World Community Grid & IBM - OpenPandemics Initiative to Fight COVID-19 (Now Live)

ZipSpeed

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It looks like there will be a third major player soon in the fight against COVID-19. I noticed a recent shortage of Rosetta WUs so with WCG, there will be another opportunity to keep those CPUs fed at maximum capacity.


IBM.org said:
We want to stop pandemics in their tracks.
What if your computer could help scientists fight COVID-19... and future pandemics?


Scientists at Scripps Research are doing computational research to look for possible treatments for COVID-19, but to be successful they need massive computing power to carry out millions of simulated laboratory experiments.
So they’re teaming up with World Community Grid, an IBM social impact initiative that allows anyone with a computer and an internet connection to donate their device’s idle processing power to help scientists study the world’s biggest problems in health and sustainability.
The researchers want not only to help find treatments for COVID-19, but also to create a fast-response, open source tool that will help all scientists quickly search for treatments for future pandemics.
OpenPandemics will be launching soon, and we need your help.
 
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Markfw

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Well, this is easy... my last medical reasearch project... I just pause a few Rosetta, and resume WCG...
 
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StefanR5R

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Some more little bits of info from the WCG forum:

The launch is said to be "a matter of weeks".

On April 1 WCG admin jhindo said:
  • The OpenPandemics project will have two objectives: first, to screen chemical compounds as potential treatments for COVID-19; second, to develop and make available tools & methods to streamline the computational drug discovery process, to be deployed against future pandemics.
  • We haven't finalized the specific system requirements for the project yet. The research application currently runs on Windows, Mac and Linux.
  • At launch, the project will run on CPU.
[...] we may port the research application over to Android at some point but the priority right now is to get the project launched as quickly as possible.

[...] Folding@Home and Rosetta@Home are leveraging different computational research techniques - predicting the protein structure of the virus, whereas OpenPandemics which will be predicting which chemical compounds dock against COVD-19 protein targets. Both approaches are valid and valuable.
(source 1, 2, 3)

On April 2 WCG admin jhindo said:
Scripps is considering docking against multiple ligand libraries, including clinically tested compounds. We don't yet have an estimate of the project's likely duration - it depends on many factors including overall number of work units, average runtime per work unit, volunteer interest in the project, etc. We'll have a better idea closer to launch.

Good question about the tools development. Large scale, high-throughput computational research efforts like this require a ton of work for researchers to prepare and organize their input data, and even more work to store, process and analyze the output data generated. These tools aim to ease that burden by streamlining these pre and post processes to make it easier to carry out computational drug docking experiments in the future.

Finally, scientists believe that future pandemics caused by newly emerging pathogens are unfortunately likely to become more common. The OpenPandemics project can therefore be leveraged to address such future outbreaks too.
(source)

On April 1 WCG admin jhindo said:
  • The research application will be AutoDock, which is developed by Scripps and has been used on a number of World Community Grid drug discovery projects in the past.
  • At this time, AutoDock runs on Windows, Mac and Linux but not Android.
  • We are working very aggressively towards launch, but don't yet have an expected launch date. We will keep you posted as we get further into the onboarding process.
(source)

On April 3 WCG technician knreed said:
Since we got the go ahead for the project I have been working with Keith on estimating the characteristics of this project in terms of how it is going to impact the system from the perspective of bandwidth, storage, cpu and other capacity factors. Fortunately, this project appears to be very favorable to volunteer computing and the ratio of cpu time/file size is very high (in fact our early estimates suggest that 5000 years of cpu time/day for the OpenPandemics project will use less bandwidth and storage than 15 years of cpu time/day for the African Rainfall Project). However, storage and bandwidth are only two of the factors we need to estimate.

We are assuming that we are going to see some explosive growth in the number of users and devices contributing to World Community Grid. I am putting together a plan that will be finalized today or Monday that will detail the steps we need to do before launch to accommodate that growth. We will be implementing this plan before launch and will be prepared for recording breaking participation (we have been watching the experiences of Rosetta@Home and Folding@Home to help us gauge what to expect).
(source)

On April 3 WCG technician uplinger said:
Due to an issue with Android work units clogging the system, we started working on a mechanism that would limit the number of concurrent workunits allowed per core based on application version id. This means that a device that downloads windows 64 bit version of it may be limited to say 2 for every core they have. An 8 core machine would only be allowed to have 16 total work units on their machine. We are still working on this feature but hope to have it deployed in advance of OpenPandemics. This will be a configuration on the database side so limits can be easily lifted or shifted.
(source)
 
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ZipSpeed

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Thanks for the update. I was wondering when we'll start to see beta units, but it looks like it's still at least weeks away.
 

