BioBrew is a collection of open-source applications for life scientists and an in-house project at Bioinformatics.Org. The BioBrew Roll for Rocks can be used to create Rocks/BioBrew Linux, a distribution customized for both cluster and bioinformatics computing: it automates cluster installation, includes all the HPC software a cluster enthusiast needs, and contains popular bioinformatics applications.Bio Brew is an open source Linux distribution based on the NPACI Rocks cluster software and enhanced for bioinformaticists and life scientists. While it looks, feels, and operates like ordinary Red Hat Linux, BioBrew Linux includes popular cluster software e.g. MPICH, LAM-MPI, PVM, Modules, PVFS, Myrinet GM, Sun Grid Engine, gcc, Ganglia, and Globus, *and* popular bioinformatics software e.g. the NCBI toolkit, BLAST, mpiBLAST, HMMER, ClustalW, GROMACS, PHYLIP, WISE, FASTA, and EMBOSS.
The Bioinformatics Organization, Inc. serves the scientific and educational needs of bioinformatic practitioners and the general public. We develop and maintain computational resources to facilitate world-wide communications and collaborations between people of all educational and professional levels. We provide and promote open access to the materials and methods required for, and derived from, research, development and education.
Membership
The Bioinformatics Organization provides associate (non-voting) membership to individuals. This type of membership is divided into two categories: Basic and Professional.
The Organization was established in 1998 by J.W. Bizzaro as a place to host collaborations in bioinformatics. In 2000, it had more than 100 members and a dozen projects. The Organization became incorporated in 2003 and currently has about 25,000 members and over 300 projects. It is now one of the largest affiliations in the field of bioinformatics, and the number of resources that we offer is on-par with the number offered by NCBI and EBI. However, we distinguish ourselves with our open membership and project hosting: anyone, anywhere can participate. The Organization is also well-known for its emphasis on open access to biological information as well as on Free and Open Source software.
Services
* Life sciences R&D: The Bioinformatics Organization provides group hosting services and a number of online tools, databases and forums, all free to use. Through our Bioinformatics Core Facility, we provide fee-based data analysis and software development services to cater to the needs of scientists and biomedical researchers.
* Education: In addition to the hosted resources, which are also available for educational use, the Bioinformatics Organization offers professional development courses for continuing scientific education. These are short, graduate- or postgraduate-level courses on computational topics of interest to prospective and practicing researchers in the life sciences.
Bio Brew is an open source Linux distribution based on the NPACI Rocks cluster software and enhanced for bioinformaticists and life scientists. While it looks, feels, and operates like ordinary Red Hat Linux, BioBrew Linux includes popular cluster software e.g. MPICH, LAM-MPI, PVM, Modules, PVFS, Myrinet GM, Sun Grid Engine, gcc, Ganglia, and Globus, *and* popular bioinformatics software e.g. the NCBI toolkit, BLAST, mpiBLAST, HMMER, ClustalW, GROMACS, PHYLIP, WISE, FASTA, and EMBOSS.
BioBrew is "FREE AS IN BEER"! Use a mirror to download ISOs and documentation:
Rocks distributions (and thus BioBrew RPMs) are compatible with the following Linux distributions:
We encourage users familiar with the software packages used in BioBrew to contact us with their experiences, problems, successes, and suggestions so that we can improve the distribution. We have an email list for users:
biobrew-users@bioinformatics.org
You can subscribe to the list here:
http://bioinformatics.org/lists/biobrew-users
A very active and helpful Rocks email discussion list exists at:
npaci-rocks-discussion@sdsc.edu
You can subscribe to the list here:
https://lists.sdsc.edu/mailman/listinfo.cgi/npaci-rocks-discussion
Please only post general Rocks cluster installation, configuration, customization, and management questions to that list, and not any BioBrew bioinformatics software questions. They won't be able to help you with any bioinformatics queries.
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