[BiO BB] Bioinformatics Benchmark System version 3 released

Martin Gollery mgollery at unr.edu
Fri Aug 13 16:52:33 EDT 2004

Thanks Joe. One addition that might be useful would be to have a space 
where people could post their results, with complete information about 
the system, of course. This would allow people to see how their system 
compares to any other.


Joe Landman wrote:

> Version 3 of the Bioinformatics Benchmark System (BBS v3) has been 
> released. Many new features, bug fixes, and suggested changes have been 
> made. New benchmarks have been added and updated for mpiBLAST, HMMer, 
> NCBI BLAST, and others in the baseline tests.  The version 1 tests are 
> still there if you wish to run them.
> The Bioinformatics Benchmark System is an attempt to build a flexible 
> and power testing framework, and meaningful tests,  to enable end users 
> and vendors to probe the performance of their systems.  As the most 
> important benchmark is your benchmark, and not a pre-packaged benchmark, 
> the system is specifically designed to allow you to easily modify or add 
> new tests.
> Moreover, the source to these tests are available under GPL, and are 
> hosted on Bioinformatics.org (http://bioinformatics.org/bbs) and 
> Scalable Informatics (http://www.scalableinformatics.com/BBS).
> For those who wish to run their own tests by hand without any testing 
> framework, the --dryrun switch will emit the final command line that 
> would be run.
> Additional documentation on the XML input format is forthcoming.  A 
> submission system for results, and baseline curation and data set 
> tagging will commence in short order.  Better handling of errors is in 
> place, as are better IPC methods.
> You can pull the binary tarball from 
> http://downloads.scalableinformatics.com/downloads/bbs/bbsv3.tar.gz .  
> Please note that this includes data for a rather large mpiBLAST job.  If 
> someone has a sizeable cluster they are willing to play with, mpiBLAST 
> installed and some time, we would like to see the speedup curve for 16 - 
> 256 nodes (or higher).  We would be happy to help out with this.
> Joe

Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
Marty's Law- the number of Bioinformatics acronyms will double every 18 

More information about the BBB mailing list