BioBrew Roll 4.1 - Bioinformatics.org

J.W. Bizzaro • November 28, 2005

BioBrew Roll 4.1

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.

More information on BioBrew can be found here:
http://biobrew.org

Brewmaster Glen Otero writes...

BioBrew-4.1 rolls for use with Rocks-4.1 (http://www.rocksclusters.org) on x86 and x86_64 architectures are here (finally). The rolls can be downloaded from the FTP mirror:
ftp://ftp.bay13.net/pub/biobrew/

Application upgrades for 4.1:
upgraded MrBayes to 3.1-1
upgraded hmmer to 2.3.2-4
upgraded wwwblast to 2.2-12
upgraded EMBOSS to 3.0.0-1
upgraded NCBI BLAST to 2.2.12-1 (using Joe Landman's NCBI-2.2.12-1static.src.rpm srpm)
upgraded mpiBLAST to 1.40-1 (using Joe Landman's mpiblast-1.4.0-1.src.rpm srpm)
upgraded Phylip to 3.65-1

New applications:
biopython-1.40b-1
clustalw-mpi-0.13-1
modeltest-3.7-1
Numeric-24.0b2-1
primer3-1.0.0-1
probcons-1.10-1
reportlab-1.20-1
t-coffee-2.66-1

There were several packages that I wanted to include, but I was delaying the release for much too long. I will try to create incremental releases that include new packages. All SRPMS are posted on the FTP mirror:
ftp://ftp.bay13.net/pub/biobrew/srpms/4.1/

You can subscribe to the BioBrew mailing list here:
http://bioinformatics.org/lists/biobrew-discuss

Thanks to Joe Landman of Scalable Informatics, Luc Ducazu of BioLinux, Susan Chacko at NIH, and Rudi Chiarito and Bent Terp of the BioRPMS project at the BEA core facility at NOVUM (http://apt.bea.ki.se) for the packages and SRPMS they make available to the community, and from which I borrowed liberally. Their efforts helped make this release a reality.

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