Rosetta's role in fighting coronavirus

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Profile yoerik
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Message 96513 - Posted: 15 May 2020, 6:54:21 UTC - in response to Message 96482.  

Exactly. One of the major issues with Distributed Computing has been keeping users active.
Updates are one of the best ways to do that.


It's not much to ask to be kept up to date, within reason. We don't need daily updates - but it's reasonable to request updates more frequently than once every few months.
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Message 96749 - Posted: 23 May 2020, 14:54:20 UTC - in response to Message 96439.  
Last modified: 23 May 2020, 14:54:39 UTC

You should post these updates on the Rosetta@home website and send out a notice.
https://twitter.com/RosettaAtHome/status/1260368548976713730 and https://twitter.com/RosettaAtHome/status/1260368892695699457

"COVID update:

Our project scientists submitted over 28M "scaffold design" work units in recent weeks.

Those helped enable a further 200M "binder design" calculations!

Initial laboratory testing of these candidate COVID treatments is underway.

Thanks to all crunchers!"

"This is just the first wave. Expect hundreds of millions of additional work units to be issued in the coming weeks and months.

We need you now more than ever!"


Bit of a let down that no one from Rosetta@home posted this update on Rosetta@home in the 10 days since it was posted on Twitter.
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Message 96753 - Posted: 23 May 2020, 23:47:54 UTC - in response to Message 92000.  
Last modified: 24 May 2020, 0:00:22 UTC

CoVid19 Projects

Folding @ home (f@h)[ uses its own client software to distribute work units.

https://foldingathome.org/ (Project Home Page)
https://foldingathome.org/start-folding/ (f@h client download site)

https://www.worldcommunitygrid.org/research/opn1/overview.do (Open Pandemics-World Community Grid Home Page)

Proposed Solutions*
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.

*Taken from Open Pandemics Home Page
Introductory paragraph of the Proposed Solutions section.
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Message 96754 - Posted: 23 May 2020, 23:48:18 UTC - in response to Message 96749.  

Yep. I check this thread every 2-3 days just to see if anything new is posted. Bit of a let-down that there was a lot of communication early on, and now radio silence for a while.
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Message 96758 - Posted: 24 May 2020, 6:58:20 UTC - in response to Message 96754.  

Yep. I check this thread every 2-3 days just to see if anything new is posted. Bit of a let-down that there was a lot of communication early on, and now radio silence for a while.


It's not entitled to ask to be kept informed - it's disappointing that we have to do more work to find the latest news, than it would take for them to share that news here.
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Message 96781 - Posted: 25 May 2020, 18:12:09 UTC - in response to Message 91772.  

Very cool!
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Message 96792 - Posted: 26 May 2020, 10:00:30 UTC - in response to Message 96758.  

Yep. I check this thread every 2-3 days just to see if anything new is posted. Bit of a let-down that there was a lot of communication early on, and now radio silence for a while.


It's not entitled to ask to be kept informed - it's disappointing that we have to do more work to find the latest news, than it would take for them to share that news here.



It's in Rosetta's self-interest to update their volunteers. I can't possibly understand why they could not have copy pasted their tweet, post here and send out a notice to BOINC clients.
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Message 96797 - Posted: 26 May 2020, 15:28:15 UTC - in response to Message 96792.  
Last modified: 26 May 2020, 15:32:59 UTC

it's hard to fathom. You and I are both familiar with WCG's efforts to keep us up to date - it takes minimal effort to keep us informed. The lack of this communication as a newer volunteer is concerning.

I've taken steps to reduce my contribution to Rosetta - I will crunch WCG full time if this communication issue continues into next month. I just cannot justify a higher electricity bill for a project that doesn't have the will to issue the simplest of updates. It's almost insulting.
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Message 96895 - Posted: 30 May 2020, 17:58:53 UTC

I'm just here for the free beer, what no beer?
Damn stupid Covid 19 research, wait.. research can save beer workers?
WOOHOO!









With beer all things are possible, although some of them should not be done.
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Erich56

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Message 97354 - Posted: 13 Jun 2020, 10:24:08 UTC

I've noticed that all of my computers have barely received any new Covid tasks for crunching during the past few days :-(
Has research in Covid been stopped by Rosetta? Please let us know.
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Message 97355 - Posted: 13 Jun 2020, 11:53:30 UTC - in response to Message 97354.  
Last modified: 13 Jun 2020, 11:54:39 UTC

I've noticed that all of my computers have barely received any new Covid tasks for crunching during the past few days :-(
Has research in Covid been stopped by Rosetta? Please let us know.


Each of your pc's has several tasks on it now, each is taking around 6 hours to finish each task so it depends on your cache settings. But remember there is a 3 day return deadline for each task here so a large cache is not a good idea.
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Message 97358 - Posted: 13 Jun 2020, 12:59:06 UTC - in response to Message 97354.  

I've noticed that all of my computers have barely received any new Covid tasks for crunching during the past few days :-(
Has research in Covid been stopped by Rosetta? Please let us know.

not all COVID-19 tasks are labeled COVID-19 - so unless it is clearly labelled for us lay people to understand - we have no way of 100% knowing which ones are COVID related, and which ones aren't.
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Message 97364 - Posted: 13 Jun 2020, 14:19:53 UTC - in response to Message 97358.  

not all COVID-19 tasks are labeled COVID-19 - so unless it is clearly labelled for us lay people to understand - we have no way of 100% knowing which ones are COVID related, and which ones aren't.
which is too bad, though; I would very much be interested in knowing.
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Erich56

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Message 97366 - Posted: 13 Jun 2020, 20:00:59 UTC

I guess, some time ago someone here mentioned that tasks with "robetta" in their name (starting with "rb_...") are also related to Covid? Is this correct?
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Message 97368 - Posted: 13 Jun 2020, 20:51:01 UTC - in response to Message 97366.  