ZipSpeed

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Another update from a WCG tech:

WCG Tech Uplinger said:
Hello,

I want to update everyone that we have started Alpha testing against the actual COVID-19 target. We have a sample set of small ligands to compare against COVID-19. This Alpha testing is on devices that are owned by members of the World Community Grid team. We are doing this to help give us an idea if the binaries work well and the work units do not crash. So far things are looking well as we work through issues. Alpha testing will hopefully be short, but one of the things we are testing is work unit sizing as different ligands take different times to complete, sometimes exponentially. We are getting a larger subset of ligands to test on Alpha later today to help with the sizing problem.

Thanks again for your interest and look forward to a BETA soon :p
-Uplinger
 
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ZipSpeed

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Beta testing has officially begun!

Greetings,

We are starting a new beta test that will be version 7.08 for Autodock. This is the new project that was announced here: https://www.worldcommunitygrid.org/forums/wcg/viewthread_thread,42232

The initial group of work units will range in size from 3 minutes to 6 hours. We will be sending out 2 copies of every work unit to help check the validator works against the answers. Each work unit should check point 49 times. Please test the check points out.

Also, we are not hiding the screen saver graphics, so you may catch a glimpse of what it will look like.

Thanks,
-Uplinger
Hi everyone,

A quick update: we just started an initial Beta test. For now, we’re using manually created work units, which are actually targeting a protein in the virus. The aim of this initial beta run is to test the science application (AutoDock), results validation and work unit sizing. The initial validation will be with redundancy (where we send out two copies of each work unit), which will help us confirm the validator works against all CPU types within the same operating system. However, at launch, this project should run similarly to other previous AutoDock-based World Community Grid projects - i.e. besides random comparison checks, work units will run with no comparison/redundancy.

In the meantime, we are testing the automation of work unit generation on our Alpha environment and once those tests are complete, we’ll proceed with automatic work unit generation on beta.

For the latest on this beta test, please visit this issues thread: https://www.worldcommunitygrid.org/forums/wcg/viewthread_thread,42310

If you’d like to participate in this test, make sure you’re signed up for beta testing here: https://www.worldcommunitygrid.org/ms/device/viewBetaProfiles.do .

Many thanks for your continued interest in OpenPandemics,
Juan
 

Markfw

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How do you become a beta tester ?
 

Markfw

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Under the beta testing tab, I have checked the boxes. So I should automatically get the units ? Now ???
 

ZipSpeed

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Under the beta testing tab, I have checked the boxes. So I should automatically get the units ? Now ???
Yup, the next time BOINC syncs with WCG, you will automatically download the beta work if there are any available. 40,000 isn't a whole lot considering how many WCG users there are. Most of the time, I'd be lucky to grab a handful, if that.
 

ZipSpeed

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OpenPandemics - COVID19 is officially underway!

World Community Grid said:
Problem

COVID-19 is a disease caused by SARS-CoV2, a virus of the coronavirus family. These viruses cause diseases that affect mainly the human respiratory system and potentially other major organs. COVID-19 can lead to serious illness or even death.


As of the launch of this project, there is no treatment, cure, or vaccine for COVID-19.

Proposed Solution

Scientists at Scripps Research are doing molecular modeling simulations to look for possible candidates for the development of treatments for COVID-19, but to be successful they need massive computing power to carry out millions of simulated laboratory experiments.


So Scripps Research is partnering with World Community Grid, an IBM social impact initiative that allows anyone with a computer and an internet connection to donate their device’s computing power to help scientists study the world’s biggest problems in health and sustainability. By using this donated computing power, the scientists aim to identify promising chemical compounds for further laboratory testing.


The research team wants not only to help find treatments for COVID-19, but also to create a fast-response, open source toolkit that will help all scientists quickly search for treatments for future pandemics. And in keeping with World Community Grid's open data policy, all data and tools that are developed through this project will be shared freely in the scientific community.


The project’s primary goal is to search for potential treatments for COVID-19, so studying proteins from SARS-CoV2 (the virus that causes COVID-19) is the highest priority.


Additionally, scientists want to fight not only the current emergency, but also prepare for the ones that will likely follow. 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. So, the research team is including proteins from the 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.

How You Can Help

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 will automatically run a simulated experiment in the background which will help predict the effectiveness of a particular chemical compound as a possible treatment for COVID-19.Then, your computer contacts the World Community Grid server to let it know that it has completed the simulation, which is automatically and securely sent back to us.


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 receives the results you send back (often called work units or research tasks), combines them with hundreds of thousands of results from other volunteers all over the world, and sends them to the Scripps Research team. The researchers then begin the difficult work of analyzing the data. While this process doesn't happen overnight, it accelerates what would otherwise take many years, or might even be impossible.
 

