beowulf apps for bioinformatics

[Eric Billings]

On Thu, 22 Jun 2000, Borries Demeler wrote:

> My idea was to find a list of applications that can be run on a beowulf 
> system and may be useful to researchers in our dept. We have X-ray
> crystallographers, molecular biologists, kineticists, geneticists and all
> flavors of biochemistry represented in our dept. Once we have a good list
> of available software that may address a subject dealt with by one or the
> other faculty, we could come up with a viable proposal for a medium scale
> beowulf system, geared towards the software packages most useful to us.

You can find a terrific list of software applications at:

http://cmm.info.nih.gov/modeling/software.html

The page is maintained by Peter Steinbach of the Center for Molecular
Modeling.  Many of the applications are becoming available for Beowulf-class
machines and several of the free applications are already running under
Linux.  Of particular interest to the molecular biologists and geneticists
are the BLAST suite (http://www.ncbi.nlm.nih.gov/Tools/index.htmli).
We've been running the BLAST suite under Linux for a year or so.  It is
quite parallelizable and several of the algorithms fit into the 
"embarassingly parallelizable" category for essentially independent
searches.

- Eric 


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Dr. Eric Billings                                Voice: (301) 496-6520
Laboratory of Biophysical Chemistry              FAX:   (301) 496-2172
National Institutes of Health            email: billings at helix.nih.gov
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