Linux, Optimized for Science

When Glen Otero worked as a postdoc at the San Diego Supercomputer Center, he noticed a project called NPACI Rocks, which fine-tunes the operating system for cluster computing. That software now forms the core of Otero's own Linux distribution called BioBrew http://www.bioinformatics.org/biobrew.Based on Red Hat Linux kernel 7.3, BioBrew is optimized for cluster computing and bioinformatics. Besides the usual collection of networking and programming tools, the distribution includes such clusteri

Sam Jaffe
Jan 18, 2004

When Glen Otero worked as a postdoc at the San Diego Supercomputer Center, he noticed a project called NPACI Rocks, which fine-tunes the operating system for cluster computing. That software now forms the core of Otero's own Linux distribution called BioBrew http://www.bioinformatics.org/biobrew.

Based on Red Hat Linux kernel 7.3, BioBrew is optimized for cluster computing and bioinformatics. Besides the usual collection of networking and programming tools, the distribution includes such clustering tools as Sun Microsystems' Grid Engine, and bioinformatics programs such as HMMER, CLUSTALW, and BLAST.

And all of it is free and open-sourced. "If you wanted to do a Linux cluster in the past you would have to download dozens of programs from dozens of different places and then get them to work on your system," says Otero. "Now you can pop three CDs in and it's ready to go."

Even while the program was still in beta...

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