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Profile valterc
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Message 1698 - Posted: 14 Mar 2020, 19:07:17 UTC - in response to Message 1697.

We are actually expanding a lot of human genes, prioritizing them according to the scientists' interests. Among them this one (ACE2) https://www.ncbi.nlm.nih.gov/gene/59272 which is closely related to the SARS-CoV-2 virus. Don't expect we will be able to 'find a cure' but we are trying to add something to better know our enemy.

In the mean time, please, take care.

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Message 1708 - Posted: 19 Mar 2020, 15:55:13 UTC - in response to Message 1698.
Last modified: 19 Mar 2020, 15:55:32 UTC

We are actually expanding a lot of human genes, prioritizing them according to the scientists' interests. Among them this one (ACE2) https://www.ncbi.nlm.nih.gov/gene/59272 which is closely related to the SARS-CoV-2 virus. Don't expect we will be able to 'find a cure' but we are trying to add something to better know our enemy.

How about expanding the 400 proteins involved in SARS-CoV-2 processing and replication???

https://www.nytimes.com/2020/03/17/science/coronavirus-treatment.html?action=click&module=Top%20Stories&pgtype=Homepage
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Message 1709 - Posted: 19 Mar 2020, 19:35:29 UTC - in response to Message 1708.

How about expanding the 400 proteins involved in SARS-CoV-2 processing and replication???

That is a great article. If expanding the 400 proteins would do them any good, I am all for it and can put more machines on it. (The experts will have to decide if it is relevant.)

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Message 1712 - Posted: 19 Mar 2020, 23:08:59 UTC

We just added some other genes related to ACE2, according to this https://string-db.org/cgi/network.pl?taskId=fBQjTFzroyIX

They are AGT AGTR1 AGTR2 REN MME DPP4 PRCP MEP1B MEP1A XPNPEP2, among them we already expanded MME and DPP4. You may see the others' names coded inside the workunits string.

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Message 1713 - Posted: 19 Mar 2020, 23:10:46 UTC - in response to Message 1708.
Last modified: 19 Mar 2020, 23:17:05 UTC

We are actually expanding a lot of human genes, prioritizing them according to the scientists' interests. Among them this one (ACE2) https://www.ncbi.nlm.nih.gov/gene/59272 which is closely related to the SARS-CoV-2 virus. Don't expect we will be able to 'find a cure' but we are trying to add something to better know our enemy.

How about expanding the 400 proteins involved in SARS-CoV-2 processing and replication???

https://www.nytimes.com/2020/03/17/science/coronavirus-treatment.html?action=click&module=Top%20Stories&pgtype=Homepage


Interesting stuff, I will send the information to my colleagues (BTW we already did the expansion of BRD2, cited in the article, in the past).

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Message 1726 - Posted: 28 Mar 2020, 23:01:43 UTC
Last modified: 28 Mar 2020, 23:02:11 UTC

Added a few genes, related to DPP4, according to StringDB:
INS GIP SLC5A2 SLC5A5 ADA GCG GLP1R

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Message 1727 - Posted: 29 Mar 2020, 11:01:29 UTC - in response to Message 1726.

Thanks for the update, got a few INS workunits.

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Message 1731 - Posted: 2 Apr 2020, 10:57:27 UTC - in response to Message 1727.

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...

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Message 1732 - Posted: 2 Apr 2020, 14:00:16 UTC - in response to Message 1731.

Thanks for the precious update
So, for the end, how many wus will be related to COVID-19?

Profile Buro87 [Lombardia]
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Message 1733 - Posted: 2 Apr 2020, 15:49:39 UTC - in response to Message 1732.

Thanks for the precious update
So, for the end, how many wus will be related to COVID-19?


1242(genes) *294(wu) *2(copies) = 730296 wu

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Message 1734 - Posted: 2 Apr 2020, 15:59:26 UTC - in response to Message 1733.

Thanks for the precious update
So, for the end, how many wus will be related to COVID-19?


1242(genes) *294(wu) *2(copies) = 730296 wu


Grazie!
All'attacco!! Let's squeeze all cpu's cores!!

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Message 1735 - Posted: 2 Apr 2020, 18:13:28 UTC

Got some of those new SARS-CoV-2 WU's already.
Thanks for the update.

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Message 1736 - Posted: 2 Apr 2020, 18:59:15 UTC

Arte these available for RaspberryPi?
Thanks.

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Message 1737 - Posted: 2 Apr 2020, 20:19:15 UTC - in response to Message 1736.

Arte these available for RaspberryPi?
Thanks.

We have applications for ARM based devices. It should work, just try.

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Message 1738 - Posted: 2 Apr 2020, 20:25:06 UTC - in response to Message 1737.

Arte these available for RaspberryPi?
Thanks.

We have applications for ARM based devices. It should work, just try.


I'll keep on going with my little Pi 2 :D.
Thanks.

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Message 1740 - Posted: 3 Apr 2020, 14:22:33 UTC - in response to Message 1731.

This is really a great news!
Nonetheless it makes me raise a question... As far as I understood of this project (the science behind is a bit difficult for the non-scientists) I know that one of your main goal is to publish the "OneGeneE" database, where you are going to provide to the researchers with all the gene networks expansions we are computing.
Now, I assume that you are going to publish this database after the computation of all the queued genes for the Homo Sapiens research. This, according to the "science status" page, will require 3,37 years from now. This can be ok if we consider a "normal" basic research with a large possible timespan. Things are different if we are talking about knowing more of the pandemic that is struggling the world now: it is evident that science needs all the results as soon as possible, in terms of months.
So I was wondering, could it be possible that you publish the OneGeneE database just after we finish the computation of the SARS-CoV-2 related genes? In this way researches from all over the world could benefit immediately from the great job you do in Trento and perhaps speeding up the search for a cure. After all, at the actual pace, the computation on the 1242 genes you inserted would require only 24 days!
Is this possible? Or must the computation go through other steps before the publication? In particular I've read somewhere on this site about another software you have to run after boinc's results plus lab tests that of course require time and work of human beings. Is this the case also for the publication of the database?
Thank you for answering my doubts and thank you for your job.

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Message 1742 - Posted: 3 Apr 2020, 16:00:13 UTC - in response to Message 1740.
Last modified: 3 Apr 2020, 19:55:46 UTC

We already published the OneGenE (expansion of all the genes) results for a Vitis vinifera dataset (Vespucci).

The OneGeneE project for Homo sapiens FANTOM-5 gene expression dataset is our 'background' job, and it is a very long one. We normally put genes in the queue in alphabetic order (actually it is by 'number of isoforms', but it would be the same). At the very beginning we started by prioritizing genes related to neurovegetative diseases, then to some types of cancer, right now any gene possibly related to COVID-19 (you guess why...).

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.

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Message 1744 - Posted: 3 Apr 2020, 16:34:55 UTC - in response to Message 1742.

This is a very interesting answer, thank you!

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Message 1748 - Posted: 3 Apr 2020, 18:08:22 UTC

This project is quite good at keeping volunteers updated.
Keep it up!

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Message 1750 - Posted: 4 Apr 2020, 2:47:38 UTC - in response to Message 1742.

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.
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