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Knights against Covid-19 coronavirus

 
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LanDroid
Prince
Prince


Joined: 11 Jun 2002
Posts: 4448
Location: Cincinnati, OH U.S.

PostPosted: Sat Mar 07, 2020 5:50 pm    Post subject: Knights against Covid-19 coronavirus Reply with quote

There are two projects analyzing SARS-CoV-2, the virus that causes the Covid-19 disease. The first is Rosetta.

https://www.ipd.uw.edu/2020/02/rosettas-role-in-fighting-coronavirus/

The second project is Folding@Home, which is non-Boinc.

https://foldingathome.org/2020/02/27/foldinghome-takes-up-the-fight-against-covid-19-2019-ncov/

https://foldingathome.org/
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LanDroid
Prince
Prince


Joined: 11 Jun 2002
Posts: 4448
Location: Cincinnati, OH U.S.

PostPosted: Sat Mar 07, 2020 6:02 pm    Post subject: Reply with quote

My thought was to shrub Rosetta with CPU and also Fold with GPU. However that may not be possible? Folding@Home uses a web interface to report what the local client is doing. It appears to be saying the current WU is about 2/3 done, with 82% CPU and 9% GPU. If that is accurate it would appear one has to choose either / or = Boinc Vs. Folding? It has been a VERY long time since I Folded anything. Do any Knights have a better understanding of Folding and whether it's possible to shrub it along with Boinc?

I set Boinc to run only when the system is idle, then set Folding to run all the time. Checking the Task Manager, it shows Folding using all CPU and GPU resources. So this does appear to confirm it's one or the other, ya can't shrub both. Hmmmm... Decision time... Shocked
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LanDroid
Prince
Prince


Joined: 11 Jun 2002
Posts: 4448
Location: Cincinnati, OH U.S.

PostPosted: Sat Mar 07, 2020 6:12 pm    Post subject: Reply with quote

I also wonder if the Covid-19 disease could be an inflection point that encourages significantly more people to participate in distributed computing? Seems like this sort of fight might capture the imagination of folks who understand what "idle" computers can accomplish.

Folding@Home is attempting to gain 1 million people. This seems like a modest goal given the enormous resources that are available, but they are only 11% on the way.
https://foldingathome.org/iamoneinamillion/

Seti@Home going into hibernation is another discouraging sign. There's enough computing power to shrub raw data, but not nearly enough to process further?

Every computer cycle is sacred. #ni-2
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LanDroid
Prince
Prince


Joined: 11 Jun 2002
Posts: 4448
Location: Cincinnati, OH U.S.

PostPosted: Fri Mar 13, 2020 8:02 pm    Post subject: Reply with quote

WCG is working on identifying a suitable project.

https://www.worldcommunitygrid.org/forums/wcg/viewthread_thread,42191_offset,0?linkId=84296303#622244
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Plomos
Prince
Prince


Joined: 26 Apr 2011
Posts: 858

PostPosted: Mon Mar 16, 2020 12:56 am    Post subject: Reply with quote

I do not have any gpus to add but I have added my cpu power to rosetta to assist in killing the beer virus.
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Michelle
Moistened Bint
Prince


Joined: 28 Oct 2004
Posts: 10214
Location: At my desk

PostPosted: Sun Mar 22, 2020 4:47 am    Post subject: Reply with quote

I haven't heard anything about distributed computing mentioned but I have heard people on telly talking about citizen science. I guess it's pretty much the same thing.
I'll have to go through the projects I'm doing and just focus on the medical research for a little while.
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Plomos
Prince
Prince


Joined: 26 Apr 2011
Posts: 858

PostPosted: Sun Apr 05, 2020 2:12 pm    Post subject: Reply with quote

Looking at the Ralph@Home message board the admin posted the following there

Quote:
The COVID-19 related updates to the 4.13 rosetta and rosetta_for_devices and 4.14 rosetta linux versions include a new target clash energy and fold-tree options to improve the interface design protocol. It will allow sampling with the ACE2 binding helix motif fixed along with the target and a fast target clash energy check. Successful binders using this protocol are already being tested and optimized in the wet lab but this will allow us to design many more candidates to increase our chances of designing successful binders with the most promising binder properties.

Please spread to word to help our Ralph@home testing efforts for this app. A broad range of platforms is desired. Thanks!


Looks like they need more help testing the things they have added to rosetta so let's pitch in Ni!

Ralph is at http://ralph.bakerlab.org/
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Mifun
Duke
Duke


Joined: 08 Jan 2012
Posts: 265
Location: Russia

PostPosted: Wed Apr 08, 2020 8:41 pm    Post subject: Reply with quote

Something wrong with folding@home team settings https://stats.foldingathome.org/team/117

Website is kinda weird. #ni-2
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LanDroid
Prince
Prince


Joined: 11 Jun 2002
Posts: 4448
Location: Cincinnati, OH U.S.

PostPosted: Thu Apr 09, 2020 4:24 am    Post subject: Reply with quote

Boinc@TACC is also researching the Covid-19 virus. (May be a little tricky to get WUs, I had to suspend other projects.) Here's an article describing the University of Texas at El Paso’s School of Pharmacy running simulations through the Texas Advanced Computing Center, which this Boinc project supports.

https://elpasoheraldpost.com/utep-school-of-pharmacy-developing-covid-19-vaccine-drug-treatments-using-supercomputing/

Here's part of a Boinc@TACC thread on this project.
https://boinc.tacc.utexas.edu/forum_thread.php?id=44&sort_style=&start=40

Main web page
https://boinc.tacc.utexas.edu/index.php
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Atomic Booty
Prince
Prince


Joined: 10 Sep 2005
Posts: 589
Location: New Orleans

PostPosted: Wed Apr 29, 2020 9:54 pm    Post subject: Reply with quote

Shrubbing Rosetta now!
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