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Profile robertmiles

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Message 93545 - Posted: 5 Apr 2020, 20:17:18 UTC - in response to Message 93534.  
Last modified: 5 Apr 2020, 20:22:48 UTC

I notice that, on several recent days including today), Rosetta has "no running tasks." Is something wrong? Do I need to change something?

Increasing the amount of time you're willing to wait for more tasks should be best - new users are now trying to download new tasks faster than they can be created.

You might want to add World Community Grid as another BOINC project on your computer. They are planning to add a COVID-19 subproject soon, but don't have it ready yet.

https://join.worldcommunitygrid.org?recruiterId=480838

Select at least one of their existing subprojects so that your account will set up properly. Be sure that you enable adding any new subprojects when they are created.

I expect the flow of tasks from their COVID-19 subproject to be very thin at first. This is typical for their new subprojects.

This gives your computer something useful to do while waiting for an increased number of COVID-19 tasks.
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Message 93657 - Posted: 6 Apr 2020, 18:44:00 UTC

I have a few devices running BOINC (Windows desktop and laptop, Android), and especially now that SETI is hibernating, I wanted to add extra power to Rosetta. However, whenever I try updating the desktop, I get a brief 'Communication deferred' and then no apparent response - no workunits at all, and from the numbers, no workunits for quite some time either (i.e., pre-December). I saw the note about '[Increase] the amount of time you're willing to wait for more tasks' but aside from not being sure where that setting is, it doesn't really explain the 'communication deferred'.

BOINC Manager 7.14.2 (x64)
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Message 93661 - Posted: 6 Apr 2020, 18:52:17 UTC - in response to Message 93657.  

Let's find out?
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13737&postid=93660
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Message 93677 - Posted: 6 Apr 2020, 20:49:40 UTC - in response to Message 93545.  

Thanks for the suggestions. I've looked in my configuration online and I don't see a setting that clearly controls the amount of time I'm willing to wait for new tasks. Where should I look?

I'll certainly check into World Community Grid if I can run that from BOINC.
--hedera

Never be afraid to try something new. Remember that amateurs built the ark. Professionals built the Titanic.

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Message 93702 - Posted: 7 Apr 2020, 1:52:20 UTC - in response to Message 93677.  

Thanks for the suggestions. I've looked in my configuration online and I don't see a setting that clearly controls the amount of time I'm willing to wait for new tasks. Where should I look?

I'll certainly check into World Community Grid if I can run that from BOINC.

I don't think there is such a setting.

World Community Grid has been compatible with running under BOINC for over 12 years now. Just find the item under Tools for Add project.
(Assuming you're using the Advanced view.)
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Message 93709 - Posted: 7 Apr 2020, 4:53:15 UTC - in response to Message 93702.  

Yes, I have a project running right now. Thanks again.
--hedera

Never be afraid to try something new. Remember that amateurs built the ark. Professionals built the Titanic.

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Message 93902 - Posted: 8 Apr 2020, 20:11:20 UTC
Last modified: 8 Apr 2020, 20:12:03 UTC

Good day-

I am doing some BETA tests with running x86_64-pc-linux applications using the Linux emulation capabilities of FreeBSD. For the last 14 years, the FreeBSD port net/boinc-client has only supported the i686-pc-linux applications, but updates to FreeBSD's kernel mean that 64 bit Linux binaries can used.

My client side efforts have been successful, but am looking for some assistance with the data validation and acceptance portion of the game.

I have 4 sitting as "Completed, awaiting validation" here. Who should I contact or where should I post about having Rosetta validate my test WU's? Is this something that is project specific? Or does it need to be escalated to modify/fix something in BOINC?

Thanks.
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Message 93925 - Posted: 8 Apr 2020, 22:23:07 UTC - in response to Message 93902.  

No it is just that so much work is coming in right now that the validator is a bit behind. Once it catches up to your results, they will be issued credit. Any computation problems should already be visible in your results page.
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Message 94034 - Posted: 10 Apr 2020, 3:29:59 UTC

I've seen a claim that zinc adheres to the RNA dependent polymerase enzyme of the COVID-19 virus in a way that disables it.

Is Rosetta@home doing anything to check that claim?

A newspaper article that looks relevant to this claim:

NY doctor reports 100% success treating coronavirus with drug combination

https://www.thepostmillennial.com/ny-doctor-reports-100-success-treating-coronavirus-with-drug-combination
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Message 94036 - Posted: 10 Apr 2020, 5:23:28 UTC - in response to Message 94034.  
Last modified: 10 Apr 2020, 5:28:51 UTC

I heard Zelenko's interview, he sounded knowledgeable but he was certainly claiming success too early.
He'd only been treating patients for 9 days at the point that article was written, only a small fraction of those people he treated were vulnerable enough that he gave them the medicine - and the average time to death from first symptoms was calculated in China as 15 days.

I checked back a few days later and the New York Times was saying his people had seen 900 patients, actually given his protocol to 300 something of them, 6 were in the hospital and 2 were on ventilators.

Now that may not be a bad outcome for such a vulnerable subgroup, but he's certainly gonna get some deaths. The probability of surviving COVID-19 if you're on ventilator is only 1 in 3.

