WCGrid News and Talking Points!!

[phill]

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]

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.


HIV is difficult to stop because when it replicates, it does not do so perfectly and is thus continually changing. Scientists are studying HIV intensively to find ways to stop the onset of AIDS. The FightAIDS@Home project was created to search for drugs that can disable a key step in HIV's life cycle — specifically by blocking HIV-1 protease.

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.

Not all proteases are good. HIV makes and uses a particular protease, HIV-1 protease, which it uses to make the virus's different proteins.

This is where ligands play an important role. Ligands are small molecules that come from outside the cell that attach, or "bind," to pockets in proteins. You can think of a ligand binding to its receptor like a key fitting into a lock. The FightAIDS@Home project specifically searched for ligands (drugs), which can attach to the HIV-1 protease receptor in a way that blocks its ability to function as an enzyme. This prevents the virus from spreading further in the body and developing into AIDS. Molecules that block HIV protease are called "protease inhibitors."

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.

In a recent paper, the FightAIDS@Home research team detailed their findings on new, interesting, potentially druggable regions on the surface of HIV-1 capsid protein, which were then targeted with virtual screenings on World Community Grid to search for compounds capable of binding on these regions.

The structural characterization, biochemical and virological assays discussed in the paper show that the identified site could be amenable to antiviral targeting.

​

"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]

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]

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]

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]

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]

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.

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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.

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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]

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]

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]

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]

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]

Joy oh joy Vina is back.
SCC has been re-launched. Time to switch your dual boot to Linux.

 

[phill]

Most of my rigs run Linux, so hopefully I'll have a bit of a points boost

 

[Arjai]

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
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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
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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).

AutoDock has been refined and improved over the past three decades. Many of these changes are described in an invited paper about the history and evolution of AutoDock in the journal Protein Science. You can read the full article here.

Thank you to all volunteers who have supported FightAIDS@Home, OpenPandemics – COVID-19, and other projects searching for new and better treatments.

Full Story, HERE
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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

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.



Click here to learn more about World Community Grid's monthly project updates.

Full Update, HERE
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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
  Average of 99.7 batches per day
• Estimated backlog: 34.6 days

Click here to learn more about World Community Grid's monthly project updates.

Full Update, HERE
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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
  Average of 25 batches per day
• Estimated backlog: 33 days

Click here to learn more about World Community Grid's monthly project updates.

Full Update, HERE
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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.

 

[windwhirl]

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

 

[Arjai]

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!!

 

[windwhirl]

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!

 

[phill]

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

 

[phill]

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??.....

 

[Deleted member 202104]

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.

 

[Arjai]

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.

 

[Operandi]

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.

 

[mstenholm]

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.

 

[Deleted member 202104]

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.

 

[phill]

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!!