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Mr P Hucker
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Message 99505 - Posted: 2 Nov 2020, 14:15:25 UTC - in response to Message 99490.  

Someone will be along to correct me
No point.
You have your beliefs, which aren't going to be impacted by any facts.

I don't have any beliefs. I'd have at least thought the purpose of the project was to remove the need for beliefs by finding something - or even close to something.
Pick the very best link of all. I promise to read every word.
Because by saying "no point" it doesn't make me think there's anything. It makes me think you already know there literally is nothing.


Either there's nothing, or there's nothing within reach of current technology. We had to try. And we have to try again in the future with better sensors and/or calculations.
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Mr P Hucker
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Message 99506 - Posted: 2 Nov 2020, 14:18:47 UTC - in response to Message 99491.  

Understandable and I don't disagree, just that I'm doing all of them as they come.
They don't have any bad sub-projects, so I'm happy to contribute time to any and all of them.


Sometimes I concentrate on just one that I read something good about. The immune system project sounds very useful indeed. It could provide insight into many different diseases. And sometimes I have a good bash at the rainfall project, since they're long tasks and I get the feeling some people don't do them for that reason.

It's the ideal co-project for Rosetta imo as some of them use Rosetta code aiui


Is that what it is? I saw a Rosetta program running in WCG and thought Rosetta was perhaps farming out processing time to WCG to get more power. So they've just used the same code?
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Mr P Hucker
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Message 99507 - Posted: 2 Nov 2020, 14:29:24 UTC - in response to Message 99494.  

It depends on the gpu, some do and some don't....you are correct it's not a blanket AWLAYS do it thing, it's much more of a case by case basis due to the better gpu's than we used even 3 years ago. It's best to leave one cpu core free and track your numbers, then use the cpu core for ie crunching and see what the numbers are.


Another strange thing - number of WUs per GPU. I run Collatz, Milkyway, and Einstein on GPU. When I restarted doing BOINC about a year ago, I tried each project in turn with 1, 2, and 3 WUs per GPU, timing how long a WU took. On all my 6 computers, 2 was quite a lot faster than 1, and 3 sometimes provided a bit more than 2, especially if the CPU was slow and the GPU fast. With Collatz it didn't make much difference, as that needs very little CPU time, but Einstein and Milkyway both benefited from multiple WUs per GPU. However just recently I noticed one computer taking an absolute age to do a task, and tried it back on 1 WU, it sped up! So I tried all the others, testing as before, and now 1 WU is always faster on every project and every computer, including Collatz which used to make no difference. They're the same CPUs as a year ago and the same GPUs. I can only conclude either all 3 projects have changed the coding, or something is old and tired at my end. Computers don't do that do they?

And back to what we were discussing, the same applies to leaving a core free. It used to help but now it doesn't. Something has improved somewhere so it does it automatically. It could even be a Windows update which for once actually made a worthwhile change!

Personally I always leave at least one cpu core free because I remote into most of my pc's to manage them and when using every cpu core for crunching the delay is horrible. The gpu benefitting from that is just an offshoot.


That's weird. I remote in using "Remote Utilities Viewer" which is freeware. That doesn't slow down at all, even if both ends are processing stuff in Virtualbox for LHC.
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Mr P Hucker
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Message 99508 - Posted: 2 Nov 2020, 14:30:40 UTC - in response to Message 99504.  

I am not getting any work for Rosetta is there an outage?


No, I'd call it a shortage. We've done all the work they've come up with. There will be more.....

TNGrid and World Community Grid do similar things if you want to use them in the meantime.
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Message 99509 - Posted: 2 Nov 2020, 14:38:10 UTC - in response to Message 99506.  
Last modified: 2 Nov 2020, 14:42:21 UTC

WCG's Microbiome Immunity Project uses the Rosetta software. One of the scientists on that project, Dr. Rich Bonneau, was a student of Dr. Baker and participated in the development of the Rosetta code (WCG says he was one of the initial authors.)
The Human Proteome Project at WCG was also run by Dr. Bonneau and also used Rosetta.


The version being used at WCG is older than what is run at Rosetta@home. That project launched in 2017 and it never received an update since it works as the scientists want.
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Message 99511 - Posted: 2 Nov 2020, 17:41:07 UTC - in response to Message 99505.  

