneously can be increased and each batch will have shorter total simulation times.
> 
> We first prototyped this new technique on our own BOINC-powered grid at Temple University. Over the past year and a half, the World Community Grid software developers have worked with us to test, refine, and now to implement the same technique on the World Community Grid platform. This effort is the largest replica exchange simulations (by two orders of magnitude) ever performed.



For more information about this work, see these two articles:

http://onlinelibrary.wiley.com/doi/10.1002/jcc.23996/abstract

http://www.sciencedirect.com/science/article/pii/S0010465515002556

*New Team Members*​We’re excited to welcome four new members of the Levy Group as research team members for the FightAIDS@Home project.




> *Bin Zhang*
> Associate Research Professor
> 
> Bin Zhang is an associate research professor from Ron Levy's Group at Temple University. He holds a Ph.D degree in physics from the University of Pittsburgh. Bin joined Dr. Levy's group in 2013. His research focuses on developing advanced sampling and reweighting(sp) algorithms in biophysics and computer simulations.





> *Di Cui*
> Assistant Research Professor
> 
> Dr. Di Cui is a computational chemist with an interest in biomolecular modeling. Currently, he is an assistant research professor in the Department of Chemistry, Center for Biophysics and Computational Biology, Temple University. His research has been focused on understanding the mechanisms and estimation the binding affinity of small-molecule ligands to protein active sites using molecular dynamic simulations. His current work involves the application of molecular modeling techniques to analyze the binding affinities to the target proteins, with the goal to design new ligand molecules that could serve as leads and optimized compounds for drug discovery.





> *Avik Biswas*
> Graduate Student
> 
> Avik Biswas is currently a Ph.D (Physics) student in the Ron Levy group at Temple University, Philadelphia. Prior to joining the Levy group in 2016, Avik completed his Integrated BS-MS from the Indian Institute of Science Education and Research (Bhopal, India) where his research involved using molecular dynamics and ab initio methods (Density Functional Theory) to understand the mechanics of rolling graphene. Currently, his research is focused on using Potts Hamiltonian models of protein evolutionary fitness to study the inter-relations between protein sequence, structure, and fitness, with a particular interest in the evolution of drug resistance in HIV.





> *Shima Arasteh*
> Graduate Student
> 
> Shima Arasteh is a Ph.D student from Ron Levy's group at Temple University. She holds a bachelor's degree in physics and a master's degree in biophysics from the University of Tehran. Before joining Dr. Levy's group in 2015, her research focused on the functions and stability of membrane ion channels. Currently, she is studying the conformational transitions of protein kinases, and developing advanced algorithms to measure the free energy changes of these transitions.


*Thank you to everyone who is supporting FightAIDS@Home. We couldn’t do it without your donated computing power. *

 Sounds good to me!!

Edited, slightly. Full article, HERE.


----------



## Arjai (Mar 13, 2019)

*"We can feel the heartbeats of the crunch for science."*





By: Jerome Doussy 
CRUNCHERS SANS FRONTIERES

*12 Mar 2019*

*Summary*
Meet Jerome Doussy, a volunteer from France who shares his own words why he supports World Community Grid and scientific research.






> My name is Jérôme Doussy. I'm French and I live near Bordeaux. I work in the industrial sector for the Mondelez International company. I'm 43 years old and a father of two lovable children. My hobbies include computers, science, astronomy, photography, and sports.
> 
> I started distributed computing with the SETI@Home project as an astronomy fan more than 10 years ago. I felt concerned with the fact that humanity is not alone in our universe, so helping scientists with SETI@Home and BOINC (the software that World Community Grid and other distributed computing projects are run on) was quite an obvious choice for me.





> It was at this time that I met Thomas H.V. Dupont, who recruited me to his former team on the SETI@Home project, BRIGADE DU COSMOS (BDC). After a time, the BDC team was dissolved because we wanted to turn to distributed computing projects which address more tangible issues. So CRUNCHERS SANS FRONTIERES (CSF) was born--a dynamic team of dedicated people and serious crunchers.





> We joined World Community Grid because it seemed to us to be a serious entity with great scientists, great staff behind the scenes, great scientific feedback, and a great community of crunchers. Besides, it deals with many of the serious diseases all around the world, such as AIDS, Zika, Ebola, and cancer. Overcoming these deadly diseases via distributed computing instills a new dynamic and a new hope. We can do something to help so let's go!





> In CRUNCHERS SANS FRONTIERES, we can feel the heartbeats of the Crunch for Science. It's in our DNA. We are not a large team, but we are deeply concerned and aware of the importance of the projects we support. We are an international team, and we organize challenges such as THOR CHALLENGE or ATHENA TROPHY to help motivate World Community Grid crunchers to remain very active.





> The CSF team is my engine and especially a second family. Each member has the same purpose and it make me feel important and keeps me motivated!* I'm very proud to have a chance to help scientific research on disease with World Community Grid. It's a great opportunity for ordinary people to contribute to the building of a better world...it's priceless for sure!*



_I wholeheartedly agree with the highlighted text, quoted above._

Full Story, and pic, can be found HERE.


----------



## AmioriK (Mar 13, 2019)

Arjai said:


> _I wholeheartedly agree with the highlighted text, quoted above._


Yes, same. For me, WCG (and F@H) combines too of my passions; computer technology and microprocessors, and helping people. This is why I'm so heavily invested in it. I'm going to watch this thread, I didn't know it was here until I clicked on it this morning.

With all the negative and upsetting news in the world, this is a ray of light I sorely need. Thanks


----------



## hat (Mar 15, 2019)

That was how I felt when I first started doing such projects. Especially before WCG was a thing (at least at TPU) and we were all running the single core command line FAH client, multiple instances of it if we had dual core or better processors. I almost felt like some kind of researcher myself, watching those FAH cores crunch away in those command prompt windows. Then the SMT core came along, and GPU folding, and WCG... and then I started collecting hardware to build multiple rigs. It's the reason I ever had a second computer to begin with (I later found other uses for it, but it was originally so I could fold and crunch more). It's also the reason that by this time next year I might be eyeballing some Ryzen hardware myself for my second computer (once my loan is paid off and I have more free money for things). Or maybe a used workstation. There's a lot of options.

But, in reality, all I'm doing is installing a program and sending results to someone else to mull over. But, without all of us making up the distributing computing project that is WCG, those researchers would have far less to work with. They turned to the masses, asking to borrow their unused computing power, for their research, relying on the good will of man... and here we are. Collectively, the Grid is also far more powerful than any supercomputer they could have rented.


----------



## phill (Mar 15, 2019)

I do wonder how many researchers are sat there looking at all the data that we (TPU) and the rest of the teams submit..  I mean there's literally thousands, if not a million or so of results returned each day..  Compare this back to when I first started in 2007 with single core CPUs, my world how things have moved on.  I can crunch what I did in 2007/2008 in a year in a day with the hardware I have working now.  How scary is that??


----------



## hat (Mar 15, 2019)

I remember crunching on a single core AM2 Sempron for a while... overclocked to 3GHz. It ran Battlefield 2 and Fallout 3 decently. Then I got my 7750BE.

I started FAH with a Athlon64 5200+ though, I believe. I upgraded to an OG Phenom x4, but I blew up my board trying to overclock it. Still wish I hadn't done that.  That's how I wound up with the single core chip for a while...


----------



## phill (Mar 16, 2019)

My first Crunching machine was an AMD XP CPU.  I remember also crunching on a EPIA 533Mhz system as well that I used for a server back years ago..  Man that thing was very very slow... lol   I believe I still have pictures of that too....


----------



## Arjai (Mar 17, 2019)

I started on a Socket A Duron!, With the help of some TPU WCG-er's, I ran about 4 different CPU's until I found a mobile chip, a 2600m? That would clock at 1.1GHz stable, 24/7! 

I burned the board out after a couple of years. I tried to revive it but, have been unable to find a working Socket A motherboard. LOL. I have bought a few duds, but they were inexpensive. Given a larger budget? I could possibly find a working board. I have also thought of having one of them repaired, but that is still money I can't spend. Hardly seems worth it, now. Maybe someday, when I have nothing better to do!


----------



## TheoneandonlyMrK (Mar 17, 2019)

phill said:


> I do wonder how many researchers are sat there looking at all the data that we (TPU) and the rest of the teams submit..  I mean there's literally thousands, if not a million or so of results returned each day..  Compare this back to when I first started in 2007 with single core CPUs, my world how things have moved on.  I can crunch what I did in 2007/2008 in a year in a day with the hardware I have working now.  How scary is that??


Folding @ home is similar, i think it took me a few years to get to a million points yet that's a day flat out now.
My first foray into wcg was with my old trusty q6600 now i have 12 cores at it with my dream of a 32 core monster ,soon it could be much more  since this chip would then be my server chip (12 core +32)yay.


----------



## phill (Mar 17, 2019)

I must admit now with Ryzen, they are monsters   Two running at the moment, can't fault it.  Fans are quiet, temps are reasonably good for the air coolers I'm using and what more could I ask for in a cruncher?  Some of the earlier work units I was doing the wattage meter read 125w at best for a full system and that's 16 threads..  Now it's a little higher, 155w but still better than my 6700k and E3-1245v3 together as they are only 8 threads each


----------



## Arjai (Mar 22, 2019)

*Meet Your Fellow Volunteer Computing Enthusiasts at the BOINC Workshop 2019*

*19 Feb 2019* 





*Summary*
We're excited host this year's BOINC Workshop in Chicago, Illinois, USA. If you're reading this, you're part of the BOINC community and we'd like to meet you. 

It's almost that time of year again...the 13th annual BOINC Workshop is happening from July 9 to July 12, and registration is now open. This year, the workshop is being hosted by World Community Grid in IBM's Chicago offices. 



> Attendees to the 2019 workshop are invited to give a 15-30 minute presentation about the work they are doing with BOINC.
> 
> All scientists, project administrators, developers, volunteers, and anyone with an interest in volunteer computing will be welcome to attend. Past BOINC Workshops have covered topics such as presentations on the science supported by BOINC projects, ideas for future development, how GDPR may affect the ways that BOINC projects handle data, and suggestions for simplifying volunteer registration. You can see all of the presentations from last year's workshop here, and listen to audio from the workshop here.
> 
> At the workshop, attendees will have the opportunity to learn what other attendees are doing with BOINC software and volunteer computing, learn about what has happened with BOINC since the last workshop, participate in a hackfest where we attendees team up to solve some challenges, and get to know others in the community.





> Registration is free. We'll update the BOINC Workshop 2019 page as more information becomes available, but in the meantime feel free to ask any question in the workshop forum thread.