I guess, some time ago someone here mentioned that tasks with "robetta" in their name (starting with "rb_...") are also related to Covid? Is this correct?


Some Robetta tasks are COVID-19 related but not all.

See: robetta.bakerlab.org/queue.php

You can check if there's any COVID-19 work available. You can search using the "target" field for keywords like "cov" "covid" "sars".
If some of the jobs are marked active, it likely means there is work available or in progress at rosetta@home.
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Message 97425 - Posted: 16 Jun 2020, 16:48:56 UTC - in response to Message 97358.  

I've noticed that all of my computers have barely received any new Covid tasks for crunching during the past few days :-(
Has research in Covid been stopped by Rosetta? Please let us know.

not all COVID-19 tasks are labeled COVID-19 - so unless it is clearly labelled for us lay people to understand - we have no way of 100% knowing which ones are COVID related, and which ones aren't.

it's too bad that there is no clear indication as to whether a task is related to COVID or not.
In fact, none of the tasks my computers have received during the past 3 or 4 days were labeld "COVID" - so I assume that most of them were NOT Covid-related.
In a way it seems rather unlogical that some of the COVID tasks are labeled as "COVID", others are not. What sense does this make?

Given the fact that so many people joined Rosetta recently as they wanted to help with COVID research, facts should be made clear. I would even suggest that we people can choose between COVID-related and other tasks.
This is possible, for example, at Folding@Home and WordCommunityGrid. So any cruncher is free to make his/her choice - which is exactly the way it should be.

Meanwhile, I have switched some of my machines to projects where I can choose COVID exclusively. For me personally, it's important to use my computational power for fighting agains COVID.
As soon as I can do this here at Rosetta, too, I'll be glad to come back. with all my computers.
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Message 97426 - Posted: 16 Jun 2020, 17:20:58 UTC - in response to Message 97425.  
Last modified: 16 Jun 2020, 17:24:44 UTC

I reject any tasks that don't have a label covid-19 and in recent days for some reason they are almost absent
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Message 97427 - Posted: 16 Jun 2020, 17:54:45 UTC

Robetta tasks are not run by the Rosetta@home scientists but by outside scientists. It's a public service.
Tasks are named by those outside scientists.
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Message 97430 - Posted: 17 Jun 2020, 1:59:48 UTC - in response to Message 97425.  

I've noticed that all of my computers have barely received any new Covid tasks for crunching during the past few days :-(
Has research in Covid been stopped by Rosetta? Please let us know.

Not all COVID-19 tasks are labeled COVID-19 - so unless it is clearly labelled for us lay people to understand - we have no way of 100% knowing which ones are COVID related, and which ones aren't.

It's too bad that there is no clear indication as to whether a task is related to COVID or not.
In fact, none of the tasks my computers have received during the past 3 or 4 days were labeled "COVID" - so I assume that most of them were NOT Covid-related.
In a way it seems rather unlogical that some of the COVID tasks are labeled as "COVID", others are not. What sense does this make?

This isn't an assumption you can reasonably make. Some will, some won't.
My understanding is tasks that come via Robetta are from other labs who use their own naming convention, not under the control to Rosetta.
Checking back, I note the Veesler Lab submits tasks - they're the ones who discovered that antibodies to the original SARS-Cov (2003) virus also apply to SARS-Cov-2 as i posted in Cafe recently.
Also note tasks can focus on interfacebinders to specific sites and I'm not clear these fragments get labelled CV19 when they're highly relevant to the issue.

Meanwhile, I have switched some of my machines to projects where I can choose COVID exclusively. For me personally, it's important to use my computational power for fighting against COVID.
As soon as I can do this here at Rosetta, too, I'll be glad to come back. with all my computers.

I agree completely, but I'm concentrating my resources here with only the occasional switch to WCG's Open Pandemics sub-project on my PCs (exclusively WCG on my phone while there's the issue with Rosetta on BOINC Android)[/quote]
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Message 97449 - Posted: 18 Jun 2020, 21:19:40 UTC - in response to Message 92747.  

There has been a discussion that Folding@home is likely to produce a BOINC version soon, Not ready yet, though.

Is that right? That's a project I've always wanted to run - especially now they're doing COVID work - but I've also been put off by it not being available via Boinc

The discussions are very preliminary; I have been a part of them. But the developers have to do the real work, and I would guess that it won't come in the midst of the current rush.

But the Folding client works well enough once you get past its idiosyncrasies setting it up; look to their forum for help - especially on Linux.
I run my GPUs on Folding (by deleting the CPU slot when setting it up), and then run my CPUs on BOINC. It works great.

I would not recommend F@H on Linux. I just left there because of the issues concerning software dependencies. As much as F@H likes to state their software will run most anywhere (which is why they suggest ignoring dependencies during install), I and others, have found that to not be the case. I never could get FAHControl running on 3 different distributions without having to go back and install deprecated software. If one is running a Long Term Support release of a distribution (which tends to be back-leveled) then the chances are greater that the install will work. It wasn't worth fiddling with. Just one man's opinion of course

I've seen, but not investigated, a project that does COVID-19 work on GPUs, but under Linux only. You might want to check if it has similar dependency problems. NOT a BOINC project.

Quarantine@Home (GPU only for Linux)

https://quarantine.infino.me/
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