Glen Otero, Linux Prophet
Track: Bioinformatics.Org
Date: Wednesday, February 05
Time: 11:30am - 12:15pm
Location: Plaza
The biopackage repository is a project that collects, builds, and maintains popular bioinformatics software packages for download in .rpm format. Currently available software includes BLAST, Phylip, ClustalW, BioPerl, and HMMER RPMs. These are the same RPMs to be included in the first release of the BioBrew Linux cluster distribution. Future bioinformatics packages will be added based on availability of code and community requests.
BioBrew is a Linux distribution that combines the NPACI Rocks cluster software with several popular open source bioinformatics software tools like BLAST, HMMER, ClustalW, BioPerl, and Phylip. The result is a Linux distribution that can be used to install a workstation or a Beowulf cluster for bioinformatics analyses. With BioBrew, users can build a Linux workstation that includes several bioinformatics applications “out of the box” and later expand that workstation into a Beowulf cluster by networking additional computers to the original workstation via a second network interface.
Otero, a co-founder and administrator of both projects, delves into the following BioBrew Linux and Biopackage repository topics:
-Goals of both projects
-Project backgrounds and explanation of how both projects are intertwined
-Project components and tools
-Structure and dynamics of both projects at Bioinformatics.Org
-Directions for using BioBrew Linux for workstation and cluster installations
-How to run bioinformatics applications on BioBrew workstations and clusters
-How to use the Biopackage repository
-Project administrators and mailing lists
-Call for participation in both projects
The BioBrew Linux and Biopackage repository projects are the first known attempts at creating and freely distributing easy-to-use clustering software designed for life scientists. The software is built upon established clustering methods and well known bioinformatics applications.
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