Posts by Jim1348

1) Message boards : Science : What is the Nipah virus and why is it more deadly than COVID-19? (Message 1140)
Posted 9 Sep 2021 by Jim1348
Post:
we should do HTVS also for NIPAH. Do you have an idea which protein to target?
Thanks, but you credit me with too much knowledge. That part is beyond me.
I just think that as a cruncher, the sooner we can start on them the better. They usually get worse.
2) Message boards : Science : What is the Nipah virus and why is it more deadly than COVID-19? (Message 1137)
Posted 8 Sep 2021 by Jim1348
Post:
https://www.yahoo.com/news/nipah-virus-why-more-deadly-185533487.html
This one is not related to COVID-19, so any vaccine or treatment will probably have to start from the beginning.
3) Message boards : News : Targets six, seven, eight (Message 1118)
Posted 29 Aug 2021 by Jim1348
Post:
Are those targets solved by AlphaFold already? How to compare Sidock to AlphaDock ?

Where do you see that "AlphaDock" exists? AlphaFold is for protein folding, not docking.
4) Message boards : News : Targets six, seven, eight (Message 1116)
Posted 28 Aug 2021 by Jim1348
Post:
I am glad that you are able to switch to more promising targets when they appear. This is no doubt still a rapidly-developing field, and everything is evolving rapidly (including the virus).
5) Message boards : Science : COVID-19 news (Message 1108)
Posted 12 Aug 2021 by Jim1348
Post:
A New Covid Variant On The Loose: B.1.621
A group of seven residents in a Belgian nursing home died after infection with a new variant, all of whom were fully vaccinated according to virologists on the scene. Though the vaccine used in these residents was not made public, it was likely either AstraZeneca or an mRNA vaccine such as Pfizer and Moderna, among those most frequently used in the country.

The new variant, B.1.621, has yet to receive a greek letter designation from the World Health Organization. The variant already accounts for around 2% of coronavirus infections in the United States, and as much as 10% in Miami, according to Carlos Migoya, CEO of Jackson Health System. The variant can be traced back to identification in samples from Colombia in March 2021 and according to the GISAID coronavirus database, the variant has been identified in as many as 28 countries, but potentially more.

Despite not having the official label of Variant of Interest or Concern, it should be noted that B.1.621 has certain characteristics that suggest it may be worth watching, as it could become a variant of interest or concern in the near future. Here we analyze those mutations and summarize what we know about their likely effects on transmissibility, virulence, vaccine evasion, and pathogenesis.
https://www.forbes.com/sites/williamhaseltine/2021/08/12/a-new-killer-on-the-loose-b1621/?sh=6f04c0ea3d1f

Looks interesting.
6) Message boards : Science : Other uses of docking than viruses? (Message 1106)
Posted 11 Aug 2021 by Jim1348
Post:
I am wondering too, but they may want to finish up the current work on CPUs for scientific consistency before jumping to GPUs.
And it will be interesting to see if they go entirely to GPUs, or whether they reserve some work for CPUs. I expect we will know more toward the end of the current batch.
7) Questions and Answers : Web site : COVID-19 news (Message 1100)
Posted 6 Aug 2021 by Jim1348
Post:
Licensed drug could reduce SARS-CoV-2 infection by up to 70 per cent, reveals study

That is quite interesting, but would probably be seen by more people in the other thread.
https://www.sidock.si/sidock/forum_thread.php?id=20
8) Message boards : Number crunching : Self reporting. (Message 1037)
Posted 13 Jun 2021 by Jim1348
Post:
You can use an app_config.xml:

<app_config>
<report_results_immediately/>
</app_config>
9) Message boards : Number crunching : Deadline is too short (Message 907)
Posted 11 May 2021 by Jim1348
Post:
The default buffer of 0.1 + 0.5 days works for me. I have no SD High Priorities, and it works for practically all of my projects.
But if you load up on too many projects, BOINC sometimes has a problem handling all of them in time also.
10) Message boards : Science : Other uses of docking than viruses? (Message 767)
Posted 3 Apr 2021 by Jim1348
Post:
We will explore in the future also other targets than for corona; that would be not neccessarly connected with viruses.

Excellent. That is what I was hoping for.

