Index  | Recent Threads  | Unanswered Threads  | Who's Active  | Guidelines  | Search
 

Quick Go »
No member browsing this thread
Thread Status: Active
Total posts in this thread: 36
Posts: 36   Pages: 4   [ 1 2 3 4 | Next Page ]
[ Jump to Last Post ]
Post new Thread
Author
Previous Thread This topic has been viewed 69990 times and has 35 replies Next Thread
manalog
Cruncher
Joined: Apr 9, 2015
Post Count: 18
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
(please, forward to Scripps' researchers): two less known DC-projects working on Sars-Cov2

Hi all,
I assume Scripps' researchers are aware of the existence of other distributed-computing projects participating in this fight against this invisible enemy: Rosetta@Home, Folding@Home, Ibercivis. I am aware that each one of those is doing research with a different approach, that everything helps, and I assume that the researchers behind OPN1 knows if they need some data from these projects and how to contact them. In science verification is important, but mere replication without communication is obviously a waste of precious resources.
I would like to show in brief two other projects that are working on Covid: they are less know, and perhaps OPN's researches does not know them. Perhaps they know them, in case ignore my post :)

The first is TN-Grid, from the University of Trento, Italy. They are running a project, gene@home, that is doing "gene network expansion" with an algorithm called PC-IM. They looks like a small but very serious project, with a good number of publication and very precise in the work they are doing. They did this "gene expansion" thing for many genes involved in some human pathologies but, during this outbreak, they expanded all the genes related to Sars-Cov2 according to recent papers, as can be seen in this forum post. Onestly, I do not know what a gene expansion is, but I am sure Scripps' researchers does. They completed this part of the research (1242 genes in 730296 WUs), and they are ok with sharing the data with the scientific community as soon as they need them. So, if this kind of research can be of any use for the purpose of OPN1, you should contact them!

The second is called Quarantine@Home and it is maintained by researchers from the University of California, San Francisco, as can be seen in this reddit post. This project is really new and much less known than Tn-Grid. But I think it can be interesting for Scripps' researchers to see what they are doing because:
1) They are performing Autodock simulations between molecules from the ZINC database and three Sars-Cov2's targets: mpro-1, spike-1, spike-2;
2) Their software runs also on Nvidia GPU's on a docker, and I have seen that it runs very well, with a speed way faster than the one of OPN1 on CPU (of course);
3) Despite being very "spartan" their website is outstanding: results are updated real time and you can see all the binding energy calculated by users in a public database! So the data are immediately available to everyone, including your researchers of course. The best binding energy they've found so far is -14,8
Perhaps it could be very useful for you to compare their results with yours.

Let me know if this post was useful even if just a tiny bit in this fight.
Thank you for your job!
----------------------------------------
[Edit 1 times, last edit by manalog at May 17, 2020 12:48:01 PM]
[May 17, 2020 12:45:49 PM]   Link   Report threatening or abusive post: please login first  Go to top 
Aurum
Master Cruncher
The Great Basin
Joined: Dec 24, 2017
Post Count: 2391
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: (please, forward to Scripps' researchers): two less known DC-projects working on Sars-Cov2

The first is TN-Grid, from the University of Trento, Italy. They are running a project, gene@home, that is doing "gene network expansion" with an algorithm called PC-IM. They looks like a small but very serious project, with a good number of publication and very precise in the work they are doing. They did this "gene expansion" thing for many genes involved in some human pathologies but, during this outbreak, they expanded all the genes related to Sars-Cov2 according to recent papers, as can be seen in this [url=https://gene.disi.unitn.it/test/forum_thread.php?id=265&postid=1804]forum post. Onestly, I do not know what a gene expansion is, but I am sure Scripps' researchers does. They completed this part of the research (1242 genes in 730296 WUs), and they are ok with sharing the data with the scientific community as soon as they need them. So, if this kind of research can be of any use for the purpose of OPN1, you should contact them!
Excellent point. I sent valetrc an article about a group that mapped all the proteins involved in SARS-CoV-2 processes and he found their published paper https://www.biorxiv.org/content/10.1101/2020.03.22.002386v3. He submitted all 480 proteins and we completed those gene expansions in days. I see he's added some more Covid-19 tasks since.
WHO currently lists 16,461 articles in their database related to Covid-19.
https://search.bvsalud.org/global-literature-on-novel-coronavirus-2019-ncov/
PubMed currently lists 12,959 papers related to Covid-19 https://www.ncbi.nlm.nih.gov/pubmed/?term=covid-19 and 5,535 papers on SARS-CoV-2 https://www.ncbi.nlm.nih.gov/pubmed/?term=sars-cov-2.
I've never seen anything like the current explosion of communications on a given topic. Nobody can read that many papers, not even a grad student :-) Sharing ideas is a great way to speed things up.
----------------------------------------