I think his main insight is that ALL studies show that the virus' outcome is mostly improved when virus suppressing medications are given BEFORE serious symptoms appear.

Also there are OTHER (and safer) ionophores that have been shown to let zinc into cells, if zinc turns out to work (note that the South Koreans use zinc and chloroquin). There's a doctor in Canada who is using quercetin as an ionophore along with zinc to treat COVID-19. That's a bioflavinoid that you can get over the counter. His protocol is 50 to 100 mg per one Kg of a person's weight. Don't know how much zinc.

You know, if a medication helps but not very much, then I think the math is that may take a huge sample to be sure that it's helping and you're not just seeing random variation. I get that impression from calculating ELO scores, it sure takes a lot of games to nail down an ELO score difference.
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Message 94073 - Posted: 10 Apr 2020, 13:12:51 UTC - in response to Message 94034.  
Last modified: 10 Apr 2020, 13:17:02 UTC

I do not know the scientific merits here. The Science message board would be the best place to ask.

I know that very early on, batteries of computational tests were run on an IBM supercomputer to search several thousands of existing compounds to see if they would interact with COVID. If something as simple as zine would have an effective interaction, I should think that would have turned up. Oh! I even got lucky and found the article I had read on that.
OK, BBCode doesn't seem to support blanks in a URL, and the website didn't resolve %40, so you'll have to copy it:
https://sciencenode.org/feature/The race against coronavirus.php

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Message 94092 - Posted: 10 Apr 2020, 18:39:39 UTC

My software thinks %20 works better than %40, so you might also try that in the future.

The race against coronavirus

https://sciencenode.org/feature/The%20race%20against%20coronavirus.php


A paper that article was derived from:

Early research on existing drug compounds via supercomputing could combat coronavirus

https://www.ornl.gov/news/early-research-existing-drug-compounds-supercomputing-could-combat-coronavirus


Neither said much about the limits on what types of compounds were tested. Many of the simulation programs don't allow any compounds that include any metal atoms, so they might not have tested any of the compound often used in zinc supplements.

It was mentioned that over 8000 compounds were tested, but I doubt that zinc ions would qualify.
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Message 94094 - Posted: 10 Apr 2020, 18:58:32 UTC - in response to Message 94092.  

HA! That probably WOULD work better... but blanks are x'40' in EBCDIC!
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Message 94906 - Posted: 19 Apr 2020, 16:56:08 UTC

Hi there. New to the message boards, but member since 2011. I just saw R@H is helping with Covid. Is there any way to tell if your computer is working on a file FROM the covid material based on the application name? Or will it just still show up as "roestta 4.15 or Rosetta mini.."....? Curious.

Would be nice to know if my system is actually helping on such a project!

Thanks!
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Message 94910 - Posted: 19 Apr 2020, 17:19:10 UTC - in response to Message 94906.  

The actual application is the one you've been running all along, this is the tool that you've been contributing to for nearly a decade. So yes, defniitely, your contribution was used to make the tool that is now being used to study COVID as well as continue to develop the tools. The place to look is the name of the work units. Some of them specifically say COVID in the name. There are others that are studying fragments and the spikes and things that might dock with it that do not explicitly say COVID in the name.
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Message 95539 - Posted: 29 Apr 2020, 13:09:35 UTC - in response to Message 9860.  

Hello. I would like to write a non-commercial post regarding Rosetta and the COVID emergency.
I was wondering if I can re-use some of the 3D protein models images that are visible in the site (in particular
in the news, regarding the mini protein models).
Would it be possible to have the 3D structures that are visualized with VMD?
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Message 95601 - Posted: 30 Apr 2020, 12:43:22 UTC
Last modified: 30 Apr 2020, 12:44:28 UTC

Could you perhaps enable automatic subscribing to a given thread if a user posts a reply?

It took me some time to realize that this was not done here and I think many who post questions here don't realize that they need to check back manually to see if they have any answers (unless they click the oddly hidden "subscribe" button at the top).
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Message 95675 - Posted: 1 May 2020, 19:52:42 UTC

https://boinc.bakerlab.org/rosetta/stats.php This page continue to link to "BOINC Statistics for the WORLD! developed by Zain Upton" which appears to now be a spam site. Would it be possible to have this removed? Thanks.
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Message 95697 - Posted: 1 May 2020, 23:12:49 UTC - in response to Message 95601.  

Could you perhaps enable automatic subscribing to a given thread if a user posts a reply?
Hell no.
Things like that should always be opt-in never opt-out.

If you want to be notified, then make use of the Subscribe button at the top of each thread you want to know about.
You could post a suggestion on the BOINC message boards for an option in the "Message boards and private messages Community preferences" for automatic subscription to threads that are posted to. With the default being No.
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Message 95779 - Posted: 2 May 2020, 8:23:26 UTC - in response to Message 95697.  
Last modified: 2 May 2020, 8:25:04 UTC

FYI. It defaults to on on most forum systems I use.

Why would you want to post to a thread if you aren't interested in the response? Although I have seen people like that, I don't think that it's valuable to the community.
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