With hopes of bringing together FreeBSD users in bioscientific fields, Johann Visagie of Electric Genetics has set up a mailing list for those interested in working toward a more “bio-friendly” free Unix.
FreeBSD, a version of the original BSD (Berkeley Software Distribution) Unix created by the University of California, has made its mark as an industrial web server platform — it powers Yahoo! among over 2,400 other websites — but hasn’t yet found its way into many bioinformatics departments.
This may be because the FreeBSD ports tree, which currently offers over 5,200 applications, offers a very slim selection of bioinformatics applications. Proponents tout the port system’s ability to integrate third-party applications into a Unix-based operating system as FreeBSD’s greatest feature. Visagie and a small core of other FreeBSD users in the bioinformatics field have started an informal movement to encapsulate more bioinformatics applications within the port system.
“Many bioinformatics applications are rather arcane and take quite a bit of hacking to get going properly,” Visagie said. “As far as I’m concerned, if I can do it once and allow all the other users of the operating system to gain the benefit of my experience of being able to install it with single command, that’s great.”
Visagie hopes that the core group of users will benefit from others’ experiences as well. “Someone else may come up with a better way of doing it and that might become integrated with the port,” he said.
There are 13 bioinformatics applications encapsulated at present, including ClustalW, Emboss, Genpak, Hmmer, and the NCBI toolkit. These are available at www.freebsd/ports/biology.html. Visagie said he’s working on “basic things” like BioPerl, BioPython, and applications built on top of them.
One advantage of the FreeBSD port, according to Visagie, is that it permits users to define dependencies — a plus for packages that depend on graphics libraries like Emboss. “It makes it very easy for a user to type one command and sit back and wait for every single dependency to be downloaded, unpacked, and installed properly,” Visagie said.
While usage is still at a “very humble scale,” Visagie said that since he started the mailing list a number of users have contributed new packages.
“It’s picked up slowly, but it’s not something that’s meant to take over the world,” Visagie said. “Call it the open source philosophy extended to system administration: Install something once and let others share the experience and maybe contribute improvements.”
Information about joining the mailing list is available at www.plig. net/mailman/listinfo/freebsd-bio.