...KRI please cancel all shadow-banning
----------------------------------------
[Edit 4 times, last edit by Aurum420 at May 17, 2020 1:23:07 PM]
[May 17, 2020 1:17:58 PM]   Link   Report threatening or abusive post: please login first  Go to top 
manalog
Cruncher
Joined: Apr 9, 2015
Post Count: 18
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: (please, forward to Scripps' researchers): two less known DC-projects working on Sars-Cov2


WHO currently lists 16,461 articles in their database related to Covid-19.
https://search.bvsalud.org/global-literature-on-novel-coronavirus-2019-ncov/
PubMed currently lists 12,959 papers related to Covid-19 https://www.ncbi.nlm.nih.gov/pubmed/?term=covid-19 and 5,535 papers on SARS-CoV-2 https://www.ncbi.nlm.nih.gov/pubmed/?term=sars-cov-2.
I've never seen anything like the current explosion of communications on a given topic. Nobody can read that many papers, not even a grad student :-) Sharing ideas is a great way to speed things up.

This is the curse of contemporary science :(
Definitely it is very important to build a network at least of Dc-computing projects against Covid-19
[May 17, 2020 1:24:26 PM]   Link   Report threatening or abusive post: please login first  Go to top 
Falconet
Master Cruncher
Portugal
Joined: Mar 9, 2009
Post Count: 3315
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: (please, forward to Scripps' researchers): two less known DC-projects working on Sars-Cov2

I think TN-Grid is a great little project indeed.
I linked this thread to the Forli Twitter account.

I tried Quarantine@home a few days ago but couldn't get it to run.
Errors out with 404 not found when it's downloading some files, even after it performs a successful update.
----------------------------------------


- AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W
- AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W
- AMD Ryzen 7 7730U 8C/16T 3.0 GHz
[May 17, 2020 1:41:56 PM]   Link   Report threatening or abusive post: please login first  Go to top 
Aurum
Master Cruncher
The Great Basin
Joined: Dec 24, 2017
Post Count: 2391
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: (please, forward to Scripps' researchers): two less known DC-projects working on Sars-Cov2

Thanks for the Quarantine@home link. I'm trying to install it for Linux Mint 19.3 (Ubuntu 18.04 bionic) but the instructions are not clear.
Does anyone have a clear set of instructions for Linux??? TIA

This is where it goes bad:
curl -s -L https://nvidia.github.io/nvidia-docker/$distribution/nvidia-docker.list | sudo tee /etc/apt/sources.list.d/nvidia-docker.list
# Unsupported distribution!

----------------------------------------

...KRI please cancel all shadow-banning
----------------------------------------
[Edit 4 times, last edit by Aurum420 at May 17, 2020 2:00:30 PM]
[May 17, 2020 1:47:30 PM]   Link   Report threatening or abusive post: please login first  Go to top 
manalog
Cruncher
Joined: Apr 9, 2015
Post Count: 18
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: (please, forward to Scripps' researchers): two less known DC-projects working on Sars-Cov2

I have Mint too, you have to consider it as Ubuntu, so put in the variable $distribution this value "ubuntu18.04".
[May 17, 2020 2:25:13 PM]   Link   Report threatening or abusive post: please login first  Go to top 
manalog
Cruncher
Joined: Apr 9, 2015
Post Count: 18
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: (please, forward to Scripps' researchers): two less known DC-projects working on Sars-Cov2

I think TN-Grid is a great little project indeed.
I linked this thread to the Forli Twitter account.

I tried Quarantine@home a few days ago but couldn't get it to run.
Errors out with 404 not found when it's downloading some files, even after it performs a successful update.

Thank you :)
[May 17, 2020 2:30:02 PM]   Link   Report threatening or abusive post: please login first  Go to top 
Aurum
Master Cruncher
The Great Basin
Joined: Dec 24, 2017
Post Count: 2391
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: (please, forward to Scripps' researchers): two less known DC-projects working on Sars-Cov2

I have Mint too, you have to consider it as Ubuntu, so put in the variable $distribution this value "ubuntu18.04".
Thanks, progress.
I've seen slick commands like: distribution=$(. /etc/os-release;echo $ID$VERSION_ID) before where the variable returns tricia but what's needed is bionic.
This worked:
curl -s -L https://nvidia.github.io/nvidia-docker/ubuntu18.04/nvidia-docker.list | sudo tee /etc/apt/sources.list.d/nvidia-docker.list
----------------------------------------

...KRI please cancel all shadow-banning
[May 17, 2020 2:36:19 PM]   Link   Report threatening or abusive post: please login first  Go to top 
manalog
Cruncher
Joined: Apr 9, 2015
Post Count: 18
Status: Offline
Project Badges:
Reply to this Post  Reply with Quote 
Re: (please, forward to Scripps' researchers): two less known DC-projects working on Sars-Cov2

Happy crunching!
[May 17, 2020 2:40:39 PM]   Link   Report threatening or abusive post: please login first  Go to top 
Posts: 36   Pages: 4   [ 1 2 3 4 | Next Page ]
[ Jump to Last Post ]
Post new Thread