Posts by Jim1348
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1) Message boards : Science : Miscellaneous gene-related news (Message 2390)
Posted 9 days ago by Jim1348
CDC/ClinGen collaboration results in a significant new genetic variant resource

The Centers for Disease Control and Prevention’s (CDC) Genetic Testing Reference Material Program (GeT-RM) has partnered with the Clinical Genome Resource (ClinGen) to develop a publicly available list of 546 expert curated pathogenic variants in 84 genes for use in next-generation sequencing (NGS) genetic testing. This list serves as a knowledge resource for designing comprehensive analytical validation studies and creating computer-modulated or simulated reference materials for clinical genomic test development by defining variants that are either major contributors to disease or difficult to detect. Their work is presented in The Journal of Molecular Diagnostics, published by Elsevier.

Genetic testing has evolved from interrogating small sets of known pathogenetic variants in one or a few genes to examining hundreds or thousands of genes simultaneously using NGS. For these large assays, it is logistically difficult (and often impossible) to obtain genomic DNA reference materials containing the full scope of variants and variant types needed to perform a comprehensive validation study.

It can be challenging for laboratories to maintain the expert knowledge to identify representative variants appropriate for inclusion in validation studies to assure analytic and clinical validity. In addition, a comprehensive validation study using traditional reference materials can be costly. The new expert curated variant list will help address these complexities. This is important because well designed and validated clinical assays can provide accurate and reliable results to patients, enabling accurate diagnoses and appropriate treatment decisions.

https://www.elsevier.com/about/press-releases/research-and-journals/cdc-clingen-collaboration-results-in-a-significant-new-genetic-variant-resource

This was cited by Jim Slade on the WCG/MCM forum. I don't know how relevant it is here, but maybe it is of interest to someone.
2) Message boards : Number crunching : Work Generator Down (Message 2348)
Posted 28 Jul 2021 by Jim1348
Thanks. That raises the question of whether it is just a server glitch, or whether they are out of work. I am sure that they can do more, but it is almost August.
3) Message boards : Number crunching : FMA application for windows_x86_64 (Message 2328)
Posted 19 Jun 2021 by Jim1348
As far back as my log goes, to 6 June, my i9-10900F was running avx. Then on 17 June it switched over to sse2, with no obvious change in the run times.

I will try forcing it to fma.

FMA brought it down from 3:17 (with avx or sse2) to 3:10. Nice, but no big deal.
4) Message boards : Number crunching : FMA application for windows_x86_64 (Message 2327)
Posted 19 Jun 2021 by Jim1348
It only makes sense that all i9s should work best using the same instruction set.

From what I've seen on i9 new builds that start with a fresh slate and run the test over all 3 instruction sets I'm seeing 7% improvement of fma over avx and 4% for fma over sse2.

As far back as my log goes, to 6 June, my i9-10900F was running avx. Then on 17 June it switched over to sse2, with no obvious change in the run times.

I will try forcing it to fma. I don't want to wait until Christmas to see what happens.
As I recall, my i7-8700 ended up on fma eventually, as did my Ryzen 3000s. For some reason, this project favors Intel. That is not always the case.
5) Message boards : Number crunching : World Gene Expansion Challenge 2021 (Message 2243)
Posted 8 Mar 2021 by Jim1348
My buffer is down to 9 work units, a bit low for an i7-8700.

But they have plenty from SiDock in Ljubljana, less than 300 km east of Trento.
https://www.sidock.si/sidock/server_status.php
Buy local.
6) Message boards : Science : SARS-CoV-2 virus (Message 2196)
Posted 6 Feb 2021 by Jim1348
In current weeks, scientists have sounded the alarm about new variants of the coronavirus that carry a handful of tiny mutations, some of which appear to make vaccines much less efficient.

But it’s not simply these small genetic modifications which can be elevating issues. The novel coronavirus has a propensity to combine giant chunks of its genome when it makes copies of itself. Unlike small mutations, that are like typos within the sequence, a phenomenon known as recombination resembles a main copy-and-paste error during which the second half of a sentence is totally overwritten with a barely totally different model.

https://us.newschant.com/health/the-coronavirus-is-a-master-of-mixing-its-genome-worrying-scientists/

I don't know if this is relevant to the TN-Grid work, but it looks like it might be.
7) Message boards : Number crunching : Compiling for AVX-512 (Message 2085)
Posted 18 Nov 2020 by Jim1348
It only cares if there is consensus reached between the two samples of matching or closed matched results.

