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Profile valterc
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Message 1751 - Posted: 4 Apr 2020, 11:14:22 UTC - in response to Message 1750.
Last modified: 4 Apr 2020, 11:14:36 UTC

Any result we get is immediately available to the scientific community (biologists etc.), for example the ACE2 expansions we completed a few days ago will soon be analyzed by a immunologist, etc.

We are also studying the possibility of doing some work on specific gene datasets recently made up from cells of SARS-CoV-2 infected individuals. In this case we will put 'on hold' the OneGenE Hs project.

Outstanding!!! Are these Covid-19 patients from a specific cohort??? E.g., the hyperimmune, deceased, etc.

I do not know the details yet, the biologists are looking at it, I will keep you updated if there is any news.

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Message 1752 - Posted: 4 Apr 2020, 11:46:30 UTC

What do you think to make a public announcement on other medias and / or the front page news, that TN-Grid is also computing COVID-19?

If it's public published, it can attract a lot of more users to the BOINC and also TN-Grid.

In the moment, there is a big run onto Rosetta and Folding@home.
Both projects have not permanently work.

Profile valterc
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Message 1754 - Posted: 4 Apr 2020, 15:09:02 UTC - in response to Message 1752.
Last modified: 4 Apr 2020, 15:09:29 UTC

What do you think to make a public announcement on other medias and / or the front page news, that TN-Grid is also computing COVID-19?

If it's public published, it can attract a lot of more users to the BOINC and also TN-Grid.

In the moment, there is a big run onto Rosetta and Folding@home.
Both projects have not permanently work.

Same old reason: our very limited server resources. The server is running right now at almost its full speed, say that doubling the users will just hassle the server with no real benefits. We just submitted a project to answer a governmental call (COVID-19 related), among other things we asked for a server, hoping to get some money for it.

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Message 1755 - Posted: 4 Apr 2020, 15:19:48 UTC - in response to Message 1754.

We just submitted a project to answer a governmental call (COVID-19 related), among other things we asked for a server, hoping to get some money for it.

I was just thinking that this is like Sputnik, where everybody rushed into science and engineering (my masters degree was paid for by the government).
You will have more resources than you know what to do with before long.

Profile valterc
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Message 1758 - Posted: 4 Apr 2020, 16:39:36 UTC - in response to Message 1755.
Last modified: 4 Apr 2020, 16:40:03 UTC

We just submitted a project to answer a governmental call (COVID-19 related), among other things we asked for a server, hoping to get some money for it.

I was just thinking that this is like Sputnik, where everybody rushed into science and engineering (my masters degree was paid for by the government).
You will have more resources than you know what to do with before long.

Yep, in 'normal' times no one (politics, majority of people) really cares about education, healthcare and basic research. We needed a crisis like this one in order to open a discussion about the errors made in the past, at least here in Italy, we'll see after that...

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Message 1759 - Posted: 4 Apr 2020, 16:43:30 UTC

It hasn't been that long ago that whenever I checked the Science Status page it said we were doing 27 a day. Now it's 50 a day. Doubling in weeks is impressive. This is the most reliable BOINC project I run and I hope it stays that way. Good luck on getting that new server.

http://gene.disi.unitn.it/test/gene_science.php

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Message 1761 - Posted: 6 Apr 2020, 20:09:10 UTC - in response to Message 1754.

What do you think to make a public announcement on other medias and / or the front page news, that TN-Grid is also computing COVID-19?

If it's public published, it can attract a lot of more users to the BOINC and also TN-Grid.

In the moment, there is a big run onto Rosetta and Folding@home.
Both projects have not permanently work.

Same old reason: our very limited server resources. The server is running right now at almost its full speed, say that doubling the users will just hassle the server with no real benefits. We just submitted a project to answer a governmental call (COVID-19 related), among other things we asked for a server, hoping to get some money for it.



How much you think a new server will cost you?
Have you considered doing a gofundme or something similar? I have no experience with such things on the receiving end, but could throw in few bucks.
I guess I wouldn't be the only one...

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Message 1762 - Posted: 7 Apr 2020, 8:30:12 UTC - in response to Message 1761.

Im in as well.

I have been monitoring the server status and it can't produce above 2K ready to send tasks.

I am now attaching couple machines more (I know is not gonna be a difference but if 10 guys like me do the same, sever will be exhausted).

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Message 1764 - Posted: 7 Apr 2020, 10:22:32 UTC - in response to Message 1758.

We just submitted a project to answer a governmental call (COVID-19 related), among other things we asked for a server, hoping to get some money for it.

I was just thinking that this is like Sputnik, where everybody rushed into science and engineering (my masters degree was paid for by the government).
You will have more resources than you know what to do with before long.

Yep, in 'normal' times no one (politics, majority of people) really cares about education, healthcare and basic research. We needed a crisis like this one in order to open a discussion about the errors made in the past, at least here in Italy, we'll see after that...


Very that to hear, that it's so problematic to get fundings.
Is it possible to get some fundings from the EU?

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Message 1777 - Posted: 17 Apr 2020, 4:37:17 UTC
Last modified: 17 Apr 2020, 4:39:38 UTC

A way to think about for getting servers:

World Community Grid gets servers from a non-profit division of IBM, and also staff to run them and a site (in Canada) for these servers.

They have a site in California where they examine the source code before allowing the resulting tasks to be available on the servers.

They are not the origin of the work they offer; however, they make it reach a much wider selection of users (including me). They call work from each origin a subproject.

It may be a problem if you change your programs very often - each new version has to pass their source code inspection again.

They don't mention whether the origin sites can put programs on the IBM servers to condense the volume of data sent back to the origin site.