> See you in Chicago!



_This just a repost that showed up in my 'Notices'. But is a reminder to Register and attend. I am more than likely going to attend. I am thinking of Registering next week when my Holiday time is approved._


----------



## Arjai (Mar 28, 2019)

*Volunteer opportunities in BOINC for Mac Developers*


*26 Mar 2019*

*Summary*
Are you a Mac developer? The team of volunteers supporting BOINC is looking for experienced Mac developers to help support and maintain the software that World Community Grid and other distributed computing projects depend on for scientific research. 



> The Berkeley Open Infrastructure for Network Computing (BOINC) is an open-source software platform that makes projects like World Community Grid possible. BOINC, which is maintained by a team of volunteer developers, is searching for Mac experts who are willing to volunteer alongside them. This is a chance for volunteer computing enthusiasts with Mac development skills to contribute to the development and maintenance of a crucial program.
> 
> Tasks include monitoring BOINC developer email lists and GitHub list for reports of Mac-related issues, investigating and resolving issues, and creating builds of the BOINC Mac client for testing and distribution.



The Whole Post, including "Skills Needed" and links to the application...

*HERE.*


----------



## Arjai (May 1, 2019)

"FightAIDS@Home Team's New Simulation Technique Published in Industry Journal
	

	
	
		
		

		
		
	


	




"

To be updated on Thursday the 2nd...I have been working a ton, been extremely worn out, but, I have the afternoon off on Thursday. (Yea!)

Stay tuned...


----------



## Arjai (May 2, 2019)

*FightAIDS@Home Team's New Simulation Technique Published in Industry Journal*


*22 Apr 2019*


*Summary*
The _FightAIDS@Home - Phase 2_ team teamed up with *World Community Grid* to examine and refine the results of Phase 1 of the project. Over the past 18 months, they've created a new technique called asynchronous replica exchange, which drastically increases the effectiveness of their computations and may have implications for other researchers who use the same software for drug discovery. The results of this work were recently published in the Journal of Chemical Information and Modeling. 




​


> Computer-based experiments in drug discovery require accurate and highly detailed simulations of molecular interactions. Unfortunately, conventional computing resources, even high-performance computer clusters like *World Community Grid*, often cannot provide the level of detail on these complex interactions to make them as accurate as scientists need to further their work. Similarly, *World Community Grid*'s computing resources are enormous, but its basic design was not a perfect fit for the particular molecular simulation techniques that the _FightAIDS@Home_ scientists were using.





> For more than 18 months, the research team worked closely with *World Community Grid* developers Keith Uplinger and Jonathan Armstrong to create and test asynchronous replica exchange, a new sampling protocol which provides very fine-grained dynamic molecular simulations. Asynchronous replica exchange, which is detailed in a paper recently published by the research team, could have implications for future work in drug discovery for scientists who use the same software for computer simulations.





> You can read the abstract of the paper here. *Thanks to everyone who is donating computing time to support FightAIDS@Home.*



_Keith and Jonathon, super stars working out the answers to FAH's issues! Another step towards ridding this Planet of  the AIDS!!_


----------



## Arjai (May 23, 2019)

*Student and Teacher Become First Volunteers to Visit Mapping Cancer Markers Research Team*

*16 May 2019* 

*Summary*
In a first for _World Community Grid_, high school student Dylan Bucci and teacher Robert Esposito recently traveled to Toronto to meet the scientists running the *Mapping Cancer Markers* project at Krembil Research Institute. This is the first time _World Community Grid_ volunteers have ever visited a research institution to meet with scientists who use the program. 



> In mid-January, Dylan Bucci, a sophomore at Sisler High School in Winnipeg, Canada, finished reconfiguring twelve high-end servers to provide computing power for the _*Mapping Cancer Markers*_ project, which uses_ World Community Grid_ to accelerate the search for cancer biomarkers.
> By early May, Bucci and Sisler High School teacher Robert Esposito, who guided Dylan’s work, were headed to Toronto to meet the _*Mapping Cancer Markers*_ research team at the Krembil Research Institute. There, they spent the day with scientists to see first-hand how volunteer computing contributes to the fight against cancer.






​


> “This visit has gotten me thinking about the many options someone can have with a tech background,” says Bucci. “And a major highlight was getting to meet Dr. Jurisica. Talking to him was so uplifting, and he explained his research so well.”
> “There’s not a lot of interdisciplinary study on science and technology at the high school level, and there’s a huge need for it,” adds Esposito. “_World Community Grid_—and this visit—is something that can help a student literally see the integration between the two. It can also help them feel that they’re a part of something bigger than themselves.”



*Click here** to see a CTV Toronto News video about their visit. *

More of this story, HERE


----------



## Arjai (Jun 25, 2019)

*Help Stop TB Team Continues Learning and Searching*

*By: Dr. Anna Croft
University of Nottingham, UK 
18 Jun 2019 

Summary*
While the Help Stop TB researchers continue the search for new team members, they are also learning from the data they receive from World Community Grid.  

Rest of story, HERE.

_Sorry for the short posting...I have been working 7 days a week, 13 hours a day, since the 4th._


----------



## phill (Jun 25, 2019)

Arjai said:


> *Help Stop TB Team Continues Learning and Searching*
> 
> *By: Dr. Anna Croft
> University of Nottingham, UK
> ...



Understandable mate but you need rest and to take care of yourself, don't burn yourself out   But on the other hand, it will help pay for the electric on the crunching


----------



## Arjai (Jun 26, 2019)

phill said:


> Understandable mate but you need rest and to take care of yourself, don't burn yourself out   But on the other hand, it will help pay for the electric on the crunching


I work on Salary...I'd be very wealthy if I were hourly!!


----------



## phill (Jun 26, 2019)

Arjai said:


> I work on Salary...I'd be very wealthy if I were hourly!!



That's a shame, so I'd consider asking for a pay rise if you're doing that many hours!!  Give yourself a break mate


----------



## Boatvan (Jun 26, 2019)

Arjai said:


> I work on Salary...I'd be very wealthy if I were hourly!!


I hate when employers exploit salaried workers for free overtime. Luckily I work somewhere that respects this, but generally techies are expected to work free overtime if needed. Seems to be in the culture of this field.


----------



## Peter1986C (Jul 1, 2019)

Free overtime is against the law here, afaik.


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## Arjai (Jul 9, 2019)

Just got here to the workshop, here in Chicago. There will be a live stream starting in about an hour.

Here is the YouTube link

P.S. Just met Keith Uplinger (sp?) from WCG.

Edit: Lunch break update David Wallom, CPDN, Weather@Home, OpenIFS@Home and Shawn Kwang, Einstein@Home and Keith, WCG have all had interesting presentations. This afternoon another couple of presenters and a interactive Intro to Design Thinking: Volunteer Challenges & Opportunities.

Tonight, we are gathering at Goirdano's for some Chicago Deep Dish 'Za!

I will do my best to update w/ some interviews and info on presentations, later tonight.

Sitting at the bar, at Giordano's. Meetup with the workshop group, for dinner, isn't for another hour. Rather than train back to the hotel, during rush hour, then back, 2 blocks from IBM, I will hang out here and try to NOT to get drunk!


----------



## phill (Jul 9, 2019)

I hope you have a great time @Arjai !!     Take care and post up whatever you can when you get back, it'll be great to hear all about it


----------



## Arjai (Jul 10, 2019)

Ok, to start, Chicago is just as much fun as always. If you like the urban bustle, Chicago is more Midwestern than the craziness of NYC, which is fun but, in a much different vein.

The Workshop.

The turnout, today was about half the number of sign ups. About 36 attendees, from all over. Germany, UK and Italy, were all there. Texas, Atlanta, NY and me, Minnesota. I almost forgot about Beijing, with 2 attendees.

Introduction was done with Juan (jew-ann) Hindo and Erica Tuttle. Both with IBM Chicago and member's of the BOINC team there.

Keith Uplinger, with WCG and PMC Chair with BOINC, spoke about the state of the Community and about the Contributes meetings (more about that, when I get back).

David Wallom, from ClimatePrediction.net, spoke about climate change and the contributions from Weather@Home, OpenIFS@Home and the original CPDN. He spoke about the problems they face with storage of data and the issue of member retention (one of the main subject's of the workshop).

Shawn Kwang, Einstien@Home, described their mission and what they track. Astrophysical signals, Pulsar Searches and LIGO, dealing with gravitational waves. I found this interesting, personally, due to a young woman I know from the local Speedway. She is studying astrophysics. I mentioned to her that I would here and tried to explain what BOINC is and what we do at WCG. She was fascinated and exclaimed, 'I love science'. I think Einstien@Home would be right up her alley, so to speak.

Germany Massulo, from Italy, with CERN, gave a general overview of LHC@Home. He is new, 3 months old, with CERN, so he was not as knowledgeable about the BOINC needs of CERN. He did speak about being introduced to WCG, and BOINC, by his father as a young boy. Which fostered his interest in Science.

Eric Korpela, SETI@Home, talked about what they are doing to search for ET transmissions and the evolution of the process and the issues they face with a new site coming online.

Steven Clark, with Nano@Home, spoke about NanoHub.org. One can visit the site and use their 600+ tools to run an experiment or simulation that is solved with BOINC workunits. They also use 5 other platforms, due to the specific tool needs. About 300 tools online use BOINC, running WU's that have runtimes in the seconds up to a week!

After Lunch, we worked with Evan Starkweather and Rafeal Hernandez-Chavez. They are IBM-er's and they introduced us to a version of Design Thinking. It deals with problem solving using a model developed at Stanford. We worked through some collaborative exercises using tools that are hard to describe. Essentially, creating a personal, using it as a base of thought both empathically and literally. Creating thoughts and feelings for the persona and then approaching that persona with BOINC.

The upshot I came away with is all 6 teams had a focus of ease of use for new user's. Also, we all had a secondary focus result, dealing with promotional ideas for BOINC. Tomorrow, we are to use these tools for a Brainstorming session.

There will be another Live Stream at 9 central time zone 1 and 3pm CT. Use the same link as posted above. We had 20 viewers today. I like to think many of them were TPU-er's that read my earlier posting!

Tomorrow' agenda...





Should be interesting. I spoke with Jonathan tonight at dinner.


----------



## phill (Jul 10, 2019)

Thanks for the update Arjai   I hope you're having a blast


----------



## mstenholm (Jul 10, 2019)

Not the kind of news that @Arjai normally post here but this is from the 8th of July and is about OpenZika jobs and of intresst for mobile phone plus Linux cruncher


Re: Likely pause in work available​
 

      Hi all,

We had another conference call with the research team today. The prerequisite tasks for the new batches are progressing slower than expected. The current updated estimate is for new work to be available 1-2 weeks from now. Thank you all for your patience.