Someone will be along to correct me
No point.
You have your beliefs, which aren't going to be impacted by any facts.

I don't have any beliefs. I'd have at least thought the purpose of the project was to remove the need for beliefs by finding something - or even close to something.
Pick the very best link of all. I promise to read every word.
Because by saying "no point" it doesn't make me think there's anything. It makes me think you already know there literally is nothing.

Either there's nothing, or there's nothing within reach of current technology. We had to try. And we have to try again in the future with better sensors and/or calculations.

I understand the idea of having to try. But people did try and there was nothing at all discernible.
Whether people have to try again in future, I don't know. There'd have to be a good reason imo.
Without a good reason, all the current evidence is that it would both futile and impotent, and come at the cost of reducing work on far better projects, of which we have many both here and at WCG

"If at first you don't succeed, try, try again
If you still don't succeed, give up. There's no point being a damn fool about it"
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Sid Celery

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Message 99513 - Posted: 2 Nov 2020, 18:01:06 UTC - in response to Message 99506.  

Understandable and I don't disagree, just that I'm doing all of them as they come.
They don't have any bad sub-projects, so I'm happy to contribute time to any and all of them.


Sometimes I concentrate on just one that I read something good about. The immune system project sounds very useful indeed. It could provide insight into many different diseases. And sometimes I have a good bash at the rainfall project, since they're long tasks and I get the feeling some people don't do them for that reason.

The African Rainfall Project is weird. I ask for tasks all the time, but recently, even when 120 tasks came down in one go, I only get 1, with the others spread around Mapping Cancer Markers, Open Pandemics, Microbiome Immunity Project and Smash Childhood Cancer. It's not a matter of runtime as far as I can tell. I don't know why I get so few. Usually it's none at all when 30 or 40 tasks come down at a time.

It's the ideal co-project for Rosetta imo as some of them use Rosetta code aiui

Is that what it is? I saw a Rosetta program running in WCG and thought Rosetta was perhaps farming out processing time to WCG to get more power. So they've just used the same code?

The way I've seen it described is they "use the Rosetta engine", so the way I see it, the more Rosetta can be improved over time, it has knock on benefits to other projects with more targeted purposes. And that's also why I continue to run Rosetta even if there are no targeted CV19 tasks here. Improvements in Rosetta code enables Rosetta itself and several other projects to improve at the same time
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Sid Celery

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Message 99514 - Posted: 2 Nov 2020, 18:04:44 UTC - in response to Message 99509.  

WCG's Microbiome Immunity Project uses the Rosetta software. One of the scientists on that project, Dr. Rich Bonneau, was a student of Dr. Baker and participated in the development of the Rosetta code (WCG says he was one of the initial authors.)
The Human Proteome Project at WCG was also run by Dr. Bonneau and also used Rosetta.

The version being used at WCG is older than what is run at Rosetta@home. That project launched in 2017 and it never received an update since it works as the scientists want.

Thanks for the confirmation.
A pity old Rosetta code is used, especially as Rosetta was updated in April so all the latest improvements could be employed in the CV19 tasks we've run here
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Mr P Hucker
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Message 99515 - Posted: 2 Nov 2020, 18:34:28 UTC - in response to Message 99511.  

I understand the idea of having to try. But people did try and there was nothing at all discernible.
Whether people have to try again in future, I don't know. There'd have to be a good reason imo.
Without a good reason, all the current evidence is that it would both futile and impotent, and come at the cost of reducing work on far better projects, of which we have many both here and at WCG

"If at first you don't succeed, try, try again
If you still don't succeed, give up. There's no point being a damn fool about it"


As I said, it would be worthwhile if we had stronger telescopes, or a different way of looking at the data. But to try more with the current tech would be like looking for a needle in a haystack. The needle may or may not be there, but we need a brighter torch to be likely to find it.

But we didn't know it would be that hard to find when we started, so it was not a waste of time.
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Mr P Hucker
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Message 99516 - Posted: 2 Nov 2020, 18:42:38 UTC - in response to Message 99513.  