They are already planning to add some COVID-19 work. It might be worthwhile to ask them to add more, from a different origin site, if your current server can handle the condensed volume.

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.

Profile Buro87 [Lombardia]
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Message 1778 - Posted: 17 Apr 2020, 12:45:48 UTC - in response to Message 1777.

@robertmiles
I don't understand your point.
TN-grid platform is is provided by Trnto University and National Research Council of Italy (CNR).
They are currently crunching on gene@home project
I think (and hope) they are planning to expand and add other projects to TN-grid platform in the future

robertmiles
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Message 1782 - Posted: 18 Apr 2020, 14:55:46 UTC

World Community Grid is a way to get a lot more people contributing computer time, by making projects international rather than mostly in just one country. Are you implying that this would not be good for TN-Grid?

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Message 1783 - Posted: 18 Apr 2020, 18:13:13 UTC - in response to Message 1782.

The WCG also contains more competition. TN-Grid will not get a big chunk of the processing power just like that. It's not a free, unlimited resource. Even the WCG will set priorities and you might not like them.

Within boinc, it is your choice to do TN-Grid. Within WCG it is not.

Put TN-Grid on the official boinc project list, get a Twitter, Facebook, ... compaign going. Put posters up at local universities or wherever. And first upgrade the backend so the tn-grid doesn't end up like Rosetta (out of work and untested, badly failing WU in the wild) or F@H (haven't seen a WU in the last week's).

Also: the results from the current batches at F@H, Rosetta,... will contribute to fighting covid-19 sometimes in the future. Research on biology is on the timescale of years, not weeks. Getting all twitchy now doesn't solve the current problem, it just shows that humans as a group cannot plan well in advance.

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Message 1784 - Posted: 18 Apr 2020, 20:12:09 UTC - in response to Message 1783.

WCG allows the users to select which of their subprojects to put their efforts to. Would you object if a lot of users put their efforts to whichever subprojects help COVID-19 research the most?

Profile Buro87 [Lombardia]
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Message 1785 - Posted: 18 Apr 2020, 20:52:06 UTC - in response to Message 1783.

The WCG also contains more competition. TN-Grid will not get a big chunk of the processing power just like that. It's not a free, unlimited resource. Even the WCG will set priorities and you might not like them.

Within boinc, it is your choice to do TN-Grid. Within WCG it is not.

Put TN-Grid on the official boinc project list, get a Twitter, Facebook, ... compaign going. Put posters up at local universities or wherever. And first upgrade the backend so the tn-grid doesn't end up like Rosetta (out of work and untested, badly failing WU in the wild) or F@H (haven't seen a WU in the last week's).


I agree. That' the point
TN-Grid, with their current servers, can't handle such a large number of users resulting from pubblication on the official boinc project list. As saod, they are planning to upgrade it. If all goes well, with new servers, with , maybe a Gpu app, and Android app, TN-Grid will scale up

For scientist a constant data flow is important.
Users want a full queue on their machine. Otherwise they get upset

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Message 1787 - Posted: 19 Apr 2020, 4:28:11 UTC
Last modified: 19 Apr 2020, 4:30:12 UTC

I've found a group that should be willing to provide some new users for TN-Grid, although not as many as WCG.

However, what I've seen at TN-Grid indicates that I should wait to see if you want them contacted.

Muscular Dystrophy Association

https://www.mda.org/

I'd recommend that you write at least a paragraph giving a good explanation of what gene expansion is, to have it ready to send to them.


Rosetta is now providing work most of the time.

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Message 1788 - Posted: 19 Apr 2020, 11:24:07 UTC

Why should TN-Grid move to WCG?

with their own server and project, they can act more quickly.
its the same as you would say, why can't intel and amd produce their cpus together, they could produce more cpus together.

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Message 1793 - Posted: 20 Apr 2020, 10:46:01 UTC - in response to Message 1787.

I've found a group that should be willing to provide some new users for TN-Grid, although not as many as WCG.

However, what I've seen at TN-Grid indicates that I should wait to see if you want them contacted.

Muscular Dystrophy Association

https://www.mda.org/

I'd recommend that you write at least a paragraph giving a good explanation of what gene expansion is, to have it ready to send to them.


Rosetta is now providing work most of the time.

Thank you for the info, I just forwarded this to our biologists.

Profile valterc
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Message 1794 - Posted: 20 Apr 2020, 10:47:01 UTC - in response to Message 1787.

I've found a group that should be willing to provide some new users for TN-Grid, although not as many as WCG.

However, what I've seen at TN-Grid indicates that I should wait to see if you want them contacted.

Muscular Dystrophy Association

https://www.mda.org/

I'd recommend that you write at least a paragraph giving a good explanation of what gene expansion is, to have it ready to send to them.

Thank you for the info, I just forwarded this to our biologists.

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Message 1804 - Posted: 23 Apr 2020, 20:54:38 UTC - in response to Message 1731.

I just put into the queue all the genes related to SARS-CoV-2 according to this paper https://www.biorxiv.org/content/10.1101/2020.03.22.002386v3

The data we used are available here https://public.ndexbio.org/#/networkset/4b4a9769-6ad1-11ea-bfdc-0ac135e8bacf?accesskey=abb250cd4e341423f3e913d71c171068c75c722e54649a83868feff7f239a548

Description: Interactomes for SARS-CoV-2 (coronavirus) the virus causing COVID-19. Interactomes have been performed in multiple cell lines, including HEK-293T, and a lung cell line, A549.

Workunit's id will start at 165735_Hs to 166977_Hs, that's the expansion of 1242 gene isoforms, each one will be 294 workunits, so there is plenty of work to do...



166817, getting close.

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