Seippel


----------



## phill (Jul 10, 2019)

Where's the new to @mstenholm ?  Do you have a link at all please?


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## mstenholm (Jul 10, 2019)

phill said:


> Where's the new to @mstenholm ?  Do you have a link at all please?


Here you are


----------



## phill (Jul 10, 2019)

Do they have a new thread of downtime etc?  I couldn't see much on it before..  I take it its in the forums than on the main page?


----------



## Arjai (Jul 11, 2019)

OK, Day 2 of the BOINC Workshop...

Angelo Koutsogiannis. He works for Honeywell and has developed over 60 apps on the Apple store. His main topic was crunching on NUCS and Compute sticks. He talked about the power consumption, 10 watts and 5 watts of the NUCS and Compute Sticks. Their cost's and the ease of use, along with temperatures. He lives in Arizona and and was concerned with the temps his Apple 8 core and 6 core computers vs. the tiny Nuc's and sticks.

He also pushed for the Boinc  developer's to work with Apple to break the wall and make it useable on iOS.

Patrick Schofer, with SETI, talked about retention vs. recruitment. Which is a better focus. He made a point about the cost of running BOINC vs. other hobbies and the benifit of acknowledging the small contributors and using better communication in  forums.

Something this team is good at, thanks to the Daily Numbers and Milestones, currently run by @phill , and all the other teammates before him that posted on those threads.

Kevin Reed, IBM WCG, spoke about the Client updates and the need for more 'Contributers'. They are volunteers that help develop and fix the releases. I will be posting more regarding the help they need in another post, or post's in other threads.

The latest update, 7.14.2 was in Oct. 18. It was the first Linux update, in some time and included auto attach for Windows. Meaning, on a new installation, after log in it will attach you to the project and team automatically.

The next release is due in a couple of weeks. It will be an update for Android, big one for Android, and fixes for Windows and Linux. Number 7.16.

There was a Server Update, detailing the steps involved with Server Updates, by Germano Mussulo.

Giuseppe Aceto, a designer from Italy, outlined a new interface for developer's and a new user experience via a designed user interface, making it simpler to use.

He also is designing tools for projects to use to simplify their updates and websites. He is looking for marketing and designer help.

He can be reached at iamgiuseppeacetto@gmail.

He works with a number of Italian firms, including Ducati and Ferrari.

Andy Bowers outlined some research on Heat and Power Use of the BOINC manager. The research was done at a company with 2 rooms, equal size and equal number of identical computers. One room had BOINC, the other, did not. The peak temp was recorded on a hot day, with no WU:s running. So, despite the attempt, I think it was inconclusive.

Then, Johnathon Starr, jringo@gridcoin.world. He was recorded so I could post more about him and his ideas. Essentially, he, and the other presenter's (Max and Alex, gridcoin programmers, Jason Lee, BOINC Planet www.Boinc.io, from China and John Heeter, Boid.com) talked about Crypto Currency as an incentive to recruit and retain new Crunchers. All of them have succeeded in different ways and through different avenues. I will be posting more about this subject, in a different thread, later.


----------



## Arjai (Jul 12, 2019)

Day 3 of the BOINC Workshop.

Today was an all day Hack-a-thon. We broke up into groups, by subject's. 1 session in the morning and another in the afternoon.

My morning session was about making BOINC easier to use for new user's. Giuseppe was tasked with doing some research with subject's with no knowledge of BOINC. I proposed that his research be posted in the Boinc forums then implemented either before, or at the next Workshop.

The afternoon was spent talking about recruitment and retention of new user's. With the majority of attendees being project managers and developer's their were just 2 of us as simply volunteer Crunchers. We talked about our experience, mine revolving around TPU, and Mark's, the other Cruncher, experience as a solo user. He would like more WCG involvement with the Crunchers, essentially letting him know his work is appreciated. I told him I my needs were fulfilled by my membership with this team. I mentioned that he should find or create a team.

I am most excited by the work that Giuseppe will be doing. I will also be posting more about that, when I am back home, next week.

Boinc is in need of 'Contributers' that can help build fixes and upgrades to the BOINC manager. I will be posting more about that, also.

Tomorrow a River Walk is planned as the final activity. Sat, I will be travelling home. Sunday I may start posting, if time permits, more on the above subject, and include links to the post's in the member's thread.

It seems likely the next Workshop will be back in Europe, this being the first US Workshop. When the location is announced, I may have to start a GoFundMe page! My current employment does not pay enough for a week in Europe. I may have to start putting money away, next week!


----------



## Arjai (Jul 25, 2019)

*200,000 Newly Predicted Protein Structures and Counting: The Microbiome Immunity Project's Plans for the Future*







*By: Tomasz Kosciolek, PhD*UC San Diego Center for Microbiome Innovation*23 Jul 2019 *



*Summary*
The Microbiome Immunity Project has led to the prediction of almost 200,000 unique protein structures (so far), and the project has gone international. Learn more in this video update. 









​


> Dear World Community Grid Volunteers,
> 
> As of July 2019, you’ve donated close to 70,000 CPU years to the Microbiome Immunity Project, which helped us to predict almost 200,000 unique protein structures!
> 
> ...


​Total Transcript of video, is HERE.

_Awesome!!
 _


----------



## Arjai (Aug 16, 2019)

*Stockholm Science & Innovation School Competition Donates 25 Years of Computing Time to Cancer and Microbiome Research*

*15 Aug 2019  *

*Summary*
A high school in Sweden chose to support Mapping Cancer Markers and the Microbiome Immunity Project during a one-month competition between five World Community Grid teams. Here’s what they learned during the process.







​Read the full post, *HERE.*


----------



## Arjai (Aug 24, 2019)

*We're Switching to Email-Based Login*

*21 Aug 2019

Summary*
On August 28, World Community Grid will be switching from a username-based login system to an email-based login system. Learn what this means for existing and new volunteers in this article. 



> *Background*
> 
> Since World Community Grid was created in 2004, volunteers have been required to create a username in order to sign up and begin to receiving work from our servers. Now, we're switching to email-based login in order to bring World Community Grid into closer alignment with the process used by other BOINC projects. (BOINC is the open source software platform used by World Community Grid and other volunteer computing projects to distribute work units.) And for new volunteers, an email-based signup process will cut down on the number of fields required for initial registration.





> *Current volunteers*
> 
> We plan to cut over to the new system on August 28, 2019. *Current volunteers will not need to take any action, as your username and email address will remain the same. *However, we encourage you to make sure that the email address associated with your account is up to date.



*Questions?*

Please visit our forum to see a Q & A thread about this change, and check to see if your question has already been asked and answered before you post.

Thanks to all volunteers for your support of humanitarian science.


_Complete story, one more paragraph, for new user's, is HERE._


----------



## Arjai (Sep 5, 2019)

*Planned Maintenance on Thursday, September 5, 2019






4 Sep 2019

Summary*
We are updating the operating system on our servers on Thursday, September 5, beginning at 19:00 UTC 

We will be applying an important operating system update to our servers on Thursday, September 5, beginning at 19:00 UTC. We anticipate that the work will take approximately four hours. 

During some of this time, volunteers will not be able to upload or download new work, and the website will not be accessible.

Volunteers will not need to take any particular action, as your devices will automatically retry their connections after the maintenance work is completed.

We appreciate your patience and participation.


----------



## Arjai (Sep 8, 2019)

*THOR Challenge Attracts a Record Number of Teams in 2019* 

*6 Sep 2019* 

*Summary*
The THOR Challenge, one of_ World Community Grid_'s largest team competitions, is back for another record-breaking season. Learn more in this article. 

Every September, the CRUNCHERS SANS FRONTIERES team issues the *THOR Challenge*, which begins this year on September 9 and runs for four weeks. You can learn more about how the THOR Challenge is structured in this post by Thomas H.V. Dupont, Captain of the CRUNCHERS SANS FRONTIERES team.

At the time of publication, this year’s Challenge has attracted 70 teams—a new record. And since this year’s Challenge is actually two competitions in one, there will be two winning teams with the THOR Challenge Pure (a fifth week of challenge).

*If you are a team captain, register your team today. And if you're a team member, tell your captain that you'd like the team to be part of a challenge that aims to donate a record amount of computing time to six worthy projects.

Thanks for supporting the THOR Challenge and World Community Grid!  @Norton *


----------



## Boatvan (Sep 8, 2019)

I hope everything is OK with @Norton 
It has been a while since he logged on but I see his systems still crunching away


----------



## Arjai (Oct 13, 2019)

*Help Cure Muscular Dystrophy Researcher Developing New Methods for Deciphering Protein-Protein Interactions

12 Sep 2019 

Summary*
Dr. Alessandra Carbone, the primary investigator for the Help Cure Muscular Dystrophy project, recently published a paper along with several colleagues to propose new techniques for looking at the complexities of protein-protein interactions. 












> Unlocking the mysteries of protein-protein interactions will lead to a greater understanding of many biological processes, and could help scientists better address human health and disease. However, predicting and visualizing all possible protein interactions is highly complex and challenging. Some protein surfaces are involved in many interactions with other proteins, while others are not. Predicting the nature of these protein surfaces continues to be a challenge.
> 
> To help address this complexity, *Dr. Alessandra Carbone* and her colleagues, *Dr. Chloé Dequeker* and *Dr. Elodie Laine*, conducted a study which made use of Help Cure Muscular Dystrophy results from _*World Community Grid*_. The study combines different types of information to predict protein surfaces which interact with other proteins and disentangles the complexity of the interacting surfaces. Their results were recently published in _Proteins: Structure, Function, and Bioinformatics._
> 
> This open-access paper includes details of their findings, as well as links to their data and software. You can read the full paper here.





> *Thank you to all the volunteers who helped make this study possible by supporting the Help Cure Muscular Dystrophy project.*



_Dr. Alessandra Carbone, and her esteemed colleagues, has a small ton of papers that have been published with our research and her brains. She is an awesome scientist with an awesome sounding name, that I love saying... "Alessandra Carbone", beautiful!_


----------



## Arjai (Nov 16, 2019)

*Announcing the Africa Rainfall Project*

*30 Oct 2019

Summary*
What if your computer could run weather simulations that could help farmers in Africa successfully grow their crops? We're excited to announce the Africa Rainfall Project, our first project in partnership with The Weather Company.









