[BiO BB] Re: bioclusters
jfreeman at variagenics.com
Thu Aug 23 17:56:56 EDT 2001
I could have used such a group when I built our in house cluster at
Variagenics last year, and there has been a great deal of evolution in
the tools and techniques since then. I concur with Chris and would be
happy to lend a hand to this group.
Thanks for suggesting this Jeff,
chris dagdigian wrote:
> 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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