Bioinformatics High Performance Computing (Hpc) Forums/Mailing Lists

Question

[Jcd]

Hello all,

I have several fairly non-specific questions about HPC in bioinformatics and am looking for a good place to ask them. Are there any active forums or mailing lists for this? My background is engineering and I am looking for a better understanding certain problems in computational biology.

[Casey Bergman]

Why not ask them here on BioStar or else try http://stackoverflow.com/ ?

[Neilfws]

Yes, this is an active bioinformatics forum! That said, we prefer specific questions over non-specific, whatever that means :)

[Burlappsack]

JCD, my group does some cluster work, and we had a hell of a time finding good information on parallel computing. The best source was the people administrating the cluster and the developers of the software you are using, in our case, AMBER.

[Jcd]

They are more long the lines of discussion questions. For example, I see there are 3-4 commercial products for running accelerated sequence alignment and am wondering are there other common tasks for which no accelerator exists. I could only find one paper addressing this and it only mentions sequence alignment, phylogenetics and molecular dynamics.

[Jcd]

@burlappsack: Molecular dynamics was actually the first topic I researched. I build full-custom hardware accelerators for image processing and thought, 'Why doesn't someone do this for molecular interactions?' Turns out an extremely well funded group is currently doing just that.

[Flow]

hi, did you publish those interesting results? did you find also an answer for your question?

Answer 1

[Istvan Albert]

You can ask on this forum.

For best results try to make it a specific question that is likely to have a clear answer. High level overview questions and what if scenarios do not lend themselves to good answers.