Endgame124

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Cool, they have android workunits.
Switching my phones/tablet over now :D
I saw this and had to quick check to see if they had arm on Linux support. Doesn’t look like it, so my pis shall remain on Rosetta and asteroids
 

Assimilator1

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Wouldn't phones & tablets run really hot running distributed computing??
I'm not going to run it on my phone anyway, I like the battery to last :p (total life, not just charge).
 

mopardude87

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I had to make switch to this, idk but BOINC got broken where it refused to work anymore for me. Would not connect to anything or send units. Well i am back on WGC and set up only for the Covid-19 WU. Thing hardly uses any memory but i got no idea if the first units i got are even Covid. It makes me look like a jackass for getting the 64gb of ram even if the most i ever saw used was 34gb when using BOINC/Rosetta.

Figured well lets spread the love around, give WGC some love for once. I respect they went out of their way to finally update for Covid. Will see how we do here!
 

Endgame124

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Feb 11, 2008
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I had to make switch to this, idk but BOINC got broken where it refused to work anymore for me. Would not connect to anything or send units. Well i am back on WGC and set up only for the Covid-19 WU. Thing hardly uses any memory but i got no idea if the first units i got are even Covid. It makes me look like a jackass for getting the 64gb of ram even if the most i ever saw used was 34gb when using BOINC/Rosetta.

Figured well lets spread the love around, give WGC some love for once. I respect they went out of their way to finally update for Covid. Will see how we do here!
There is a problem with multiple projects right now with an expired certificate in the windows certificate chain. I don’t think WCG has this issue in windows right now, but so far I’ve only setup Linux hosts for WCG, so I can’t say for certain. There is a manual workaround to can apply if you want to go back to running some Rosetta.

As for the ram, don’t feel bad - project ram requirements keep going up, so even if you don’t go back to Rosetta right away, the ram will be useful eventually.
 

mopardude87

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There is a problem with multiple projects right now with an expired certificate in the windows certificate chain. I don’t think WCG has this issue in windows right now, but so far I’ve only setup Linux hosts for WCG, so I can’t say for certain. There is a manual workaround to can apply if you want to go back to running some Rosetta.

As for the ram, don’t feel bad - project ram requirements keep going up, so even if you don’t go back to Rosetta right away, the ram will be useful eventually.
Yeah its been peachy :) Yup i got plans for the big top dog 4000 series and i know ram usage would go up with threads and i guess Rosetta had times some units used 3gb. I figured lets set up for anything.

I figured they put the hard work into putting Covid Wu in, i figured its only right to pay them for their hard work with some crunching!

Edit: Just wanted to add in some temps and memory readings, not bad huh? :) Pretty happy with it myself.

 
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StefanR5R

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i got no idea if the first units i got are even Covid.
The tasks with "opn1" in their name are OpenPandemics "phase 1" units. Phase 1 of OpenPandemics has got the search for COVID-19 treatments as its primary goal. To this end, it studies proteins of the SARS-CoV2 virus mostly. But because the virus mutates, proteins of the older SARS-CoV1 virus and some other viruses are included in the study as well. As a by-product, the simulation tools used in the OpenPandemics Phase 1 project are being developed to be useful to searches of treatments in future pandemics too. (Source: OpenPandemics FAQ)

There is a possibility that the OpenPandemics project will go into additional phases with new goals or new methods in the future, but (a) there aren't any definite plans for this yet, (b) WorldCommunityGrid will probably add extra opt-in switches to the "My Projects" page when a project enters a new phase.
 
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mopardude87

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The tasks with "opn1" in their name are OpenPandemics "phase 1" units. Phase 1 of OpenPandemics has got the search for COVID-19 treatments as its primary goal. To this end, it studies proteins of the SARS-CoV2 virus mostly. But because the virus mutates, proteins of the older SARS-CoV1 virus and some other viruses are included in the study as well. As a by-product, the simulation tools used in the OpenPandemics Phase 1 project are being developed to be useful to searches of treatments in future pandemics too. (Source: OpenPandemics FAQ)

There is a possibility that the OpenPandemics project will go into additional phases with new goals or new methods in the future, but (a) there aren't any definite plans for this yet, (b) WorldCommunityGrid will probably add extra opt-in switches to the "My Projects" page when a project enters a new phase.
Wow i am loving the sound of that,i think i am gonna stick with this a while then. Oh well about the ram ha. I hope they ravage this system with a packet worthy of the memory usage. Maybe add in a super Wu option of sorts for people with larger amounts of ram? It seems some Wu on Boinc/Rosetta were like this. I had only 16gb and kept non stop running out of ram LOL cause some WU consumed insane amounts of ram. I got the 64gb as a "I am done with this non sense" approach.
 
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