[Beowulf] Bioinformatics Benchmark System v3 rc1 ready

Joe Landman landman at scalableinformatics.com
Mon Jul 12 03:10:10 EDT 2004


Folks:

  Much delayed as version 2 went through many rewrites, and we did not
release early or often.  This will be corrected.

  http://scalableinformatics.com/BBS/

and

  http://bioinformatics.org/bbs

(they are identical)

  Much is new in version 3.

1)  You no longer need to modify program source
to setup your benchmark.  A simple XML input file will do. 

2) A number of examples are included.  We need to document the
format better, though if you read the format, you will see 
that it really isn't complex (this is what took so long
oddly enough)

3) A bbsv1.xml input deck that replicates the original benchmarks from
last year is included.

4) New baseline example tests have been created using HMMer, multiple
BLAST runs, and others.  Further baseline tests will be added (and
suggestions are always welcome).  We are looking at a number of codes
including ClustalW, and various chemistry and proteomics codes.

5) Output in multiple formats: plain text, csv (comma separated values),
and XML.

6) A dryrun option.  Does everything but the final execution.  Uses a 
random sleep rather than a run.  

Much more code, some of it hinting at things to come.  Quite scalable:
we ran 100 simultaneous tests on a laptop (learning some surprising
things about DBM and performance loss in the process).  Documentation
has been created at least in the form of man pages.  More documentation
should be available soon, with details of the formats, configuration,
and so forth

The code is heavily commented.  It is GPLed for GPL projects/products. 
For commercial products which need to be non-GPL and supported efforts,
please contact us.

Please give it a spin, and send us a note as to how you found it, what
else you might like on it, and what tests you would like to see.  If you
want to contribute an idea for a test, or even better, a test, please
send a note.  If you want to help out on coding, please send a note as
well.

Thanks!

-- 
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615

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