*Why are accurate rainfall forecasts particularly important for farmers in sub-Saharan Africa?*

Most farms in Africa (about 95 percent) depend on rainfall to successfully raise their crops. However, because rainfall in Africa is often localized—sometimes almost at the level of one farm—it's difficult to forecast accurately with technology such as satellite data, which shows larger weather patterns.



> The Africa Rainfall Project aims to change that by creating more accurate rainfall forecasts that use rainfall data from The Weather Company, satellite data, ground observations, and data derived from weather simulations run on World Community Grid.





> *Who is behind this project?*
> 
> The project's principal investigator, Professor Nick van de Giesen, is Van Kuffeler Chair of Water Resources Management of the Faculty of Civil Engineering and Geosciences at Delft University of Technology in the Netherlands, as well as chairman of the Delft Global Initiative, which connects scientists at Delft University with partners in developing countries to solve issues. Professor van de Giesen has been doing scientific work related to Africa for more than 20 years, and he's been interested in the field for much longer. "In high school I was very into chemistry, biology, and physics," says Professor van de Giesen. "I was also interested in science that has a positive impact on the world."
> 
> Learn more about the research team here.





> *Why are the data from the Africa Rainfall Project useful for farmers in sub-Saharan Africa?*
> 
> More accurate rainfall forecasts will help farmers make better plans for planting season. Additionally, knowledge of recent past rainfall over Africa can be used for insurance for small farmers. This insurance is an important tool to make agriculture more climate resilient. Later, rainfall information could also be used for irrigation and hydropower planning in Africa.



_To contribute to the Africa Rainfall Project, __join World Community Grid__, or if you are already a volunteer, make sure the project is selected on your __My Projects__ page._ 

Whole thing, News, is HERE. 
WCG Page to add this project






/break


*15 Years of Shining a Beacon for Science*





*15 Nov 2019

Summary*
To mark *World Community Grid's 15th anniversary*, we're asking you as volunteers, researchers, and supporters to publicly show your support for science on social media, in our forum, and on your own website or blog.

*“Basic research is performed without thought of practical ends. It results in general knowledge and understanding of nature and its laws. The general knowledge provides the means of answering a large number of important practical problems, though it may not give a complete specific answer to any one of them.”*


_Vannevar Bush,
"Science, the Endless Frontier"_




​


> _*Thanks to volunteers, researchers, and supporters of science all over the globe, World Community Grid has been a beacon for scientific research since 2004.*_ What started out as a short-term initiative has grown into a major source of computing power for 30 basic science projects to-date. So far, this has led to breakthrough discoveries for childhood cancer, water filtration, and renewable energy, as well as more than 50 peer-reviewed papers about many smaller discoveries that may one day lead to future breakthroughs.





> Future discoveries depend on the basic research of yesterday and today. And basic research projects often uncover knowledge no one expected, and lead to paths that were previously unknown. This past year, World Community Grid's contribution to advances in basic research included:
> 
> 
> Working with the FightAIDS@Home researchers to create a new, more efficient sampling protocol
> ...





> *We're inviting everyone involved with World Community Grid to shine a beacon for science this week to help us celebrate our 15th anniversary.* You can do this by:
> 
> 
> Creating your own social media posts on your favorite platform (tag us on Twitter or Facebook so we can say thanks, and use the hashtag #Beacon4Science)
> ...



_Feel free to include pictures or videos, especially if they're science or World Community Grid-related. 

Thanks for helping us shine a beacon for science since 2004, and we look forward to continuing our important work together._​
https://twitter.com/WCGrid

https://www.facebook.com/worldcommunitygrid.org/

Thread: 15 Years of Shining a Beacon for Science


----------



## Arjai (Dec 5, 2019)

*Planned Maintenance on Thursday, December 5, 2019*

*4 Dec 2019* 

*Summary*
We are updating the operating system on our servers on Thursday, December 5, beginning at 19:00 UTC.





​

We will be applying an important operating system update to our servers on Thursday, December 5, beginning at 19:00 UTC. We anticipate that the work will take approximately four hours. 

During some of this time, volunteers will not be able to upload or download new work, and the website will not be accessible.

Volunteers will not need to take any particular action, as your devices will automatically retry their connections after the maintenance work is completed.
We appreciate your patience and participation.

_*Post in it's entirety*_


----------



## Arjai (Feb 18, 2020)

*Mapping Cancer Markers Researchers Analyzing Lung Cancer Data*

*By: The Mapping Cancer Markers research team *

*31 Jan 2020

*
*Summary*
The Mapping Cancer Markers team discusses the past (lung cancer), present (ovarian cancer), and future (sarcoma) of the project in this comprehensive update. 

*Background*


> The Mapping Cancer Markers (MCM) project was designed to identify the markers associated with various types of cancer, and by refining the process of identifying these markers, identify such biomarkers for other diseases more efficiently. We aimed to analyze multiple cancer datasets in order to identify potential biomarkers for these cancers, which could eventually help scientists and physicians detect cancers earlier and create personalized treatments. The first three datasets in MCM plan are lung, ovarian, and sarcoma, representing the past, present and future of MCM. Lung processing is complete. Ovarian marker processing is underway, but nearing completion. We are now preparing for a switch to sarcoma.
> 
> Processing a dataset on *World Community Grid* over months and years produces a huge amount of data, and this data is not directly usable, but must then be collated, filtered, and analyzed in different ways. We have been focusing on this post-processing step in our lab.
> 
> In this update, we will mainly discuss some of the work done with the processed lung dataset, but first, we will take a quick glance at the future.



*Final preparations for sarcoma dataset*


> The upcoming sarcoma dataset will be MCM’s most complex dataset to-date. It contains potential biomarkers drawn from multiple sources: measurements of RNA, DNA, and protein activity, mutations, and other biological modalities.
> 
> With such detailed information about each sample in the dataset, it took some effort to reduce the dataset and result sizes to practical levels. We are currently testing work units of our draft dataset and are planning the work.
> 
> A future update will announce the launch of a new phase of the MCM project, focusing on sarcoma and provide more details.



*Results from the lung dataset*


> The biomarkers in the MCM lung dataset measure the activity of thousands of genes. Collectively, these biomarkers cover most of the human genome. The majority of MCM lung work processed on *World Community Grid* surveyed signatures randomly drawn from the entire set of biomarkers. A shorter, second phase of MCM lung drew signatures from optimized subsets of those biomarkers.
> 
> The contribution of compute cycles to the project was extraordinary. _*World Community Grid* members processed 4.5 trillion candidate lung cancer signatures in the main phase of MCM lung, 220 billion in an initial experimental phase, and 1.6 trillion signatures in the optimizing phase. _*(WOW!!)*
> 
> We will discuss some findings from the main phase of MCM lung in this update.



*       The question of signature size*


> MCM lung surveyed signatures of multiple sizes. Sizes varied from 5 biomarkers to 100, with the greatest focus on signatures in the range of 10-20 biomarkers. For a cancer signature to succeed in clinical use, signature size is a compromise between diagnostic power, complexity, and cost. Every biomarker can potentially add diagnostic information to a signature, increasing accuracy, but too many biomarkers can also add noise and unnecessarily increase cost and complexity for practical use in the clinic.
> 
> The figure below shows the effect of signature size on peak accuracy. For almost any size, a signature built from randomly-chosen biomarkers will have poor accuracy, but by testing enough such signatures, and then looking at the accuracy of the top fraction (say, the top 0.01%), we see the effect made by signature size. Carefully engineered signatures should achieve the same accuracy using fewer biomarkers.








​*       Which biomarkers are most successful?*



> In the main phase of MCM lung, signatures were built from biomarkers chosen randomly from the dataset. As such, every biomarker had an equal chance of appearing in each new signature. This does not mean, though, that all biomarkers are equally useful – as we said above, a random signature will most likely have low accuracy. If, however, we take only the most accurate fraction of signatures, and see which biomarkers they contain, we see that a few biomarkers appear frequently, and that the rest are relatively rare. (We may even notice patterns in ways that certain groups of biomarkers appear together, as we discussed in a previous update.) We can determine then how effective or useful each biomarker is from how often it appears in these top signatures.







​


> After analyzing the full set of MCM lung results, we can confirm an effect that we had noticed in earlier, preliminary studies: the effectiveness of each biomarker depends on the signature size, affecting each biomarker differently. The figure below illustrates the effect for some of the top-ranked biomarkers.






​*       Pathway enrichment among the top biomarkers*


> To get a higher-level view of the biomarkers discovered in the lung dataset, we examined them from the pathway perspective. A _pathway_ is a group of genes that cooperate to perform the same biological function. We fed lists of top-1% biomarkers into our lab’s pathDIP database [1], [2]. _pathDIP_ is a comprehensive, integrated database of known pathways (signaling cascades), and given a list of genes, it will find all pathways associated with any gene in the list. Most usefully, it will measure the _enrichment_ of each pathway in your gene list – the degree to which pathway has an above-average connection to your list. Using such analysis, we aim to find biologically meaningful interpretation of our identified biomarkers.
> 
> The figure below shows the results from _pathDIP_.








​


> Across a large number of signature sizes, _pathDIP_ consistently found five pathways enriched in our gene lists:
> 
> 
> Cyclophosphamide Pathway, Pharmacodynamics
> ...




*       Using the Gene Ontology Resource to describe top biomarkers*



> We can get a related view from the Gene Ontology Resource (GO). _GO_ categorizes each gene from three different perspectives: biological process, molecular function, and cellular component. The figures below show terms in _GO_ categories that appear frequently in top 1% biomarkers.











​


> Many of the terms reflect the themes found in pathways: oxidation, alcohol, and red-blood-cell chemistry.



*       Looking ahead*


> We are in the process of expanding and combining multiple additional analyses of the main-phase lung data, and substantial analyses of the second phase lung results. After that, the ovarian data awaits. For ovarian, some of the same techniques will apply, but some will need to be adapted, and some we’ll need to develop.
> 
> In short, the MCM project will keep us busy for a long time. In the meantime, _we would like to thank you for your interest and for your generous donation of computing power to this and other *World Community Grid* projects. We will provide updates more frequently now._




*       Additional results*
(see link at bottom of page)

*Other news*


> In other news, we have been able to secure several grants to enable funding for the project, including:
> 
> 
> Novel methods for integrative computational biology from Natural Sciences and Engineering Council of Canada,
> ...




*Thank you for all the contributed computing power that makes this research possible. *))

*The MCM Team*


[1] Rahmati, S., Abovsky, M., Pastrello, C., Jurisica, I. pathDIP: An annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. _Nucl Acids Res_ *45(D1)*: D419-D426, 2017.

