[BiO BB] Re: bioclusters

chris dagdigian dag at fedayi.sonsorol.org
Thu Aug 23 17:40:43 EDT 2001

Acually I just set up necluster.org over the past few months intending to
use it as a platform for new england area discussion of clustering :) This
idea came from some VA Linux guys that I was working with who thought that
the critical mass of clusters in New England was large enough to support a
regional interest group.

I'm interested in helping out with HOWTO documents and actually I'm trying
to get a presentation accepted at the ORA Bioinformatics conference in
February where I can talk about production quality life science
clusters. In particular I want to talk/write about the VAMPIRE cluster
that I just built for Vertex Pharmaceuticals (PR-speak info available at
http://www.vpharm.com/Pressreleases2001/pr081301.html :)

Count me in as a member of any biocluster list that comes up and please
let me know what you think of the "NECLUSTER" idea. I really do think that
there could be a pretty good local area clustering user group that may or
may not be life science specific depending on its members.

Keep me in the loop!


> Michi Kami wrote:
> >
> > In case anyone isn't aware of it and would be interested - John
> > Koza from Stanford has a 1000-Pentium Beowulf cluster set up. 
> > (As my 3-year old says, "that's a big puppy!")  He has a write-up,
> > and links to it, at http://www.xent.com/FoRK-archive/july99/0591.html
> > His area is genetic algorithms (mine also, while bridging
> > into bioinformatics), and the system runs Linux. 
> I've been considering starting a mailing list, and later posting some HOWTO's,
> for building computer clusters (e.g., Beowulf) for bioinformatics.  There are
> at least two issues that make "bioclusters" unique, requiring discussions
> outside of those for traditional clusters: (1) some bioinformatics programs
> have special hardware requirements (e.g., "embarrassingly parallel" vs.
> parallel or serial), and (2) bioinformaticians/ists may want to find and help
> each other with locating or porting bioinformatics software to these clusters
> (e.g., where can one get a parallel version of BLAST?).
> I know some people who'd like to learn more (or anything) about building
> bioclusters, but we need some people with experience willing to give advise. 
> It would be silly to have 200 people on a list with no one able to answer a
> single question.  If you are able to help, please contact me at
> jeff at bioinformatics.org.
> Also, if anyone knows of an existing discussion forum with educational
> resources like what I'm proposing, please let us know.  Maybe we don't want to
> reinvent the wheel.
> Cheers.
> Jeff
> -- 
> J.W. Bizzaro                                jeff at bioinformatics.org
> Director, Bioinformatics.org        http://bioinformatics.org/~jeff
> "As we enjoy great advantages from the inventions of others, we
> should be glad of an opportunity to serve others by any invention
> of ours; and this we should do freely and generously."
>                    -- Benjamin Franklin
> --

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