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What or Who is Linux Prophet?

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. What or Who is Linux Prophet?. Biology Bioinformatics Assess life science informatics needs

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What or Who is Linux Prophet?

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  1. The Biopackage Repository and BioBrew Linux ProjectsO’Reilly BioconBioinformatics.Org Track February 5, 2003Glen Otero, Ph.D.Linux Prophetgotero@linuxprophet.comwww.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 Rockshttp://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!!

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