[2] Rahmati, S., Abovsky, M., Pastrello, C., Kotlyar, M., Lu, R., Cumbaa, C.A., Rahman, P., Chandran, V. and Jurisica, I. pathDIP 4: An extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species, _Nucl Acids Res_, In press. 2019. https://doi.org/10.1093/nar/gkz989

[3] CTV News  Interview on IBM World Community Grid, Mapping Cancer Markers, May 3, 2019

_This is Amazing work done! I hope to see more results, soon!_​
The WHOLE thing, on _WCG.org_


----------



## Arjai (Feb 23, 2020)

*World Community Grid’s FightAIDS@Home Team Gathers at HIVE Center Meeting*

*By: The FightAIDS@Home research team
11 Feb 2020 *
​*Summary*
The FightAIDS@Home researchers recently met in California to discuss their plans for the project’s future. 



> On January 15 and 16, 2020, the HIVE (HIV Interactions in Viral Evolution) Center held its annual winter face-to-face meeting in La Jolla, California at The Scripps Research Institute. Sixty-five scientists, who are HIVE members from around the country, were in attendance. This U.S. National Institutes of Health funded Center was established by founding Director Prof. Arthur Olson, who also initiated the FightAIDS@Home (FAAH) project on World Community Grid (WCG) in 2005. FAAH and WCG play a significant part in the work of the Center, which integrates their computational research with the experimental research of virologists, molecular biologists, structural biologists, and chemists within the HIVE.
> 
> The latest research of the FAAH team was presented at the meeting, which included work from the Levy group at Temple University as well as from the Olson laboratory at The Scripps Research Institute.





> The two-day meeting highlighted the latest HIVE work on understanding the structure and function of HIV and how infected human cells interact with the virus during its life cycle. The focus of the research is in understanding how the virus evolves and its implications for both drug design and in finding a cure by elimination or complete suppression of the virus in its human host. Gratitude was expressed for the important contributions that _World Community Grid volunteers_ have made to progress of the HIVE Center’s work.





 

Edited, get the Whole Story, HERE.


----------



## Arjai (Mar 12, 2020)

*Smash Childhood Cancer Team Announces New Principal Investigator and New Project Targets* 

*By: The Smash Childhood Cancer research team*
*9 Mar 2020
*
*Summary*
The Smash Childhood Cancer researchers are pleased to announce that Dr. Godfrey Chan, a founding member of the team, will be the new Principal Investigator for the project. The project is re-starting with two new targets to investigate in the continuing search for better childhood cancer treatments.

*Thank You to Dr. Akira Nakagawara



*​


> The Smash Childhood Cancer team and World Community Grid thank Dr. Akira Nakagawara for his many years of leadership and service as Principal Investigator of the Help Fight Childhood Cancer and Smash Childhood Cancer research teams. He is stepping down as Principal Investigator to spend more time with his family, but will remain part of the research team and will be involved in future work.





> Under Dr. Nakagawara’s leadership, the Help Fight Childhood Cancer project discovered seven drug candidates that show great promise as new treatments for neuroblastoma, one of the most common and dangerous forms of childhood cancer. To help build on these discoveries, he expanded the original project into the international collaboration of the Smash Childhood Cancer project, which is searching for potential treatments for brain tumors, Wilms' tumors (malignancies in the kidneys), hepatoblastoma (liver cancer), germ cell tumors, and osteosarcoma (bone cancer).



*Welcome to Dr. Godfrey Chan 



*​


> Dr. Godfrey Chan, one of the original members of the Smash Childhood Cancer team, will be the project’s new Principal Investigator. As a pediatric oncologist and researcher focused on translational medical research and clinical trials, his specialty is the screening and development of new drugs targeting known or newly defined molecules.





> He is Head & Chief of Service of the Department of Pediatrics & Adolescent Medicine at The University of Hong Kong. He is also the Director of Molecular Laboratory for Traditional Chinese Medicine (New Drug Screening for Immunology & Cancer), and was the Deputy Director of the Stem Cells & Regenerative Medicine Consortium (Clinical Application of Mesenchymal Stem Cells) at The University of Hong Kong.
> 
> Dr. Chan serves as the Continental Chairman (Africa, Asia and Australia) of Advance Neuroblastoma Research and Executive Committee Member of SIOPEN (European Neuroblastoma) group. He has earned several international awards (ANR, SIOP, ASPR, Endeavor Executive Award-Australian Government, Outstanding Pediatrician of APPA) for his clinical and laboratory research works on childhood neurogenic tumors and stem cells biology.
> 
> Thank you to both outstanding researchers for their ongoing work in the fight against childhood cancer.


*

New Targets 

*


> The newest Smash Childhood Cancer work units will look at two potentially important targets, PRDM14 and Fox01.
> 
> PRDM14 is involved in intracranial germ cell tumors (IGCTs) that primarily affect adolescents and young adults. These are very rare brain tumors that have a much higher incidence in Japan and East Asia. In addition to IGCTs, PRDM14 also affects non-small cell lung cancer, breast cancer, leukemia (both pre-B cell and T-cell) as well as prostate cancer.
> 
> Fox01 is believed to play a role in the development of a number of cancers in addition to childhood cancers, including prostate, endometrial, pancreatic, and others.




After _World Community Grid’s_ work on these two targets is finished, we anticipate having a few more for volunteers to crunch. Thank you to everyone for supporting the Smash Childhood Cancer project.​

WCG Story, HERE


----------



## Arjai (Apr 7, 2020)

*Planned Maintenance on Wednesday, April 8, 2020 

6 Apr 2020* 

*Summary*
We are updating the operating system on our servers on Wednesday, April 8, beginning at 13:00 UTC.

We will be applying an important operating system update to our servers on Wednesday, April 8 beginning at 13:00 UTC. We anticipate that the work will take approximately four hours. 

During some of this time, volunteers will not be able to upload or download new work, and the website will not be accessible.

Volunteers will not need to take any particular action, as your devices will automatically retry their connections after the maintenance work is completed.

We appreciate your patience and participation.


----------



## phill (Apr 7, 2020)

I won't bother changing my buffered work stock then, as 4 hours should only get through a few work units   Besides I guess if they do stop working, they'll thank me for it !!


----------



## Arjai (Apr 16, 2020)

*New Version of World Community Grid Software Now Available for Windows and Mac*

*13 Apr 2020

Summary*
The newest version of the World Community Grid software application adds enhanced security measures for Windows and Mac computers. All volunteers who are currently running version 7.14.2 or older are encouraged to upgrade. 

We have released a new version of the World Community Grid software application. This new version includes security enhancements for Windows and Mac computers, as well as an update to the program's screensavers for Mac users. The new version is now available to download.

In particular, volunteers running version 7.14.2 or earlier of the application are encouraged to upgrade. To check if your PC or Mac is running an old version of World Community Grid:


Open the World Community Grid software application, which can be done either via the small World Community Grid icon on your computer's task bar, or from your computer's application menu.
In the main menu of the World Community Grid application:
(For Windows users) Click on _Help_ to display the help menu. Then click on on '_About World Community Grid - BOINC Manager.'_
(For Mac users) Click on _'World Community Grid'_ in the main menu. Then click on on '_About World Community Grid - BOINC Manager.'_

In the _About_ window, the version number is listed toward the top (see below for an example).


No update is needed at this time for Linux machines or Android devices.


----------



## phill (Apr 18, 2020)

Does anyone here run that VirtuaBox setup or is it just the standard smaller download here people use??


----------



## Peter1986C (Apr 18, 2020)

Just the BOINC client itself. The one with VB is only for very specific projects that need it.


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## blobster21 (Apr 18, 2020)

Arjai said:


> *New Version of World Community Grid Software Now Available for Windows and Mac*



How did you guys proceed to get the update ?

EDIT : Nevermind, i mistook the boinc manager client updated version with my own WCG client, which is still on v 7.14.3.



Phill said:


> Does anyone here run that VirtuaBox setup or is it just the standard smaller download here people use??



I remember using that Vbox setup for crunching datas for the LHC a couple of years ago.


----------



## phill (Apr 19, 2020)

How has the update been going for those upgraded??  I've not done all my machines but I think everything seems to be fine for the ones I've upgraded....  Anyone else had similar fortune??


----------



## Arjai (Apr 21, 2020)

*Planned Maintenance on Wednesday, April 22, 2020*

*20 Apr 2020

Summary*
We are performing database maintenance on Wednesday, April 22, 2020 starting at 13:00 UTC.

We are performing maintenance on the BOINC database in order to improve performance and capacity. This work will start on *Wednesday, April 22, 2020 at 13:00 UTC*, and will take about five hours.

During the entire time of the maintenance, volunteers will not be able to obtain new work or report completed work. Volunteers will not be able check on the status of their results, but the rest of the website will remain available.

_*Volunteers will not need to take any particular action, as your devices will automatically retry their connections after the maintenance work is completed.*_

We appreciate your patience and participation.


----------



## phill (Apr 22, 2020)

Best get some extra work lined up everyone just incase!!


----------



## Arjai (May 14, 2020)

*The Microbiome Immunity Project Must Go On!*

*By: The Microbiome Immunity Project research team
11 May 2020

Summary*
Research in the time of a pandemic is more important than ever. Here’s how the _Microbiome Immunity Project_ team is making continued progress while working from home.



> Trillions of bacteria live inside and on our bodies. The _Microbiome Immunity Project_ is using the computational power of *World Community Grid* to study the proteins produced by these bacteria, which are encoded in their genomes. This helps scientists understand the role of the microbiome in disease.
> We want to thank all of our volunteers for their help with donating valuable computer time! So far, we have run more than 300,000 protein sequences through our pipeline. With the predicted models and our new method for functional annotation, we have finally started a deeper dive into analyzing our data!



*The Context* 





> We were supposed to meet in New York City in March for our regular research general meeting. However, due to the COVID-19 pandemic, this meeting could not happen in person. Instead, we had several-hour long video calls through Zoom on those three days, March 18-20. Researchers from the USA (New York), Poland, and New Zealand participated in the meeting. Finding a time that worked for everyone in those three different time zones across the globe was hard, but we pulled it off.



*The Progress*



> Our paper about functional annotation from sequence and structure (you can check out a preprint here) has been submitted and is currently under review. We’re keeping our fingers crossed for positive reviews!





> Our research activities have always involved remote work and online communication. In these trying times we are working as hard as ever, and we are hoping that all *World Community Grid* _volunteers are taking measures to stay safe and healthy. We thank you for your continued support!_



Full story and Research info, HERE.


