1. The Biopackage Repository and BioBrew Linux Projects O’Reilly Biocon Bioinformatics.Org Track February 5, 2003 Glen Otero, Ph.D. Linux Prophet gotero@linuxprophet.com www.linuxprophet.com

2. What or Who is Linux Prophet? Biology Bioinformatics Assess life science informatics needs Solution recommendations and design Build, test, and install solutions Training and education Beowulf Clusters Business

3. The Need for BioBrew Linux Bioinformaticians and life scientists: Have more data to analyze every day Need more cpu cycles Build and/or buy Beowulf clusters/compute farms Install cluster software and applications from the far flung corners of the Internet Chaos, comedy,and costs ensue The problem: There’s no one-stop shopping for an open source bioinformatics cluster solution Until Now…

4. BioBrew Linux A Linux cluster distribution that is: Easy to install, manage, upgrade, and understand Contains all necessary cluster software Open source Contains open source bioinformatics software!!! BLAST, HMMER, ncbi-toolkit, ClustalW, mpi-blast, etc. But How?

5. NPACI Rocks http://www.rocksclusters.org http://www.rocksclusters.org A Linux cluster distribution that is: Easy to install, manage, upgrade, and understand Contains all necessary cluster software Open source Freely downloadable ISO image(s) and manual All code developed for Rocks is released in binary and source Red Hat rpms. Linux Journal, 5/1/02--The Beowulf State of Mind

6. Cluster Software Components

7. Rocks Special Sauce

8. BioBrew Additions

9. BioBrew’s First Release Impending Rocks version 2.3.1 Linux Red Hat 7.3 OpenPBS (Portable Batch System) Sun Grid Engine (SGE) Maui PVM MPI (MPICH-Ethernet and Myrinet) Modules Ganglia PVFS Benchmarks (hpl,iozone, stream)

10. BioBrew’s First Release Bioinformatics Applications BLAST Standalone Sever integrated with SGE Bioinformatics Application Roadmap NCBI-toolkit Mpi-blast HMMER ClustalW GROMACS PyMol NAMD EMBOSS Others???? (Audience Participation)

11. BioBrew’s First Release What’s taking so long?? Rocks is strictly based on rpms All integrated apps need to be built as rpms Takes time (much software distributed as tarballs) I would like software suggestions and submissions I would like volunteers Helping build rpms Testing software on BioBrew/Rocks clusters or submitting test data to me As the sole project admin, I’ll cut the iso images and post them First release planned for this month

12. BioBrew Demo

13. BioBrew--What’s the catch?? Mailing list support is the only means of support for clusters built with BioBrew downloads gotero@linuxprophet.com npaci-rocks-discussion@sdsc.edu However… There are vendors building clusters with Rocks Callident will build, test, install, and provide commercial support for Rocks/BioBrew clusters Rocks developers are on Callident’s technical advisory board

14. The Biopackage Repository The Biopackage repository project is planned to contain the BioBrew apps, and other software, built as rpms on vanilla Red Hat releases. Adoption of Debian deb packages a possibility Multiple meticulous (and busy) project administrators taking their time (much software distributed as tarballs) biopkg-admins@bioinformatics.org We would like software suggestions We would like volunteers Building rpms Testing

15. Thank You!!