The African Rainfall Project is weird. I ask for tasks all the time, but recently, even when 120 tasks came down in one go, I only get 1, with the others spread around Mapping Cancer Markers, Open Pandemics, Microbiome Immunity Project and Smash Childhood Cancer. It's not a matter of runtime as far as I can tell. I don't know why I get so few. Usually it's none at all when 30 or 40 tasks come down at a time.


WCG send out their projects in different proportions, presumably depending on how much work there is available for each. Recently there's been a surge in calculations needed for cancer research, so I get a lot of them if I accept anything. But if you narrow it down and only accept rainfall, you will get as much as you want, they have plenty. I've currently got all but coronavirus switched on, and immunity is the one I hardly get any of. Rainfall is a reasonable amount, with cancer being a lot more. Probably I'm getting them in the ratio of 1 immunity to 2 rainfall to 2 child cancer to 4 cancer.

Having said all that, they do warn you that rainfall has specific requirements (I can't remember what they are, probably PC always on (they're long tasks with short deadlines), lots of RAM (although I can run 4 on an 8GB machine), or something). So if you haven't done any before on that PC, or not for a long time, it might give you the odd one to make sure they work ok first.

I wish WCG had a status page so we can see how much there is of each available, but you have to delve into the pages of each project to find a few titbits of information.

The way I've seen it described is they "use the Rosetta engine", so the way I see it, the more Rosetta can be improved over time, it has knock on benefits to other projects with more targeted purposes. And that's also why I continue to run Rosetta even if there are no targeted CV19 tasks here. Improvements in Rosetta code enables Rosetta itself and several other projects to improve at the same time


Yeah, that's why I run coronavirus stuff sometimes, as it has other outputs - like developing a painkiller by accident.
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Mr P Hucker
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Message 99517 - Posted: 2 Nov 2020, 18:43:48 UTC - in response to Message 99514.  

A pity old Rosetta code is used, especially as Rosetta was updated in April so all the latest improvements could be employed in the CV19 tasks we've run here


They might not be improvements relevant to what they're studying over at WCG.
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Message 99520 - Posted: 2 Nov 2020, 20:13:47 UTC - in response to Message 99514.  

The code issue was raised somewhat recently on the forums, IIRC.
The answer was that the scientists were happy with the results.
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Message 99522 - Posted: 2 Nov 2020, 22:13:10 UTC - in response to Message 99516.  

The African Rainfall Project is weird. I ask for tasks all the time, but recently, even when 120 tasks came down in one go, I only get 1, with the others spread around Mapping Cancer Markers, Open Pandemics, Microbiome Immunity Project and Smash Childhood Cancer. It's not a matter of runtime as far as I can tell. I don't know why I get so few. Usually it's none at all when 30 or 40 tasks come down at a time.

WCG send out their projects in different proportions, presumably depending on how much work there is available for each. Recently there's been a surge in calculations needed for cancer research, so I get a lot of them if I accept anything. But if you narrow it down and only accept rainfall, you will get as much as you want, they have plenty. I've currently got all but coronavirus switched on, and immunity is the one I hardly get any of. Rainfall is a reasonable amount, with cancer being a lot more. Probably I'm getting them in the ratio of 1 immunity to 2 rainfall to 2 child cancer to 4 cancer.

Having said all that, they do warn you that rainfall has specific requirements (I can't remember what they are, probably PC always on (they're long tasks with short deadlines), lots of RAM (although I can run 4 on an 8GB machine), or something). So if you haven't done any before on that PC, or not for a long time, it might give you the odd one to make sure they work ok first.

I don't know. I've got 16Gb RAM on an 8-core machine (and 8Gb on a 4-core laptop) and both had 1 Rainfall task running each. Uploaded, grabbed 44 tasks on the 8-core 16Gb machine and none came down again. Also no Childhood Cancer tasks. I get what I get, I suppose.

Also, on here, it seems there have been some tasks coming down again (yesterday's 137k in progress is now 148k) and I've had none again. Aggravating...
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Message 99523 - Posted: 2 Nov 2020, 22:18:04 UTC - in response to Message 99520.  

The code issue was raised somewhat recently on the forums, IIRC.
The answer was that the scientists were happy with the results.