----------



## Flanker (May 15, 2020)

I just got a batch of work units for covid19!


----------



## Arjai (May 15, 2020)

*Help Stop COVID-19 and Future Pandemics in Their Tracks*

*By: The OpenPandemics Research Team
14 May 2020

Summary*

The OpenPandemics - COVID-19 project helps researchers at Scripps Research look for potential COVID-19 treatments. But that's just the beginning for our newest project, and we need your help.



Contribute to this Project






No treatment.

No cure.

No vaccine.

These are three grim facts about COVID-19, a disease caused by a newly identified and highly contagious virus, named SARS-CoV-2, that has, in just a few months, wrought havoc around the globe, causing severe illness and even death. But scientists and volunteers are uniting to power OpenPandemics - COVID-19, a new World Community Grid project to help address the urgent need for identifying potentially effective COVID-19 treatments.

*Why is finding potential treatments for COVID-19 so important?  *

Soon after COVID-19 was identified, scientists began the complex undertaking of creating a vaccine that could help prevent the spread of the virus. However, this process is likely to take many months--or possibly years--even with a concerted, global effort among scientists and with accelerated clinical trials. 
In the meantime, scientists are also searching for potential therapeutic agents that could help managing the symptoms, halting the progression of the disease, and ultimately speed healing from COVID-19. OpenPandemics - COVID-19 is one such effort, led by researchers in the Forli Lab at Scripps Research, who are accelerating the search by enlisting the help of World Community Grid volunteers.

*How does World Community Grid work? *

As a World Community Grid volunteer, you download a secure software program to your computer. And when your computer is not using its full computing power, it automatically runs a simulated experiment in the background which will help predict the effectiveness of a particular chemical compound in inhibiting the functions of viral proteins, as a possible treatment for COVID-19. Then, your computer returns the results of the completed simulation and requests the next simulation.
All of this happens unobtrusively, while you are going about your regular activities such as typing an email, browsing the Internet, or while your computer is idle but left on.
World Community Grid combines the results from your computer along with millions of results from other volunteers all over the world and sends them to the Scripps Research team for analysis. While this process doesn't happen overnight, it accelerates dramatically what would otherwise take many years, or might even be impossible.
*What exactly are the scientists at Scripps Research looking for?*





_Top (l to r): Stefano Forli, Paolo Governa, Andreas Tillack, Jérôme Eberhardt
Middle (l to r): Giulia Bianco, Batuujin Burendei, Diogo Santos-Martins, Martina Maritan
Bottom (l to r): Matthew Holcomb, Christina Garza
Click here to learn more about the OpenPandemics research team._

The Forli Lab is using a process known as molecular docking, which is the study of how two or more molecules fit together, to evaluate how chemical compounds might bind to SARS-CoV2 proteins and may therefore be effective as potential treatments. 
By leveraging World Community Grid's massive computational power, the research team can virtually screen millions of known and novel chemical compounds in a matter of months instead of years. Promising compounds will then proceed through the drug discovery process, including laboratory testing.

*How can this effort help address future pandemics?*

From what scientists have learned from past outbreaks, they expect pandemics caused by newly emerging pathogens to become more and more common. That's why this project is being designed to be rapidly deployed to fight future diseases, ideally before they reach a critical stage.
In order to help address future pandemics, researchers need access to swift and effective tools which can be deployed very early, as soon as a threatening disease is identified. Using the knowledge and data from looking for potential COVID-19 treatments, the researchers plan to create a software infrastructure to streamline the process of finding potential treatments for other diseases. And, in keeping with World Community Grid's open data policy, they'll make their findings and these tools freely available to the scientific community. 

In addition to searching for potential treatments for COVID-19, the scientists want to be prepared for the next emergency. Future pandemics could stem from a progressive accumulation of mutations, which can eventually lead to a new virus variant. This is what happened when the virus SARS-CoV1 mutated to become SARS-CoV2, the virus which causes COVID-19. So the research team is including proteins from SARS-CoV1 and other viruses, to be studied as part of OpenPandemics - COVID-19, which will help them assess how difficult would it be to find or design molecules capable of overcoming the inevitable mutations.

Contribute to this Project


----------



## Arjai (Jun 18, 2020)

*Help Stop TB Researchers Welcome New Team Member*

*By: The Help Stop TB Team*
*University of Nottingham*
*11 Jun 2020 *

*Summary*
Meet the newest member of the Help Stop TB research team, who will be helping with the project’s data analysis. 



> *Background*
> 
> The Help Stop TB project was created to study the sheath of the bacterium that causes tuberculosis, in order to help scientists look for better treatments.
> 
> In 2018, approximately 10 million people contracted tuberculosis, and 1.5 million people died. And in a recent publication, the World Health Organization stated, "Between 2020 and 2025 an additional 1.4 million TB deaths could be registered as direct consequence of the COVID-19 pandemic."





> *Welcome, Marko!*
> 
> Since our last update, we’ve had a new addition to the project team!
> 
> ...






​


> *Search for Additional Team Members Continues*
> 
> We are always actively looking for new team members. Our opportunities include PhD studentships available to talented UK/EU (UK resident) applicants, alongside opportunities via our European-Union-targeted scholarships. In the near future, further details for 2021 scholarships will be available at https://www.nottingham.ac.uk/pgstudy/funding/vc-scholarship-for-research-excellence-eu
> 
> ...



_Good luck Mark and Team Help Stop TB!
 _


----------



## Arjai (Jun 19, 2020)

*This is how a global community unites to find cancer biomarkers.*

*17 Jun 2020

Summary*
Sawyer created a World Community Grid team to help accelerate research after his father was diagnosed with brain cancer. In the process, he found a global community of volunteers who are helping scientists at Krembil Research Institute find cancer biomarkers, which could lead to better diagnosis and treatment.

*Meet Sawyer*

Sawyer is really into computers. He built his first computer at the age of eight, and within a couple of years he founded his own company, where he built and sold more than 20 computers. At the age of 11, he began building cryptominers.

Then, his father, Brett, was diagnosed with brain cancer.




​


> *Quick Facts about Cancer and Biomarkers*
> 
> Cancer is the second leading cause of death globally, accounting for an estimated 9.6 million deaths, or one in six deaths, in 2018. (See the World Health Organization's website for more statistics and facts about cancer.)
> 
> ...






​*Helping Cancer Patients and Finding a Community*

Sawyer was only 11 when his father (pictured above at left) began treatment for brain cancer, but he did some research, found _World Community Grid's __Mapping Cancer Markers_ project, and realized he had the power to help. "I had these powerful cryptominers in my basement and realized I could run World Community Grid on them to help people with cancer, like my dad," he says.

_More of the Story, __HERE._


----------



## Arjai (Jun 24, 2020)

*New Version of BOINC*

17.6.7

Get it HERE


----------



## phill (Jun 24, 2020)

Been running the newer version for a little while, seems ok as no issues that I'm aware of   Not sure if they give a performance boost or not but...


----------



## Arjai (Jul 6, 2020)

*FightAIDS@Home – Phase 1 researchers identified new potential targets for antivirals*

*By: The FightAIDS@Home research team*
*1 Jul 2020
*
*Summary*
A protein called HIV-1 capsid (CA), which is crucial to the replication of HIV, may have some recently discovered vulnerabilities.



> *Background on FightAIDS@Home – Phase 1
> *
> Many people live with Human Immunodeficiency Virus (HIV), and do not get sick for many years. However, because the human body cannot generate antibodies that can eradicate HIV, it can slowly infect key cells of the immune system and impair their function or even destroy them. Eventually, HIV infection results in progressive depletion of a person’s immune system, leading to Acquired Immune Deficiency Syndrome (AIDS). The immune system is said to be deficient when it can no longer fulfill its role of fighting off infections and cancers.
> 
> ...





> *Blocking HIV Protease*
> 
> Proteins are the basic building blocks in all of life's functions. Proteins are long chains of smaller molecules called amino acids. Enzymes are particular kinds of proteins that accelerate biochemical reactions. A protease (pronounced "pro-tee-ace") is an enzyme that is able to cut proteins apart at some point along the amino acid chain. While only a small percent of all of the proteins in an organism are proteases, they are very important in the proper functioning of its life processes.
> 
> ...





> *Potential New Targets for Antivirals
> *
> A protein called HIV-1 capsid *(CA)* is a structural protein crucial to the viral replication cycle as it encloses the viral genome. Its involvement in both early and the late stage of the infection led to efforts in developing antivirals targeting CA.
> 
> ...










​"The paper, which you can read here, presents the data analysis and the details of the researchers’ findings. 

*Thanks to everyone who has supported this project.*"

*Awesome! Looks like our Basic Research has started to get results!! Love this!!*



​


----------



## Arjai (Jul 23, 2020)

*Synthetic Compound May Be Useful for Developing Zika Virus Treatment*

*By: The OpenZika research team*

*23 Jul 2020*

*Summary*
As the OpenZika research team wrapped up their work on _World Community Grid_, they identified a promising compound in the ongoing search for Zika treatments.










> *Background*
> 
> The OpenZika project was created to identify potential treatments for people who were infected by the Zika virus. Specifically, the project targeted key proteins that the virus uses to survive and spread in the body, based on what is known from similar diseases, such as dengue and yellow fever. In order to develop treatments, the researchers aimed to identify which of millions of chemical compounds could be effective at interfering with these key proteins.
> 
> The researchers looked at which chemical compounds might be effective against the apo NS3 helicase crystal structure (apo means that the protein was not bound to anything else, such as a cofactor, inhibitor, or nucleic acid). The NS3 helicase is important because it is a component of the Zika virus (ZIKV) that allows it to replicate. You can learn more about helicases here.





> *A Potential Treatment*
> 
> In late 2019, the OpenZika researchers published a paper in Scientific Reports which _outlined their work showing that a synthetic compound called FAM E3 can inhibit ZIKV infection by blocking the genome replication stage._ Through molecular docking work on _World Community Grid_, the researchers were able to predict a possible interaction between FAM E3 and the ZIKV NS3 helicase. Based on the molecular docking results, _the researchers investigated the interaction in vitro and demonstrated that FAM E3 could bind to and stabilize NS3. _
> 
> You can read the paper here. The results may be useful for further development of Zika antivirals, as well as for a better understanding of how exactly this synthetic compound inhibits viral replication.





