Help in the fight against COVID-19!

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Message 93894 - Posted: 8 Apr 2020, 18:52:03 UTC - in response to Message 93880.  
Last modified: 8 Apr 2020, 18:57:49 UTC

chrislaf, since you are already running Rosetta@home, you are already helping in the study of COVID-19.

cliff, the new application version 4.12 enables some protocols that are needed to study COVID-19. There are many types of WUs related to the effort. Some of them have COVID right in the WU name. Some are studying protein fragments that might bind to COVID. Some are processing tasks from the public queue (robetta), which just basically get a batch number, and they might be COVID related, but they might not. And then there is the original mission of the lab, which is the better understand how proteins work and how to predict their structures and behaviors, and to develop a software tool to help researchers study the roles of various proteins in the body, and in nature.
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Message 93962 - Posted: 9 Apr 2020, 10:54:21 UTC - in response to Message 93202.  

Dear Brian Coventry et alia,
1. Your custom protein binding the Spike protein looks like it will put neutralizing IgGs to shame!!! Very impressive!!! {As an aside each dose of this protein therapeutic will have to be injected as it could never survive a transit of the stomach and upper GI tract with the low pH and proteolytic enzymes that would reduce it to amino acids.}

2. I'm laboring under the assumption that Rosetta code incorrectly programmed the use of the L3 cache and will bottleneck if too many Rosetta WUs are running simultaneously. I limited my use to one WU per 5 MB of L3 cache. Exceeding that limitation slows the entire CPU over 60%. This means that my fleet of Xeon E5s are running Rosetta at less than 20% capacity. Has this been fixed and is it safe to run full force now???

3. I believe that your statement implies that all WUs are contributing to Covid-19 research regardless of whether you include "Covid-19" in the WU name and that minirosetta is doing Covid-19 work as well. Is that what you mean???

4. I don't know if I'm running ARM64 Rosetta aps or not. I see from your Applications page there are numerous versions but when I look at the Properties of a given WU I'm running it says the version 3.76, 4.07, 4.08 or 4.12. What are the Linux-ARM platforms???

5. I suggest you tether these blocking proteins together like an IgM. This would more readily mark them for destruction. Also, it appears that your blocking protein is much larger than an IgG so when it binds a Spike it also blocks neighboring Spikes (like an umbrella) from binding ACE2 and being invaginated.

{Please use black text on white background for your forum to maximize contrast. This faded gray text really strains my old eyes so I never read your forums. I would not have seen this announcement except that you were nice enough to send out a BOINC Notice. Thank you in advance :-}



Hi, I did some testing and the result shows that L3 cache is not a problem. I put more details in this thread: https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13764#93961
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Message 93983 - Posted: 9 Apr 2020, 17:04:15 UTC - in response to Message 93880.  

So, am I supposed to update my client to participate in this new capability? Kind of confused as to whether this is a call to action or just a status update.


You just attach Rosetta to BOINC and that's it. BOINC automatically downloads the executable for you and updates it if necessary,
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Message 93984 - Posted: 9 Apr 2020, 17:40:23 UTC - in response to Message 93267.  

I wondered the same thing. So there is no COVID-19 but just run Rosetta@home?

Thanks for everyone coming together to help.
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Message 93991 - Posted: 9 Apr 2020, 18:52:49 UTC - in response to Message 93962.  
Last modified: 9 Apr 2020, 18:53:32 UTC

I mentioned this before. but on my Xeon E5s I find there's a bug with Numa (turn it off unless you want all instances to run on one socket) and there's a problem with hyperthreading (turn it off unless you're not going to run more than half threads).
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Message 93993 - Posted: 9 Apr 2020, 19:37:31 UTC - in response to Message 93313.  
Last modified: 9 Apr 2020, 19:40:55 UTC

I switched my pi farm across to rosetta@home after using it for seti@home for the past year, as I was hoping to contribute to the project, have got a “no work available to process “ message for the last 10 hours or so....normal for there to be fewer WU?


Also, I could be wrong but I believe you need to be running a 64-bit version of Linux on your RPI. The default installation is 32-bit. Someone please correct me if I'm wrong!

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Message 93994 - Posted: 9 Apr 2020, 19:41:50 UTC - in response to Message 93188.  

Same here, my 8 core Samsung tablet {no root) doesn't have enough "swap space" to do any work units for R@H, its short by about 600mb.
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Message 94011 - Posted: 9 Apr 2020, 22:20:05 UTC

I’ve given my entire 18 core i9 over to Rosetta because of coronavirus, I now find it’s running more non-covid tasks than covid. How do I get rid of the non-covid stuff? Because if I can’t, I consider Rosetta is abusing my generosity. There are other important non-Rosetta projects I like to support too and right now I’m starving them because of this emergency.
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Message 94013 - Posted: 9 Apr 2020, 22:30:08 UTC - in response to Message 94011.  

How do I get rid of the non-covid stuff? Because if I can’t, I consider Rosetta is abusing my generosity. There are other important non-Rosetta projects I like to support too and right now I’m starving them because of this emergency.
Many of the the non-covid tasks while not specifically for covid work, are still used for covid work. It's just that they are also useful for other work as well. Hence they are not labelled specifically as Covid Tasks so people don't get upset about that.
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Message 94018 - Posted: 9 Apr 2020, 23:15:17 UTC
Last modified: 9 Apr 2020, 23:15:43 UTC

This thread is locked.

If you are interested in the original COVID-19 information this link goes to the beginning of the thread. See both posts there from "admin".

If you have questions about Rosetta@home, or about running it on your computer or portable device, or anything else, here is a link to the message boards. Most questions should be opened on the Number Crunching board.
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Message 94723 - Posted: 18 Apr 2020, 3:17:06 UTC
Last modified: 18 Apr 2020, 3:20:31 UTC

I edited the original posts on this thread to be specific with the name of the disease (COVID-19) and the name of the virus causing the disease (SARS-CoV-2). After realizing that these posts were being used and quoted many times over, I thought it was important to fix. -- David K
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Message boards : News : Help in the fight against COVID-19!



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