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


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


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…


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?


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


Cluster Software Components


Rocks Special Sauce


BioBrew Additions


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)


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)


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


BioBrew Demo


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


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


Thank You!!


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