> *Other News*
> 
> Like many scientists with extensive experience with infectious disease research,  the OpenZika team is currently doing work related to SARS-CoV-2. In May, the team published a perspective in Drug Discovery Today regarding drug discovery projects for SARS-CoV-2. This paper mentions what they learned through their experiences with previous projects, including the OpenZika project.
> 
> The research team has also begun writing a new paper on the results from the project's virtual screening of NS3 helicase and NS2B-NS3 protease, with the results in vitro in ZIKV and also in the proteins.



*"Thank you to the many volunteers around the world who supported this project during its time on World Community Grid."*

_Pulled from HERE_

_Love that they have found something promising!!_


----------



## Arjai (Jul 28, 2020)

*Behind the Scenes with World Community Grid's Active Projects*

*27 Jul 2020

Summary*
Interested in learning more about our monthly calls with the researchers for each active World Community Grid project? You can get updates on our website, in our forum, and via email.




​Many volunteers have expressed interest in learning more about the day-to-day doings of the research teams, beyond the formal project updates.

Beginning in early August, we'll make this information more widely available in three different ways: 

1. We'll publish a short article on our website for each monthly update on each active project. You'll be able to find these articles tagged as "Research Call Notes."

2. A link to each of these articles will be automatically be posted into our News forum, along with all other World Community Grid news articles. Volunteers who have questions or comments about a specific update can post in the News forum as well.

3. You can choose to include these articles as part of a Daily, Weekly, or Monthly digest email by selecting the _Research Project News_ option in your Communications Preferences settings. (You must be logged in to access this feature.)

Full Article HERE.


----------



## Arjai (Aug 14, 2020)

*August Update: Africa Rainfall Project*

*10 Aug 2020

Summary*
The World Community Grid team had a quick monthly meeting with the Africa Rainfall Project researchers, which you can read about in this article.



*Project background*


> 95% of agriculture in Africa depends on rainfall. The Africa Rainfall Project uses massive computing power, data from The Weather Company, and other data to provide more accurate rainfall forecasts, which will help farmers more successfully raise crops.



*Looking for an additional team member*

*Upcoming conferences*

*Current status of work units*


> We're currently sending out generations 18 and 19. (A generation is a set of work--in this case, a set of computer simulations of rainfall in sub-Saharan Africa.) _The World Community Grid_ tech team is increasing the rate at which we're sending out work. We'll post about this increase in the African Rainfall Project forum as soon as it's implemented.



_Full News Item, __HERE>_


----------



## Arjai (Aug 15, 2020)

*August Update: OpenPandemics - COVID-19*

*13 Aug 2020

Summary*
OpenPandemics - COVID-19 launched in May, and the work has just begun. Learn more about the scientists' progress so far, as well as the collaborations that will help move the research forward in the coming weeks and months.








_Click here to learn more about the team._ ​*Background*



> OpenPandemics - COVID-19 was created to help accelerate the search for COVID-19 treatments. You can learn more about the details of the work on the research team's website.



*Data analysis*


> Since OpenPandemics - COVID-19 launched in May, the project has screened millions of chemical compounds that may be potential treatments for the disease. The screening is still ongoing, but the research team has analyzed the results they've gotten so far (45.7 million runs and 2.3 billion poses), and have narrowed the initial group down to approximately 1,500 compounds (0.00003 % of the total ligands docked!) that have been selected for their interactions with the target proteins and that warrant further analysis.
> 
> From the current group of 1,500 compounds, the researchers will do manual analysis to identify approximately 100 of the most promising, which will then go to their collaborators for further laboratory testing. (You can see a list of collaborators toward the bottom of the Research Participants page.)
> 
> While this testing goes on, they'll continue analyzing the data they receive from us and will continue to send new work to us.




*Additional collaborations

Grant award

GPU version*


> _The_ _World Community Grid_ development team is starting to create work units for initial alpha testing. Their current issue is creating work units that can run on both *CPU and GPU*, rather than needing to create two different versions, which would add complexity to the project. The next step within IBM will be a security review of the new version. The work is ongoing and there's currently no estimate for when it will be completed.




*Potential publications

Current status of work units*


> Available for download:  4,882 batches
> In progress:  2,052 batches (16,101,394 work units)
> Completed:  5,459 batches (2,587 batches in the last 30 days,
> an average of 86 batches per day)
> Estimated backlog: 56 days




Full News Item, HERE.


----------



## Arjai (Aug 23, 2020)

*August Update: FightAIDS@Home*

*17 Aug 2020

Summary*
Phase 2 is currently paused while the researchers plan for the future and finish up two papers.




_A few of the members of the FightAIDS@Home team are pictured above at an in-person meeting before the COVID-19 pandemic began. Learn more about the entire team here._​*Work on Phase 2 *

The project is currently paused, and the Phase 2 team has received back all work units that were run on _World Community Grid._

The researchers from both phases of the project recently held a virtual meeting, and plan to hold another one in the next few weeks. They're deciding exactly which chemical compounds they'll concentrate on to re-start Phase 2. They may also do further analysis on compounds that don't need the massive computing power of _World Community Grid._

_More info and History, HERE._

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

*August Update: Help Stop TB*

*19 Aug 2020*

*Summary*
The Help Stop TB researchers recently welcomed a new team member, and continue to research for additional students to help with the project.

*Background* 

*Search for new team members

Data formatting

Current status of work units*



> In progress: 44 batches (1,085 work units )
> Completed:  23,541 batches
> 75 batches in the last 30 days
> average of 2.5 batches per day
> _*Note:*_ For this particular project, the researchers often need to analyze the batches we send back to them before they can build more work units. This can sometimes lead to an intermittent work unit supply.



_The rest of the info is __HERE._

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

*August Update: Mapping Cancer Markers*

*21 Aug 2020

Summary*
The Mapping Cancer Markers researchers continue to analyze lung cancer marker data while working with the _World Community Grid_ tech team on new sarcoma work units.





_Members of the Jurisica Lab, the researchers behind Mapping Cancer Markers_​*Background*



> Mapping Cancer Markers aims to identify the markers associated with various types of cancer. The project is analyzing millions of data points collected from thousands of healthy and cancerous patient tissue samples. These include tissues with lung cancer, ovarian cancer, and sarcoma.
> 
> By comparing these different data points, researchers hope to identify patterns of markers for different cancers and correlate them with different outcomes, including responsiveness to various treatment options.



*Lung cancer markers

Beta testing on new sarcoma work units*



> _World Community Grid's_ tech team has taken care of a minor issue with the recently-run beta sarcoma work units. We might run an additional beta test in the near future; if this happens, we'll post a notice in our Beta Test Announcements forum so that interested volunteers can participate. (You can check your settings here to see if you're signed up for beta testing.)



*Current status of work units*



> Available for download:  842 batches
> In progress:  941 batches (7,392,542 work units)
> Completed:  64,955 batches (691 batches in the past 30 days,
> an average of 23 batches per day)
> Estimated backlog: 36 days




_More info to be had, __HERE._


----------



## Arjai (Aug 23, 2020)

Unfortunately, I only had time today, to do these 3 updates. The current format for TPU, does not allow me to separate them into separate postings, on the same day (or for how ever many hours between...).

I started my new job last Monday, I have been struggling with getting used to walking 4-6 miles a shift! The toll has been lack of time to do much other than eat, shower, sleep and work. Yesterday and today are off days, this week, and I tried to stay off my feet as much as possible, yesterday. 

Today, I am going to try and assemble my new box, parts are all here, have been since last week. With that build I will have to reconfigure my computer shelves and switch out two surge protectors, comp. rack to Living room and new Belkin 12 outlet on comp. rack. Plus a general cable clean up, that takes most of time. Cable management might take a few days to truly take care of!!


----------



## phill (Aug 24, 2020)

We could always get one of the Super Mods @Arjai to set this thread as a non auto combine thread like I've had done with the Pie threads and such   Might be worth an ask?


----------



## Arjai (Aug 25, 2020)

*August Update: Smash Childhood Cancer*

*24 Aug 2020

Summary*
The Smash Childhood Cancer researchers have given the World Community Grid tech team new work units for testing, and the researchers are also continuing analysis on the simulation results they've already received.




​*Background

Testing of new work units*


> The _World Community Grid_ tech team is currently running alpha testing (or internal testing of a small sample) for new work units that will address a protein the researchers want to study.
> 
> We'll post in the _World Community Grid_ forum once this process is done and we're ready to begin beta testing.



*Data analysis*


> ...
> Each step in the data analysis process can take many months. We'll notify everyone in future monthly updates when there's notable progress on the analysis for each protein listed above.



*Search for additional research team members*

*Current status of work units*


> Paused until alpha testing is complete (see *Testing of new work units* section above).
> 
> _Click here to learn more about World Community Grid's monthly project updates._



_Lot's more in the original __POST._


----------



## Arjai (Sep 9, 2020)

*September Update: Microbiome Immunity Project*

*3 Sep 2020

Summary*
The Microbiome Immunity Project researchers continue to analyze data while simultaneously working on three academic papers.



_Meeting info __LINK_

*Background*

The Microbiome Immunity Project uses the computational power of World Community Grid, donated by volunteers all over the globe, to study the proteins produced by the bacteria in the human gut. This knowledge could help scientists understand the role of the microbiome in health and disease.

*Looking into checkpointing*

In distributed computing, checkpointing is a technique to ensure that work units can be completed even if the device that is working on them pauses, without the work units needing to be restarted. World Community Grid's technical team recently did some work on a checkpointing issue for the Microbiome Immunity Project work units. We anticipate that there will be no loss of research data due to the issue. 

*Papers in progress*
See link at bottom

*Current status of work units*


Available for download: 3,923 batches
In progress: 5,148 batches (15,564,135 work units)
Completed: 313,375 batches (4,852 batches in the past 30 days,
an average of 161.7 batches per day)
Estimated backlog: 24 days
_Full story HERE_


----------



## mstenholm (Sep 22, 2020)

Joy oh joy Vina is back.
SCC has been re-launched. Time to switch your dual boot to Linux.


----------



## phill (Sep 22, 2020)

Most of my rigs run Linux, so hopefully I'll have a bit of a points boost


----------



## Arjai (Sep 27, 2020)

*September Update: Microbiome Immunity Project*

*9 Sep 2020

Summary*
The Africa Rainfall Project researchers recently welcomed a student to their team.

*Project background

Research team welcomes a student*


> A new student has joined the researchers to help with data analysis. They will be comparing the results of the data from _World Community Grid_ to data from other sources.



*Upcoming conferences

Current status of work units*


> _World Community Grid_ is currently sending out generations 22 and 23. (A generation is a set of work--in this case, a set of computer simulations of rainfall in sub-Saharan Africa.)
> 
> _Click here to learn more about World Community Grid's monthly project updates._


*Full Update, **HERE*
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

*September Update: FightAIDS@Home*

*11 Sep 2020

Summary*
The researchers are in the early stages of exploring new possibilities for the next phase of the project.

