[Bioclusters] Bioinformatics/computational biology focused benchmarks?

Joe Landman landman at scalableinformatics.com
Wed May 23 10:51:51 EDT 2007

Greenseid, Joseph M. wrote:
> Hi all,
> I am pretty new to the bioinformatics arena of high performance
> computing.  I am a computer guy, who has done HPC in areas like CFD,
> Earth/Space sciences, stuff like that.
> I have been asked to investigate bioinformatics (as in put together a
> system and team up with a computational biologist to do some work on
> it), and I have a system that I would like to play around with, but I
> was wondering if there were any useful benchmarks that I could run
> that would mean something to someone in this field if they saw the
> results -- something akin to HPL or HPCC for traditional
> supercomputing numbers.

Hi Joe

   There are a few serious efforts in this area:  BBSv3 is the one we 
built  (http://scalableinformatics.com/bbs) in use by a few hardware 
vendors to test/market their products, and biobench 
(http://www.ece.umd.edu/biobench/), and bioperf (http://www.bioperf.org/).



Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 734 786 8452 or +1 866 888 3112
cell : +1 734 612 4615

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