And if you get a good GPU development volunteer, maybe you can get the remarkable (100x) speedup that Autodock is getting on WCG/OPNG.
They can tackle anything now I think.
11) Message boards : Science : Other uses of docking than viruses? (Message 763)
Posted 1 Apr 2021 by Jim1348
Post:
Thanks. I had not seen that.
12) Message boards : Science : Other uses of docking than viruses? (Message 761)
Posted 1 Apr 2021 by Jim1348
Post:
I have only heard of docking (such as Autodock and VINA) being used against viruses.
But can docking be used for other types of diseases as well?
I don't know what they would be, but maybe you could give some idea.

Thanks.
13) Message boards : Number crunching : Never ending WU's ? (Message 747)
Posted 26 Mar 2021 by Jim1348
Post:
But, I think, after several days estimate time will be close to actual.

Yes, they have converged to 7 hours on one Ryzen 3950X, and 8 hours on the other, which are much closer to the actual time of about 5 1/2 hours.
14) Message boards : Number crunching : Never ending WU's ? (Message 742)
Posted 25 Mar 2021 by Jim1348
Post:
sidock is not so accurate - they plan two hours on a job, but it actually works four

It goes the other way with me on two Ryzen 3950s. They run between 5 and 6 hours, but the estimates are 9 hours on one machine, and 12 hours on the other.
They should be converging to the correct value by now, but are correcting more slowly than usual.
15) Message boards : News : Fifth Target is SARS-CoV-2 EProtein (Message 717)
Posted 21 Mar 2021 by Jim1348
Post:
Thank you for the well-considered explanation. Virology is not my field, but it shows you have given significant thought to the problem.
That is a lot better than just choosing targets at random. I will try to keep a machine on it, more or less.
(I run my machines 24/7, and will try to make up for some of the people who have to have checkpoints. The longer ones are OK with me.)
16) Message boards : Cafe : SIDock taking over! (Message 630)
Posted 7 Mar 2021 by Jim1348
Post:
In addition to that, you can shorten the time it takes for BOINC to converge to the desired resource share by using a cc_config.xml file in the BOINC Data directory.
There should be one there already, and you can just add this in the Options section:
<rec_half_life_days>1.000000</rec_half_life_days>


My entire file looks like this, and probably won't do you any harm:
<cc_config>
<options>
<rec_half_life_days>1.000000</rec_half_life_days>
<use_all_gpus>1</use_all_gpus>
<allow_multiple_clients>1</allow_multiple_clients>
<allow_remote_gui_rpc>1</allow_remote_gui_rpc>
<max_file_xfers>8</max_file_xfers>
<max_file_xfers_per_project>4</max_file_xfers_per_project>
</options>
</cc_config>

The number of simultaneous file transfers is doubled, and you can increase it more though I think it can cause problems if it goes too high.
It also allows the use of more than one GPU, and remote monitoring, though that may be irrelevant to you, but won't hurt.

Note that you can create the file in a text editor (Notepad), and then save it as an ".xml" file rather than a text file, and then place it in the BOINC data directory.
You have to activate it, as by restarting BOINC, or rebooting.
17) Message boards : News : Fourth target (corona_RdRp_v1) (Message 601)
Posted 17 Feb 2021 by Jim1348
Post:
Thank you for the update. But I have been wondering, what is next?
After you find promising candidates, do you do in vitro lab tests yourself, or publish the results for others to use?

Or perhaps you do more in-house screening to eliminate false positives?
18) Message boards : News : Release CMDock v 0.1.1 (Message 550)
Posted 6 Feb 2021 by Jim1348
Post:
I don't see it on the Applications list nor is it on the Preferences list yet.

It looks like a stand-alone program to me, not a BOINC app.
It just looks like a later version of this: https://covid.si/en/quick-start/
I ran it for a short while, but it does not give as much information or control as BOINC.
19) Message boards : News : Temporary task shortage (Message 471)
Posted 27 Jan 2021 by Jim1348
Post:
Doing the same work does not mean that they are doing it with the same programs, and therefore asking them is unlikely to help if the problem is with the programs.

I think Falconet was just responding to the point about what information the various projects give you. WCG is not bad.
20) Message boards : News : Temporary task shortage (Message 460)
Posted 24 Jan 2021 by Jim1348
Post:
If you were working for an American company, you would be busy working on your resume for a new job.
I had to explain that once to a colleague visiting from Germany. He didn't believe me.


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