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