Rosetta's role in fighting coronavirus

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Ezzz

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Message 92188 - Posted: 24 Mar 2020, 1:34:48 UTC - in response to Message 92182.  

I wanted to participate in this project to research a new dangerous virus (covid) , but than i saw that there is no specific types works, unfortunately because of this I will can not run in this project
let me know if will be created special types works to this virus


I would recommend that you reconsider. A large percentage of the work units coming out are for COVID 19 research, but not all of them are labels as such. If you keep running it, you will definitely help out!
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Mod.Sense
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Message 92189 - Posted: 24 Mar 2020, 2:49:21 UTC

Yes, try to keep in mind that these are the folks (the R@h Project Team at University of Washington) that have been trying to prepare for this day of pandemic for decades. They have been developing tools that are used in research organizations across the globe to create accurate computer models of various diseases and potential vaccines or treatments. Joining the project is both serving the robetta queue of work coming in from labs across the world, and facilitating the research done at UW.

Without tools like Rosetta to analyze a novel virus, any search for a solution would be delayed by all of the time required to physically isolate these things in the lab, and eventually perform x-ray spectroscopy, which then has to be interpreted either by hand, or with tools like Rosetta to see the underlying structure of the virus that you must devise a binder to.
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CREPOSUC

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Message 92198 - Posted: 24 Mar 2020, 7:29:54 UTC - in response to Message 92188.  


I would recommend that you reconsider. A large percentage of the work units coming out are for COVID 19 research, but not all of them are labels as such. If you keep running it, you will definitely help out!



https://en.numista.com/forum/topic93914.html#p789063
WE GO
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Profile MeeeK

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Message 92199 - Posted: 24 Mar 2020, 7:33:08 UTC

Would be better for all new volunteers, if the rosetta-guys would have named the covid-WUs correctly.
So everybody could see what the computingpower is used for.

People want to see what they are working for.
Thats quite normal.
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Dotsch
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Message 92200 - Posted: 24 Mar 2020, 8:04:55 UTC - in response to Message 92189.  
Last modified: 24 Mar 2020, 8:05:48 UTC

Yes, try to keep in mind that these are the folks (the R@h Project Team at University of Washington) that have been trying to prepare for this day of pandemic for decades. They have been developing tools that are used in research organizations across the globe to create accurate computer models of various diseases and potential vaccines or treatments. Joining the project is both serving the robetta queue of work coming in from labs across the world, and facilitating the research done at UW.

Without tools like Rosetta to analyze a novel virus, any search for a solution would be delayed by all of the time required to physically isolate these things in the lab, and eventually perform x-ray spectroscopy, which then has to be interpreted either by hand, or with tools like Rosetta to see the underlying structure of the virus that you must devise a binder to.

Thank you Mod.Sense for the update.
Could you please describe more detailed, what we are calculating with the current COVID-19 batches? What are the goals?
I would also very happy, if the project give a statement or update about the current science.
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gabriel@linux-romania.com

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Message 92201 - Posted: 24 Mar 2020, 8:41:02 UTC

Hi. Stopped sharing cpu for seti long time ago but now I set 1 linux server and 3 desktops for covid19. Hope to produce some results. Gabriel
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Profile dcdc

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Message 92206 - Posted: 24 Mar 2020, 10:31:40 UTC - in response to Message 92200.  

Hi Dotsch, I think I'm still running a machine on Dotsch UX in the office! I think it's still running on the image you made - running from a pair of compactflash cards in RAID0. There's a chance I changed it to a different Linux install but it certainly was running your image for a long time. I use it as a heater under my desk when it's cold - I treat it really badly by pulling the power on it because it's headless, and it always just works.
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gabriel@linux-romania.com

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Message 92207 - Posted: 24 Mar 2020, 10:43:15 UTC - in response to Message 92206.  

