Coronavirus update from David Baker. Thank you all for your contributions!

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S@NL - eFMer - efmer.com

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Message 99170 - Posted: 27 Sep 2020, 14:11:43 UTC - in response to Message 99169.  

I think pressing - to collapse is all you need, to stop this to happen
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Message 99171 - Posted: 27 Sep 2020, 23:10:14 UTC - in response to Message 99080.  
Last modified: 27 Sep 2020, 23:19:36 UTC

I am getting spammed continuously by You Tube with this video. I never knew it existed in the first place until it popped up.

I found a thread that says if you go into your BOINC data directory and find the notices folder and delete everything. So I did that and only threads came back. All notices are gone. Hopefully this eliminates the spamming I was getting.

Here is a short video of David Baker describing some exciting results from de novo designs targeting SARS-Cov-2.

Thank you all for your contributions to this research! Although R@h was not directly used for the work described in the publication (link provided below), R@h was used for designing relevant scaffolds. Additionally, there are currently many similar designs that bind SARS-Cov-2 and related targets that were engineered using R@h.

<iframe width="560" height="315" src="https://www.youtube.com/embed/ODEIN5V3yLg" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

https://www.youtube.com/embed/ODEIN5V3yLg

More information is available from the publication, De novo design of picomolar SARS-CoV-2 mini protein inhibitors.
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Falconet

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Message 99172 - Posted: 27 Sep 2020, 23:25:38 UTC - in response to Message 99171.  
Last modified: 27 Sep 2020, 23:27:25 UTC

If you use BOINCTasks, see the comments above yours, namely this one - https://boinc.bakerlab.org/rosetta/forum_thread.php?id=14226&postid=99169


If not, maybe disabling the "Check For Notices every X Hours" option works? Open BOINC, Options, Other Options.


And I suppose if Rosetta removed the embedded video from this post and resent the notice, the issue would go away.
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Message 99175 - Posted: 28 Sep 2020, 12:37:06 UTC

The joy of getting a reply from David Baker is great.
David and crew, a piece of advise: As the pandemic gets in ''decisive'' stages, I suggest you do a little more marketing for the project.
I think you should do something like: "Come on guys, where are almost there". Even if you are not quite there for anything.
The reason I say this is because, most people that give computation away are looking for ways to help to develop a vacine or anti-virals, but these people don't really count on the complexity of the entire project.
I could argue that it would be wise to surf the rest of this pandemic-collaboration-tsunami for the benefit of the project, because after it, probably, many people will just move on to something else.
Anyways, I will keep helping in any way i can, but with smaller computational power.
Best wished to D.B. and his team.
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Message 99176 - Posted: 28 Sep 2020, 16:00:27 UTC - in response to Message 99175.  

Insofar as I can tell, Rosetta is done with COVID-19. They have their fix in the bag, and are just testing it.
Actually, they have several fixes including the anti-viral, vaccine, and diagnostics. In fact, maybe more than one of each.

They have moved on. If there is a new virus, I am sure they will come back in a hurry.
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Falconet

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Message 99177 - Posted: 28 Sep 2020, 19:17:01 UTC - in response to Message 99175.  
Last modified: 28 Sep 2020, 19:19:15 UTC

Sure but a very large portion of the COVID-19 pandemic computing power gain is gone already.
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Chooka
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Message 99183 - Posted: 29 Sep 2020, 7:55:51 UTC

Thanks for the tips on fixing this. I came back from a holiday and it was open 107 times on my browser!!
That was the most annoying thing I've come across in my years with BOINC.

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Message 99186 - Posted: 29 Sep 2020, 13:15:48 UTC - in response to Message 99124.  

This post should be sent as a notice to all BOINC clients.
(As should all News posts)

Somebody listened. Although I was rather surprised (but not annoyed) that it opened the video for me without me touching it!

I am annoyed like hell!
Screw this!
- - - - - - - - - - - - - - -
Greetings, Jens
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Jim1348

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Message 99187 - Posted: 29 Sep 2020, 17:52:41 UTC - in response to Message 99186.  
Last modified: 29 Sep 2020, 17:53:52 UTC

I am not sure that this is relevant, but I always set the BOINC "Notice reminder interval" to "Never" when setting up a machine.
I don't have any problems with it.
(If I did, I would get rid of BOINC.)
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Message 99188 - Posted: 29 Sep 2020, 18:08:17 UTC
Last modified: 29 Sep 2020, 18:14:54 UTC

Oh, boy. Just finished catching up with this thread. Sounds like an awful issue. So sorry. It was the iframe embedded video tag that causes the BOINC client to behave this way. It should be fixed now.
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Falconet

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Message 99189 - Posted: 29 Sep 2020, 18:19:31 UTC - in response to Message 99188.  

Oh, boy. Just finished catching up with this thread. Sounds like an awful issue. So sorry. It was the iframe embedded video tag that causes the BOINC client to behave this way. It should be fixed now.



Got a new notice without the video and all that blank space.
Clicking on refresh no longer opens a tab on Windows.
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Message 99190 - Posted: 29 Sep 2020, 18:28:29 UTC

Great. This is one of those situations where you think you're doing a good thing responding to user feedback and then it explodes into something horrible accidentally. David Anderson and Charlie Fenton from the BOINC team alerted me about this issue with the client and the iframe tag, and I fixed it as soon as I realized what was happening.

