The Biopackage Repository and BioBrew Linux Projects

O’Reilly Biocon

Bioinformatics.Org Track February 5, 2003

Glen Otero, Ph.D.Linux Prophet

gotero@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!!