It's their call, but I still don't understand it.
I thought Rosetta rolled up a couple of year's worth of improvements and efficiencies in the latest version.
Maybe there's some recoding involved at their end - but I'm just guessing randomly now.

Thanks again for the info
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Sid Celery

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Message 99524 - Posted: 2 Nov 2020, 22:30:45 UTC

In support of the idea that the project here is shutting down, Neil King at King Lab along with Baric Lab, Veesler Lab, Fuller Lab and IPD UW report an ultrapotent COVID19 vaccine that produces neutralizing antibodies in mice at levels >10x higher than is seen in people who recover from COVID

Induction of potent neutralizing antibody responses by a designed protein nanoparticle vaccine for Respiratory Syncytial virus - PDF

Twitter thread

"This vaccine is headed to clinical trials. We’ve transferred it royalty-free to two companies for development:
@Icosavax (with help from @Amgen) and SK Bioscience. First-in-human trials begin late 2020 or early 2021"
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Message 99526 - Posted: 2 Nov 2020, 23:31:01 UTC - in response to Message 99524.  

I think this is the link you wanted: https://www.cell.com/action/showPdf?pii=S0092-8674%2820%2931450-1
The one you posted is for the earlier research mentioned on this thread: https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13002
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Message 99527 - Posted: 2 Nov 2020, 23:43:26 UTC - in response to Message 99524.  

They aren't shutting down so much as they have finished with COVID-19.
https://science.sciencemag.org/content/370/6515/426

Their version is probably as good or better than anyone's. But that isn't the point. There are at least dozens out there that have shown good effects in the lab. They just need testing in human trials. Those are harder to come by.

Also note that we don't do the protein design here. We help them develop the tools. So we finished our part at least weeks, if not months ago.
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Mr P Hucker
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Message 99528 - Posted: 3 Nov 2020, 0:18:32 UTC - in response to Message 99522.  

I don't know. I've got 16Gb RAM on an 8-core machine (and 8Gb on a 4-core laptop) and both had 1 Rainfall task running each. Uploaded, grabbed 44 tasks on the 8-core 16Gb machine and none came down again. Also no Childhood Cancer tasks. I get what I get, I suppose.

Also, on here, it seems there have been some tasks coming down again (yesterday's 137k in progress is now 148k) and I've had none again. Aggravating...


What happens if you change the settings in your account on the WCG server to select only one application?

If I select all applications, I get some of everything, but an uneven amount (although not as uneven as you do).
If I select one application (even leaving the "gimme other stuff if none is available" ticked), then I get only what I asked for (apart from TB which is empty just now).
But whatever I do, I get what I asked for and plenty of it.

I do have a 0+3 hour buffer - if you're asking for say a 5 day buffer, maybe they won't do that.
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Message 99529 - Posted: 3 Nov 2020, 0:20:38 UTC - in response to Message 99527.  

But that isn't the point. There are at least dozens out there that have shown good effects in the lab. They just need testing in human trials. Those are harder to come by.


I would have thought volunteers who are dying of the virus would take a trial no questions asked!
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Message 99530 - Posted: 3 Nov 2020, 0:44:28 UTC - in response to Message 99528.  

I don't know. I've got 16Gb RAM on an 8-core machine (and 8Gb on a 4-core laptop) and both had 1 Rainfall task running each. Uploaded, grabbed 44 tasks on the 8-core 16Gb machine and none came down again. Also no Childhood Cancer tasks. I get what I get, I suppose.

Also, on here, it seems there have been some tasks coming down again (yesterday's 137k in progress is now 148k) and I've had none again. Aggravating...


What happens if you change the settings in your account on the WCG server to select only one application?

If I select all applications, I get some of everything, but an uneven amount (although not as uneven as you do).
If I select one application (even leaving the "gimme other stuff if none is available" ticked), then I get only what I asked for (apart from TB which is empty just now).
But whatever I do, I get what I asked for and plenty of it.

I do have a 0+3 hour buffer - if you're asking for say a 5 day buffer, maybe they won't do that.


I have my WCG set to only get TB tasks and almost never get any tasks at all. It's okay with me, I have lots of other projects that can use my time too, but I wish I could get one per pc per day so I could get my next badge there at some point, I'm currently a bit over 3 years.
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