Sorry again to everyone who was affected.
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Falconet

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Message 99191 - Posted: 29 Sep 2020, 18:34:29 UTC - in response to Message 99190.  

I'm sure it's fine.
It's fixed and that is what matters.

We always want more feedback and updates :)
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Message 99192 - Posted: 29 Sep 2020, 21:42:27 UTC - in response to Message 99144.  
Last modified: 29 Sep 2020, 22:31:45 UTC

shows up in edge as new tab. I had about 30 of those tab page coronavirus reports as the computer runs 24/7 and edge was left up overnight.
I set the check time for new notices to 0 in boincstats, maybe that will fix the problem.

The 30 doesn't make sense. Why would it be "launching" the notice that many times, unless you have 30 computers? Not that it should be launching anything at all. If it's embedded, it should be shown inside the Boinc Manager or Boincstats, not popping up more windows. Somebody ought to tell the Boinc programmers to sort it. They don't listen to me though.

If the browser runs out of room to display tab reports, why shouldn't it start hiding or even deleting the oldest ones?

Whether the number shown stops at 30 would then depend on which browser you are using.
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Message 99193 - Posted: 29 Sep 2020, 21:53:34 UTC - in response to Message 99166.  
Last modified: 29 Sep 2020, 22:12:13 UTC

Actually, aren't the Boinc apps quite restricted to only writing data within their project folder? And if they're not run with admin rights (are they?) they certainly can't mess around with the system files.

Mind you, this opening of a webpage is hardly a security risk anyway. It's only going to be what the project admin has linked to, and no browser (well possibly Edge but who uses that?) would allow code to run willy nilly.

The BOINC scheduler is usually run with admin rights, at least under Windows; otherwise, it cannot start any tasks that use the GPU.

I haven't seen whether any other BOINC programs, such as the apps, need this.
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Message 99194 - Posted: 29 Sep 2020, 22:08:18 UTC - in response to Message 99176.  
Last modified: 29 Sep 2020, 22:25:55 UTC

Insofar as I can tell, Rosetta is done with COVID-19. They have their fix in the bag, and are just testing it.
Actually, they have several fixes including the anti-viral, vaccine, and diagnostics. In fact, maybe more than one of each.

They have moved on. If there is a new virus, I am sure they will come back in a hurry.

They NEED more than one fix of each type, in case the virus mutates in a way that disables one of the fixes. Otherwise, the mutated virus would start spreading about as much as the original.

There already three known varieties with differences on the outside of the virus, so any new fix needs to be tested against all three of these varieties. There are many other mutations affecting only the inside of the virus; these appear to be significant only if you are trying to trace where the infection came from.

The three major varieties are:

The most common variety in China. It spread to the US before travel between China and the US was almost completely shut down.

A mutation that occurred in Europe, then spread to the US. Travel between Europe on the US was not shut down in time to have much effect on spreading in the US. The spikes and more tightly bound to the body of the virus, and is therefore more infectious.

A variety that started in China, spread to Indonesia, and is now the most common variety in Indonesia. It spreads to more people, but is less likely to be fatal.
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Message 99195 - Posted: 29 Sep 2020, 22:52:43 UTC - in response to Message 99194.  

I haven't heard that the vaccines and anti-virals are not effective against all known types. It is said that the virus resists mutation, and these variations appear to be fairly minor.
The Rosetta technique is to "cap" the spike with a protein. If that doesn't work for all, I am sure that the will be back here to work on it further.

But they don't tell us about it in real-time, so we don't really know until they make a big announcement of some sort.
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Message 99196 - Posted: 29 Sep 2020, 23:07:08 UTC - in response to Message 99194.  
Last modified: 29 Sep 2020, 23:15:44 UTC

I think they mentioned on the Science Paper that because they have those 10 different antiviral candidates, the chances of there being resistance and thus rendering the treatment useless are greatly diminished.

At least, that was my understanding from this:

"The minibinders designed in this work have potential advantages over antibodies as potential therapeutics. Together, they span a range of binding modes, and in combination viral mutational escape would be quite unlikely (figs. S1 and S14 and table S1)."

And then there are the Rosetta@home engineered candidates, of which we don't really know anything about but those could be tested and further developed as well, I suppose.
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Message 99197 - Posted: 30 Sep 2020, 0:13:06 UTC - in response to Message 99190.  

I'm sorry that I partially caused this from pushing the PR subject over and over on the posts.
However, the number of responses alone in this thread point to a positive aspect, since people are participating, which is the whole point of this Forum.
Thanks again for the update, and please keep'em coming whenever possible!
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Message 99198 - Posted: 30 Sep 2020, 4:18:25 UTC - in response to Message 99197.  

I'm sorry that I partially caused this from pushing the PR subject over and over on the posts.
However, the number of responses alone in this thread point to a positive aspect, since people are participating, which is the whole point of this Forum.
Thanks again for the update, and please keep'em coming whenever possible!



Only positive out of this is that Rosetta@ home is losing participants and does not seem to care. Bye
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