Nice job. Did you received seti at home Seth Shostak awards also?
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strongboes

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Message 92213 - Posted: 24 Mar 2020, 13:23:27 UTC

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Sid Celery

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Message 92224 - Posted: 24 Mar 2020, 17:14:00 UTC - in response to Message 92199.  

Would be better for all new volunteers, if the rosetta-guys would have named the covid-WUs correctly.
So everybody could see what the computing power is used for.

People want to see what they are working for.
Thats quite normal.

The self-serving arrogance of this. They're able to construct tasks for CV19 but they can't even name a task correctly. Such dorks.

What you really mean is you can't take screenshots to make it clear to everyone else how great you are.

If CV19 tasks are available here, either 100% or 50% or 1% of those available, it's that much more than almost anywhere else. Run the project or don't.
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Jim1348

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Message 92226 - Posted: 24 Mar 2020, 17:51:08 UTC - in response to Message 92224.  

Run the project or don't.

I can only agree. They have bigger fish to fry than satisfying our curiosity at the moment.
We can quibble about it later.
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Aurum

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Message 92227 - Posted: 24 Mar 2020, 17:52:46 UTC - in response to Message 92189.  

...delayed by all of the time required to physically isolate these things in the lab...
This is the first step. Isolate the virus and sequence its genome. Then model. Not sure what your point is.
...eventually perform x-ray spectroscopy...
Most proteins do not form single crystals and cannot have their structure determined by x-ray spectroscopy.
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Message 92229 - Posted: 24 Mar 2020, 18:19:41 UTC
Last modified: 25 Mar 2020, 1:58:58 UTC

We are currently trying are best considering what is happening around here with COVID-19. We are in Seattle, which is among the worst hit regions. Some are working in the lab related to COVID-19 and supporting staff even at risk of exposure, for example, the IPD core production group has been busy making COVID-19 proteins, an antibody known to bind, and the human ACE2 receptor target for research groups around the world. Relating to this project, we are trying to update Rosetta to the latest source so we can start running protein interface design jobs to design binders to COVID-19. This has already been done at a smaller scale on our local computing resources and we have some hopeful candidates that are already being worked on within the wet lab. The hope is to have many more candidates as that increases the chance of having a legitimate binder with the potential to develop and optimize for a therapeutic.

ALL COVID-19 related jobs that come out of our lab are named with the COVID-19 tag. Jobs from other institutions running through our structure prediction service, Robetta, may or may not be labeled, which is at the discretion of the individual researchers which we have no control over.

Thank you everyone for your contributions!
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torma99

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Message 92231 - Posted: 24 Mar 2020, 19:25:12 UTC - in response to Message 92229.  

Thank you for the info!

Keep up the good work, and I really-really appreciate that you still trying to work even, when the devil is ante portas.
And don't worry about the "I just want to work for covid otherwise not guys" I think the majority understands Rosetta and is committed to support science not only in this vis maior situation, but always!
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nnneal

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Message 92234 - Posted: 24 Mar 2020, 20:09:34 UTC - in response to Message 92229.  

We are currently trying are best considering what is happening around here with COVID-19. We are in Seattle, which is among the worst hit regions. Some are working in the lab related to COVID-19 and supporting staff even at risk of exposure, for example, the IPD core production group has been busy making COVID-19 proteins, an antibody known to bind, and the human ACE2 receptor target for research groups around the world. Relating to this project, we are trying to update Rosetta to the latest source so we can start running protein interface design jobs to design binders to COVID-19. This has already been done at a smaller scale on our local computing resources and we have some hopeful candidates that are already being worked on within the web lab. The hope is to have many more candidates as that increases the chance of having a legitimate binder with the potential to develop and optimize for a therapeutic.

ALL COVID-19 related jobs that come out of our lab are named with the COVID-19 tag. Jobs from other institutions running through our structure prediction service, Robetta, may or may not be labeled, which is at the discretion of the individual researchers which we have no control over.

Thank you everyone for your contributions!


