Posts by bozz4science

1) Message boards : Number crunching : New Docker image with Virtualbox and Nvidia GPU passthrough support (Message 102917)
Posted 11 Oct 2021 by bozz4science
Sounds very exciting! Didn't know that you could pass through a virtual box designed CPU-intended WU to an NVIDIA GPU using a docker image. Will take a look later this week and test this on my system! Is there a way to limit tasks to the python tasks only for testing?

P.S. This docker image could potentially also run on Windows, right?
2) Message boards : Rosetta@home Science : DeepMind published a complete human proteome data set online - for free (Message 102277)
Posted 27 Jul 2021 by bozz4science
How about that?
Google’s DeepMind puts human proteome online for free

DeepMind partnered with the European Molecular Biology Laboratory (EMBL) to come up with the AlphaFold database, which predicts the three-dimensional structures of the human proteome – nearly all (98.5%) of the 20,000 or so proteins expressed by the human genome.

AlphaFold has doubled the number of protein structures known to research, and that could help accelerate research into how diseases affect the body, and develop new medicines that can latch on to problem proteins effectively.

It is one of the most significant contributions that AI has made to the advancement of science, according to its developers, although they acknowledge that some of the predictions will still need to be validated in experimental testing. Around a third of the structures are considered to be detailed and precise enough to allow drug design.
3) Message boards : Number crunching : A new machine for boinc and to learn. (Message 99632)
Posted 10 Nov 2020 by bozz4science
The only thing I know about them is that they tend to have smaller diameter but very powerful fans that can be quite loud, especially under load. Placement (noise and ambient temperature for more efficient cooling) is definitely something you should consider.
4) Message boards : Rosetta@home Science : Techcrunch article (Message 98964)
Posted 11 Sep 2020 by bozz4science
Yeah, there's a duplicate thread labeled "David Baker wins ..." recently.

Anyway, great news and thanks for sharing![/url]
5) Message boards : Rosetta@home Science : David Baker wins 2021 Breakthrough Prize (Message 98963)
Posted 11 Sep 2020 by bozz4science
That's a great accomplishment! Even more noble that he plans to give back to the scientific cause! Truly a great man and scientist.
6) Message boards : Number crunching : Running multiple covid projects on multiple machines, how do you personally go about it? (Message 98500)
Posted 13 Aug 2020 by bozz4science
Just my 2 cents.

Personally I have far less compute power and at most 20 threads of mostly very old CPUs to share at any time. Due to the current heat wave I was forced to temporarily pause/reduce my contribution as my small apartment immediately turns into a hostile environment when running them 24/7 at the current temps. Still, I like to think that my contribution just adds up in the end so it still counts. As I have far fewer machines, there is far less to manage, so I cannot add any value here.

Usually I dedicate my older GPU to Folding@Home. The CPUs run on multiple projects with small caches. I like to diversify my Covid-related projects as well as I think each one has a valid approach but some might yield more immediate kind-of results than others. I run OPN at WCG, even though I am also anticipating the start of their GPU client, as well as TN-Grid, Rosetta and Ibercivis.

What I see so far is, that many of the aforementioned projects do not only conduct Covid-related research and thus increasingly send out more Covid-unrelated work. To my understanding only OPN and Ibercivis have dedicated their complete WU-pipeline to Covid-only tasks. I believe that in the end all research that these projects conduct is valuable, so I don't mind that only a fraction of the completed work might have this desired link to Covid-research.

In the end it all comes down to personal preference and one own's knowledge to judge the potential benefit of each project. As I don't have a well enough understanding in medical chemistry/immunology and virology, I split my resources among these projects. However, I think that Ibercivis and OPN mainly try to find a short-term antiviral candidate by testing synthetically created and existing drugs to repurpose them for Covid. This might yield more immediate opportunities as a broadly deployable and low-cost therapeutic. TN-Grid tried by extending the gene networks related to Covid-involved genes (f.ex. ACE2) to find potentially interesting genetic links to the susceptibility and severity of the disease. And lastly, Rosetta and Folding perform structural Covid-related protein prediction to find interesting binding sites for therapeutics and provide insights for further vaccine research efforts. While Rosetta is concerned about the stable final form the amino sequence folds into, Folding@Home is also interested in the folding process itself and models the atomic dynamics of molecular structures as well. Among the most notable efforts at F@H is the ongoing Covid-Moonshoot project you can read up on the F@H website. And if I am not mistaken GPU.Grid also ran some Covid WUs as well. Earlier this year Boinc@TACC (currently #8 supercomputer in the world) also ran a larger batch of Covid-tasks but only has work sporadically. In the end I think each projects complements each other even if there might be some redundancies, but it is still only the tip of the iceberg along the ongoing race for a vaccine.
7) Questions and Answers : Wish list : Badges (Message 98146)
Posted 16 Jul 2020 by bozz4science
Again ~2 months or 1/6 of a year. Anyone would be happy to show off some protein badge I guess? Would be interested in a ballpark number of when volunteers could expect badges to be implemented? Still in 2020? What factors does it depend on? Do you need help in drafting the badges? Just tell us :)

That would include an honest and definitive answer (Yes or no) to badges. if you oppose to them and don’t want to implement them at all just tell us but don’t keep us in the dark, wondering and patiently waiting in anticipation of sth that might never come.

Keep crunching!

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