WCGrid News and Talking Points!!

[Arjai]

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]

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]

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]

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]

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]

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
• Helping the Microbiome Immunity Project researchers predict almost 200,000 unique protein structures, which is more than all the experimentally solved protein structures to-date
• Providing data to help lay the ground for new tools to analyze protein-protein interactions

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)
• Posting your thoughts about being involved in World Community Grid in our forum
• Sharing our Facebook post and/or retweeting our tweets on starting on Saturday, 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.

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]

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]

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
• Ifosfamide Pathway, Pharmacodynamics
• Ethanol oxidation
• Fatty Acid Omega oxidation
• Oxidative Stress Regulatory Pathway (Erythrocyte)

All five enriched pathways relate to metabolism, meaning the breakdown of chemicals in the body. Curiously, the first two pathways relate specifically to metabolism of chemotherapy drugs, Cyclophosphamide and Ifosfamide. The last three relate to either oxidation or the prevention of oxidative stress (free radicals) in red blood cells.

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,
• Interactome mapping of disease-related proteins using split intein-mediated protein ligation (SIMPL) from Genome Canada,
• The Next Generation Signalling Biology Platform from Ontario Research Funds
• Canadian Institutes of Health in collaboration with European funding agencies

Importantly, we also had a chance to host two World Community Grid and MCM supporters at our institute[3]. Dylan Bucci, a Sisler High School student, and network and cybersecurity teacher Robert Esposito visited our research institution to meet with us and our collaborators, the scientists who use the results from the analysis. It was interesting for us to learn about their motivation, and for them to experience direct and indirect research links to MCM.

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]

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]

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]

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]

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]

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:

1. 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.
2. 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.'
3. 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]

Does anyone here run that VirtuaBox setup or is it just the standard smaller download here people use??

 

[Peter1986C]

Just the BOINC client itself. The one with VB is only for very specific projects that need it.

 

[blobster21]

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.

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]

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]

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]

Best get some extra work lined up everyone just incase!!

 

[Arjai]

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]

I just got a batch of work units for covid19!

 

[Arjai]

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]

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!

Marko Hanževački has come to us from beautiful Croatia via Erlangen in Germany, where he recently completed his PhD thesis. He has high-level expertise in molecular dynamics and in enhanced sampling methods, including a range of computational analytical expertise that will come in useful for the next stages of the Help Stop TB project.

He’s already got stuck into work here and is shown below helping out on one of our recent outreach events, “Science in the Park,” sporting one of our “Sustainable Process Technologies” research group T-shirts.

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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

We are also happy to help support qualified applicants through our fellowships processes. These include applications for the prestigious EU-funded Marie Skłodowska-Curie fellowships, and local Nottingham Research fellowships or Anne-McLaren fellowships, alongside those from the learned societies.

If you have the drive and the skills to join us, please get in touch.

Good luck Mark and Team Help Stop TB!

 

[Arjai]

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.

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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.)

Cancer starts due to genetic or environmental changes that interfere with biological mechanisms that control cell growth. These changes can be detected in tissue samples through the presence of their unique chemical indicators, such as DNA, proteins or metabolites, which together are known as "biomarkers." A group of such biomarkers is referred to as a signature.

The pattern of biomarkers can determine whether an individual is susceptible to developing a specific form of cancer, and may also predict the progression of the disease, helping to suggest the best treatment for a given individual. For example, two patients with the same form of cancer may have different outcomes and respond differently to the same treatment due to their unique genetic profile, in combination with potentially different lifestyles.

While several biomarkers are already known to be associated with certain cancers – mostly identifying patients at risk (e.g., BRCA1 or BRCA2 mutations for breast and ovarian cancer), there are many more to be discovered. Computational research can help speed up the discovery process, but researchers need massive amounts of computing power to make this possible.

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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]

New Version of BOINC

17.6.7

Get it HERE