*Background*


> FightAIDS@Home joined _World Community Grid_ many years ago to identify new and better treatments for AIDS.
> 
> Phase 1 conducted more than 20 billion drug-target comparisons using two software programs which were created by scientists at Scripps Research who ran this portion of FightAIDS@Home. Phase 2 of the project, which is led by researchers at Temple University, used a different simulation method to double-check and further refine the virtual screening results that were generated in Phase 1. This different method is called BEDAM (Binding Energy Distribution Analysis Method).



*Future Direction*


> For several months, the research teams for both phases of FightAIDS@Home had been discussing potential new targets for the next round of work on _World Community Grid_. However, in the past few weeks their discussion has turned to how to best use new approaches and technologies to further refine and possibly accelerate their data analyses.
> 
> They are now in the very early stages of exploring what new approaches and technologies (if any) may help streamline their work. Therefore, while they do plan to have additional work to run on World Community Grid, the timeline for this will be longer than we originally thought.
> 
> We will keep everyone updated as we have more information from the researchers.



*AutoDock Suite at 30 Years

Current status of project*


> Closing Phase 2, pending new direction from research team
> 
> _Click here to learn more about World Community Grid's monthly project updates._


*Full Update, **HERE*
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

*Open-source software program helps power 30 years of progress in computational research*

*14 Sep 2020

Summary*
AutoDock, the software program that powers OpenPandemics and other _World Community Grid_ projects, was created 30 years ago at Scripps Research. Learn more about this powerful software in this article and the attached, recently-published research paper.



> Computational scientific research was a different field a few decades ago, largely due to the limits of storage space and computer infrastructure. But as the searches for new and better treatments for diseases such as AIDS became more urgent, scientists at Scripps Research created the first version of AutoDock in the early 1990s.
> 
> Today, AutoDock has been used in numerous scientific studies at institutions and pharmaceutical companies all over the globe, including in _World Community Grid’s_ FightAIDS@Home and OpenPandemics – COVID-19 projects. While these projects both focus on finding treatments for AIDS and COVID-19, respectively, AutoDock has also been used in studies on drug design methodology (or how to design treatments).
> 
> ...


*Full Story, **HERE*
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

*September Update: Help Stop TB* 

*16 Sep 2020

Summary*
The Help Stop TB researchers will soon have an additional team member to help with data analysis for a couple of months.









_What are mycolic acids, and why is studying them important to the fight against tuberculosis? Both questions are answered in the video above._​*Background

Student rotation*


> In addition to the new team member who was introduced in the last project update, the researchers will have an additional student to help with data analysis for a couple of months, beginning in October.



*Current status of work units*


> In progress:  41 batches (4,100 work units )
> Completed:   23,574 batches
> 34 batches in the last 30 days
> Average of 1.1 batches per day
> ...


*Full Update, **HERE*
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

*September Update: OpenPandemics - COVID-19*

*17 Sep 2020*

*Summary*
The researchers and the _World Community Grid_ tech team are continuing their work to get the project working on GPU.

*Background

GPU version of OpenPandemics*


> Both the research team and _World Community Grid_ tech team are continuing to make progress on porting the software that powers OpenPandemics to GPU.
> 
> The researchers are working on performance improvements for an OpenCL version. Meanwhile, _World Community Grid_ has submitted the code for IBM's Open Source review and a security review. We don't currently know exactly when the IBM reviews will be done.



*AutoDock Suite at 30

Current status of work units*


> Available for download: 3,452 batches
> In progress: 2,259 batches (18,949,527 work units)
> Completed:  9,479 batches
> 2,991 batches in the last 30 days
> ...


*Full Update, **HERE*
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

*September Update: Mapping Cancer Markers*

*22 Sep 2020*

*Summary*
Mapping Cancer Markers currently has a healthy backlog of work for volunteers, with more expected to come.




*Background

Lung cancer markers

Beta testing on new sarcoma work units*


> The _World Community Grid_ tech team is hoping to run another beta test for new sarcoma work units. Once this beta test is ready, we'll post a notice in our Beta Test Announcements forum so that interested volunteers can participate. Volunteers can check your settings here to see if you're signed up for beta testing.



*Current status of work units*


> Available for download: 844  batches
> In progress:  889 batches (7,152,542 work units)
> Completed:   65,645 batches
> 749 batches in the last 30 days
> ...


*Full Update, **HERE*
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

*September Update: Smash Childhood Cancer*

*25 Sep 2020*

*Summary*
After a successful beta test earlier this month, Smash Childhood Cancer has resumed work on _World Community Grid_.

*Background

Beta testing completed

Project resumed!*


> After the successful beta test, Smash Childhood Cancer resumed sending and receiving work with _World Community Grid_ on September 22.
> 
> For this round of work, the research team is focusing on a gene called EWSR1. This gene is significant in the development of Ewing sarcoma, a rare childhood cancer that usually begins in a bone, or in the soft tissue around a bone, and can spread to the lungs or to other bones.



*Current status of work units*


> Project resumed on September 22 with 143 batches of work units
> 
> _Click here to learn more about World Community Grid's monthly project updates._


*Full Update, **HERE*

_OK, that's all the September Updates! _

_I could not find the time, or the energy, to do all of them when they came out. The new job has been wearing me out! I walk between 3 to 5+ miles each shift. I have been saying Yes to all the shifts...I am currently off until Monday morning, meaning 3 days off!! 

So, I decided to get this Thread caught up!!

I hope you enjoy the new format, with headers but not all the text. I quoted what was in the summary, and the Current Status, for the most part. Links to each article are included at the end of each article. _


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## windwhirl (Apr 7, 2021)

Planned Maintenance on Thursday, April 8 [Completed]
					

We are updating the operating system on our servers on Thursday, April 8, beginning at 15:00 UTC.



					www.worldcommunitygrid.org


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## Arjai (Apr 16, 2021)

I apologize for the lack of updates. I am going to try and get a set schedule soon. We still need to hire a couple of guards, then we will be full staffed. Until then my schedule is a bit screwy. day shifts, nights, all mixed together. It is playing havoc on my sleep schedule. Hopefully, it will settle down soon, and I can get back to doing these on a regular basis. Thanks for being patient with me as this goes on.

I am off to bed soon, gotta a 5:50 am bus to catch! Still have a bag full of chores to do, also!!


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## windwhirl (Apr 16, 2021)

Arjai said:


> I apologize for the lack of updates. I am going to try and get a set schedule soon. We still need to hire a couple of guards, then we will be full staffed. Until then my schedule is a bit screwy. day shifts, nights, all mixed together. It is playing havoc on my sleep schedule. Hopefully, it will settle down soon, and I can get back to doing these on a regular basis. Thanks for being patient with me as this goes on.
> 
> I am off to bed soon, gotta a 5:50 am bus to catch! Still have a bag full of chores to do, also!!


It's alright, don't worry. Take care!


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## phill (Apr 23, 2021)

Arjai said:


> I apologize for the lack of updates. I am going to try and get a set schedule soon. We still need to hire a couple of guards, then we will be full staffed. Until then my schedule is a bit screwy. day shifts, nights, all mixed together. It is playing havoc on my sleep schedule. Hopefully, it will settle down soon, and I can get back to doing these on a regular basis. Thanks for being patient with me as this goes on.
> 
> I am off to bed soon, gotta a 5:50 am bus to catch! Still have a bag full of chores to do, also!!


Relax mate and make sure you rest, most important    Posts can always be done another day


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## phill (Apr 26, 2021)

I was just wondering and posting out of interest, I've been having a few issues with uploading some work units this evening 11pm UK time, I was just wondering if anyone else is experiencing any similar issues?

I couldn't see anything on the site when it worked, that any maintenance was due??.....


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## Deleted member 202104 (Apr 26, 2021)

phill said:


> I was just wondering and posting out of interest, I've been having a few issues with uploading some work units this evening 11pm UK time, I was just wondering if anyone else is experiencing any similar issues?
> 
> I couldn't see anything on the site when it worked, that any maintenance was due??.....



Had the same issue here today - Can't remember the exact message in the upload queue, but something about *edit* 'Project backoff' or something similar.

I've also had zero GPU tasks come down now for about a week.


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## Arjai (Apr 27, 2021)

I googled the issue, transient error. It seems to be an issue with the servers being busy, doing whatever. I had a load of WU's go through this morning and then backed off a couple. So, hopefully nothing serious and it will resume again, normally.

Or, there could be an issue with over crowding the servers, or somebody is trying to take it down with a bot...Or one of the servers is in Canada where a beaver chewed through a main internet cable (it's True)... or there are so many user's, like us, using multiple boxes crunching, that we are breaking the internet! LOL.


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## Operandi (Apr 27, 2021)

They are currently running a stress test on the infrastructure by releasing a ton COVID-19 GPU workloads. My GPU has been running nearly constantly since yesterday evening.


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## mstenholm (Apr 27, 2021)

weekendgeek said:


> Had the same issue here today - Can't remember the exact message in the upload queue, but something about *edit* 'Project backoff' or something similar.
> 
> I've also had zero GPU tasks come down now for about a week.


Did you/Windows update your drivers recently? Restart BOINC and look for the OpenCL 1.2 in the top of the event log. There are plenty of GPU work now. I think I have around 100 spread over 5 PCs waiting to be processed. @weekendgeek

Edit: I just looked you up. Your 3070 had plenty GPU yesterday/today.


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## Deleted member 202104 (Apr 27, 2021)

mstenholm said:


> Did you/Windows update your drivers recently? Restart BOINC and look for the OpenCL 1.2 in the top of the event log. There are plenty of GPU work now. I think I have around 100 spread over 5 PCs waiting to be processed. @weekendgeek
> 
> Edit: I just looked you up. Your 3070 had plenty GPU yesterday/today.



No driver updates and the PC get rebooted one per week

They did start coming down again yesterday with the start of the 'stress test'.  Also, I was able to get my other machine with the 1070 to start GPU work - I had to plug a monitor in.  Very odd - folding works fine without, but the Microsoft Remote Display Adapter disables WGC work.


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## phill (Jun 3, 2021)

Hey Guys and Gals 

I just thought I'd put up a post, I saw that they will be doing some Server Maintenance on the servers tomorrow I believe (4th June) so make sure you have enough work    I believe the out gage is about 4 hours with some luck, so everything should be pretty smooth I hope  

'ere tis the linky!!

Hope everyone is doing well and ok!!


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