TOPIC: Fighting Covid with Distributed Computing (you can help!)

I'm finding out that fewer people know about science done via distributed computing than I thought, so I'll drop this post here in case anyone find it interesting and possibly like to contribute.

Did you know you can use your home computer to do research to find treatments for Covid? It's done via something called distributed computing - a very large task (such as modeling how the Covid virus opens up to bind with a human cell) is divided into many small chunks and then sent out to anyone who is running the application on their home computer.

The applications themselves can be set to run to only use your idle computing power - so if you need to use your computer, great, the research pauses. But when you walk away, as long as you leave your computer running, it will work on the chunk of research data, eventually completing it, sending it back and asking for more work.

There are 2 big platforms for this. Folding@home and BOINC (Berkeley Open Infrastructure for Network Computing).

Folding at home ( foldingathome.org/ ) is a distributed computing project for performing molecular dynamics simulations of protein dynamics. Its initial focus was on protein folding but has shifted to more biomedical problems, such as Alzheimer's disease, cancer, COVID-19, and Ebola. This project is best for computers with gaming video cards that can be used for the research.

Rosetta@home via Boinc ( boinc.bakerlab.org/rosetta/ ). Rosetta@home is a distributed computing project aimed at protein structure prediction and is one of the most accurate tertiary structure predictors. The conformational states from Rosetta's software can be used to initialize a Markov state model as starting points for Folding@home simulations. This project is best for computers that are not ideal for Folding@Home.

Lots of people are participating!

March 22nd, Folding at home becomes more powerful than the top 7 super computers combined.
www.tomshardware.com/news/folding-at-home-worlds-top-supercomputers-coronavirus-covid-19?fbclid=IwAR397Ea-sjLzKYBdwtzYYL6TMJqnhV5p7hsj_DbceWW291eSF2JHLWx0hCU

March 26th, folding at home reaches 1.5 exaflops, making it more powerful than the top 100 super computers combined, which is quickly increased to 2.3 exaflops by April 8th..
www.anandtech.com/show/15661/folding-at-home-reaches-exascale-1000000000000000000-operations-per-second-for-covid-19

Want to know more?

Watch an interview from the Financial times with the Director at folding at home:


Folding@Home models the first phase of corona virus in action:
foldingathome.org/2020/04/03/capturing-the-covid-19-demogorgon-aka-spike-in-action/

High performance computing website covers rosetta:
www.hpcwire.com/2020/03/24/rosettahome-rallies-a-legion-of-computers-against-the-coronavirus/

Linus Tech tips shows how they built a work server to chop up the work and send it to participating clients:

I was not aware of this or the platforms. Thanks for sharing, I'll be looking into both further.

This is great information. Thanks!

Astronomical and Mathematical Organizations have been doing things like this for decades.

But hard pass from me. The last thing I want is some organization having access to my computer and having my identity/monies stolen from someone in that organization who is unhappy or someone outside the organization who takes advantage of this program.

I'm so glad this post reminded me that this project exists. I've created a True Dungeon team if anyone wants to join. It'd be cool to see our pooled progress. Just enter team number 261246.

I've joined.

Mike Naglee wrote: I'm so glad this post reminded me that this project exists. I've created a True Dungeon team if anyone wants to join. It'd be cool to see our pooled progress. Just enter team number 261246.

Is that a folding@home team, or a Rosetta@home team?

Doh! Folding@home.

I’m setup and running on folding at home with the TD team with an old media center pc I brought back to life.

Next step is to get a true dungeon Rosetta@home Team running, and once that is in place, I plan on launching a contest for gift cards to Trent Tokens! Watch this space for more info soon.

Very cool!

I've sent an email requesting the boinc-wide team creation (they don't have a web form due to spam submissions). As soon as that is done, I'll publish the team info. Thanks!

Mike Naglee wrote: Very cool!

I've sent an email requesting the boinc-wide team creation (they don't have a web form due to spam submissions). As soon as that is done, I'll publish the team info. Thanks!

Thanks mike!

Folding at home is now simulating existing drugs for use against covid:

foldingathome.org/2020/04/13/new-simulations-to-search-for-covid-19-treatment-via-repurposing-existing-ntp-analog-drugs-that-target-viral-rna-replication/