Thanks for taking the time to post. Is the science benefitting from an influx of new contributors?
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bcov
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Message 92237 - Posted: 24 Mar 2020, 20:45:37 UTC
Last modified: 24 Mar 2020, 20:49:50 UTC


Thanks for taking the time to post. Is the science benefitting from an influx of new contributors?


Hey, I'm one of the people on the other end here using Rosetta @ Home to do science for COVID-19.

The first thing I should say is that we only recently had the idea to use Rosetta @ Home for design calculations. Previously we've been focused on structure prediction. It's quite a bit more complicated to send out jobs that need to run once (design calculations) than it is to send out jobs that need to run thousands of times (structure prediction). This requires a lot more data to be sent as well as a lot more time spent book-keeping to make sure that everything is going through.

With that in mind, step 1 right now is to update the version of Rosetta on Rosetta @ Home to use the latest and greatest version. The structure prediction side of things is rather mature and doesn't need new features, whereas the interface design is brand new, unpublished, and rapidly being developed. We need new code that I and others have written in order to perform these calculations.


So the first question is, is the science benefitting from using Rosetta @ Home? To which the answer is a definite yes. Interface design requires first making scaffold proteins followed by designing them to make interfaces. Right now I'm designing scaffolds at an unprecedented scale with the help of Rosetta @ Home. To give you an idea, as soon as I switched, I gained 10x-100x more compute than what I had before.

The second question is, will more users help? And the answer there is definitely yes again. For all of this work, more sampling = better results. The more scaffold proteins I can make, the better the best scaffolds will be. And then, once we get interface design going, the more interfaces I can design, the better the best designs will be, and the higher the experimental success rate will be.

Additionally, we have a long list of target proteins we're interested in for COVID-19 (some of which are COVID-19 itself). The more compute we have, the faster and better we can work through these targets and the faster we'll be able to make new therapeutics. Now, I can't guarantee that we'll end up making a therapeutic that goes through clinical trials and makes it to the people, but I can guarantee that we'll make binding proteins to interesting target proteins which have the potential to be therapeutics against COVID-19.
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Jim1348

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Message 92238 - Posted: 24 Mar 2020, 20:56:13 UTC - in response to Message 92237.  

Wonderful. I am in it for the long haul. There are a lot of projects on covid-19, not necessarily distributed, but in labs all over the world.
So if you can make a contribution that is great, but there are plenty of other health problems that will be around for a long time.

If you need lots of memory, just let us know. Not all crunchers have much, though I usually have 32 GB per machine, and could do even more.
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Falconet

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Message 92243 - Posted: 24 Mar 2020, 23:56:30 UTC - in response to Message 92237.  

Posts like these from Bcov and Admin are precisely what volunteers are looking for.

Please keep them coming.
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Plomos

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Message 92251 - Posted: 25 Mar 2020, 3:04:37 UTC

I am one of those people who doesn't have a lot of power to give, but what I can give I will to run as many units through as possible. It's also the only project I'm running aside from Wuprop to maintain a focus on this important work. Thank you for allowing us to positively contribute towards this solution
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Profile MeeeK

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Message 92258 - Posted: 25 Mar 2020, 9:17:01 UTC - in response to Message 92224.  


The self-serving arrogance of this. They're able to construct tasks for CV19 but they can't even name a task correctly. Such dorks.

What you really mean is you can't take screenshots to make it clear to everyone else how great you are.

If CV19 tasks are available here, either 100% or 50% or 1% of those available, it's that much more than almost anywhere else. Run the project or don't.


I think you don't get the point of boinc. We need every volunteer for getting work done.

And of course, because that's normal, everybody wants to see some kind of success. That's what we are paying for with our electricitybill.

And sure, it's 2020.
Some of the new volunteers also want to share their screenshots via Instagram or anywhere else.

But what happens?
More people will know about us and maybe they will participate too.

So you have to be kind and invest some time and work to find new volunteers.

It's NOT "run the project or don't!"
You are not "rosetta"
We are all rosetta.
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Message boards : News : Rosetta's role in fighting coronavirus



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