BioBrew is an open source Linux cluster distribution based on the popular Rocks (www.rocksclusters.org) cluster software and enhanced for bioinformatics. BioBrew includes popular cluster software e.g. MPICH, 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, MrBayes, and EMBOSS. A BioBrew DVD iso for x86 is freely available for download at BioBrew.org, a Bioinformatics.org sponsored and hosted website. README and INSTALL docs are also available on the website.
Features you'll find in this release that differ slightly from Rocks-3.1 include:
-Infiniband support from Mellanox (/usr/mellanox)
-Myrinet support with gm-2.0.11
-Virtual Machine Interface (VMI) 2.0. (/opt/vmi-2.0-gcc)
-mpich built for VMI (/opt/mpich-vmi-2.0-gcc)
Application upgrades for 3.1:
added modules back to distro with modulesenv 3.1.6-2
upgraded modulefiles to 1.0.2, including corrections to profile.d scripts submitted by Humberto Zuazaga
upgraded hmmer to 2.3.2-1
upgraded gromacs to 3.2.1-1
upgraded EMBOSS to 2.9.0-6; EMBOSS now installs to /usr/share and not /opt/BioBrew
upgraded NCBI BLAST with ncbitoools 6.1.0-2 and ncbi.tar.gz from 10/20/04)
upgraded mpiBLAST to 1.3; mpiBLAST lives under /opt/NCBI/6.1.0/bin with the rest of the binaries
upgraded Phylip to 3.61-5 and separated it from EMBOSS
MrBayes 3.0-1 has been added to BioBrew
BioBrew rolls are also here:
BioBrew rolls for Rocks-3.1 and Rocks-3.3 on x86 are also available on the website, as is a BioBrew roll for Rocks-3.3 on x86_64. The rolls contain the same bio apps as the full BioBrew release. But know that if you build a cluster with Rocks + BioBrew roll, you will not have access to the vmi, mpich-vmi, Infiniband, or Myrinet packages in the full BioBrew release. You will be relying on Rocks' Infiniband, mpich, and Myrinet support, which is slightly different than BioBrew's, when using these rolls. The BioBrew rolls include the SRPMS as well as the RPMS.
This is the first BioBrew release for x86_64:
The BioBrew roll for Rocks-3.3 on x86_64 includes the same apps as the x86 releases, except for Java and EMBOSS. EMBOSS is not included because Java for Rocks-3.3-x86_64 was not available at the time this release was built.
Future BioBrew development is likely to consist of BioBrew rolls only. I've got more apps planned. I'm also soliciting requests. Hint, hint...
Thanks to Joe Landman of Scalable Informatics and Luc Ducazu of BioLinux for the SRPMS they make available to the community, and from which I borrowed liberally. They helped make this release a reality. Thanks to the beta testers that downloaded the releases over the past few weeks and pointed out a few problems. Thanks to Aaron Darling and Humberto Zuazaga for their help with mpiBLAST and Modules, respectively. Special thanks to the folks running BioBrew mirrors!