Sure. But it is frequently the case on some projects that "similar" outputs don't match well enough for validation. I suppose it depends on the science, and how the validator is calibrated.
8) Message boards : Number crunching : Compiling for AVX-512 (Message 2083)
Posted 18 Nov 2020 by Jim1348
Almost all my WUs are fma and if I look at the wingmen the very often receive avx or sse2 equivalents - see Workunit 25706025 or 25705750 as examples.

I have never paid any attention to this, but now that you mention it, it seems that my Ubuntu 20.04.1 machine is being validated by everyone and everything.
http://gene.disi.unitn.it/test/results.php?hostid=55080&offset=0&show_names=0&state=4&appid=
9) Message boards : Science : SARS-CoV-2 virus (Message 2073)
Posted 13 Nov 2020 by Jim1348
In an international study in Science, 10 percent of nearly 1,000 Covid-19 patients who developed life-threatening pneumonia had antibodies that disable key immune system proteins called interferons. These antibodies — known as autoantibodies, because they attack the body itself — weren't found at all in 663 people with mild or asymptomatic Covid-19 infections. Only four of 1,227 healthy patients had the autoantibodies. The study was led by the Covid Human Genetic Effort, which includes 200 research centers in 40 countries.

"This is one of the most important things we've learned about the immune system since the start of the pandemic," said Dr. Eric Topol, executive vice president for research at Scripps Research in San Diego, who wasn't involved in the new study. "This is a breakthrough finding."

In a second Science study by the same team, the authors found that an additional 3.5 percent of critically ill patients had mutations in genes that control the interferons involved in fighting viruses. Given that the body has 500 to 600 of those genes, it's possible that researchers will find more mutations, said Qian Zhang, lead author of the second study.

https://news.yahoo.com/why-covid-19-kills-certain-100211975.html
10) Message boards : Number crunching : Server Status - No Work Available (Message 2019)
Posted 19 Oct 2020 by Jim1348
I have been getting enough work to keep going, even if the server status does not show it.
11) Message boards : Science : AMD COVID-19 HPC Fund (Message 1953)
Posted 18 Sep 2020 by Jim1348
Mmm, smell like an OpenCl client.... :-P

It must have been San Zeno who interceded on your behalf, proving that science and religion mix just fine.
12) Message boards : Science : AMD COVID-19 HPC Fund (Message 1941)
Posted 16 Sep 2020 by Jim1348
Today the number of "tasks ready to send" is 0... will you get also a new server from AMD?

Thanks for posting. I had missed the part about University of Trento.
TN-Grid is one of my favorite projects, but if they can get their work done faster in-house, that is even better.
13) Message boards : Science : SARS-CoV-2 virus (Message 1873)
Posted 29 Jun 2020 by Jim1348
All very good questions that could explain why some people are more susceptible than others. It shows the huge amount of work that has already been done. It will undoubtedly take years to process it all.
14) Message boards : Science : Escherichia Coli and Biobutanol (Message 1854)
Posted 31 May 2020 by Jim1348
Very nice. I hope we can make a contribution, if some researcher can be found to make use of it.
15) Message boards : Number crunching : TN-Grid on AMD GPUs (Message 1769)
Posted 10 Apr 2020 by Jim1348
Regardless of how it turns out, you have my thanks and, I'm sure, everyone else's.

Yes, certainly. Most projects I have seen get maybe a 15X - 20X speedup with a GPU.
But TN-Grid had better start planning for more work. This will keep them busy.
16) Message boards : Science : SARS-CoV-2 virus (Message 1755)
Posted 4 Apr 2020 by Jim1348
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.
17) Message boards : Science : SARS-CoV-2 virus (Message 1709)
Posted 19 Mar 2020 by Jim1348
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.)
18) Message boards : Cafe : Coronavirus (Message 1693)
Posted 8 Mar 2020 by Jim1348
I see that Trento is right on the edge of the quarantine zone.
https://www.bbc.com/news/world-middle-east-51787238

I lived in the Friuli for a couple of years and am familiar with the area.
Best of luck to them all.
19) Message boards : News : World Gene Expansion Challenge 2020 (Message 1691)
Posted 1 Mar 2020 by Jim1348
I've just installed my new AMD Ryzen 9 3950X on my PC. 32 threads ready to run TN-Grid WUs 😁

That could be fun. It looks like they are doing 10,500 seconds on Win10.
On my Ryzen 2700, I am doing about 13,500 seconds on Ubuntu 18.04.
20) Message boards : News : World Gene Expansion Challenge 2020 (Message 1682)
Posted 22 Feb 2020 by Jim1348
I run the project all the time anyway, so there is not much more to boost. But if they really want a boost, they just need to get listed in the BOINC Manager.

I know, they do not want to exceed their server capacity and run dry, but that is a problem for the crunchers. They will merely complain about it. But it would help the science, would it not?


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