biolinux-6.0.27

Bio-Linux: Ubuntu and bioinformatics

GNU/Linux

Hi! Today I’d like to spend some words on a particular Open Source project which aims to make know, test and finally use the available tools for molecolar biology, bio-technologies and bio-informatics in general. This world is overwhelmed by a number of “tools” divided in an ocean of productors, licences, repositories and kind of package (rpm, deb, Z, tar.gz, plain code…). Enter Bio-Linux.

The Bio-Linux project starts from a branch of UK’s NERC (National Environment Research Council) dealing with biology. This NEBC proudly has took in hand this shattered cosmo of open source software for bioinformatics under his own “umbrella” and then has gone further … has created a full GNU/Linux distribution, building over the solid core of Ubuntu (on it’s Long Term Support 8.04 release). Today Bio-Linux 5 is:

  • a LiveCD operating system;
  • a fully functional operating system running on desktop and servers alike;
  • a bioinformatics repository for Ubuntu

and all this is fully supported and given the news on the NEBC and NERC there’s money to guarrantee that for the expectable future. Personally at work I’ve had chance to appreciate this distro in all the flavours listed above and also as a VMware’s appliance.

If you’ve already running an Ubuntu 8.04 box in this wiki page you’ll find how-to add the biolinux repository to your sources.list. There it’s also stated that there’s some kind of compatibility with Debian and also with the latest 9.04 release, even if for a couple of software there are occasional bugs. But, on the workplace, expecially when the user has to USE his desktop and not work to make it run, Ubuntu 8.04 (with an updated copy of OpenOffice and a couple of backports) it THE way go, at least for me.

As a personal, final note, I must regret on the strickt control of the repository … I’ve witnessed a similar Biolinux project, focused on the RPM world being abandoned in 2007 supporting ancient distros like Fedora6 and RedHat 9 … I’d prefer a strong team in the Ubuntu (or $distro) community claiming “we will take care of all things bioinformatics, like it’s done for Compitz or other focused projects in the past. A change of menthality is needed so, when the Public Administration (or a private) invests on an open source technology the RoI must be seen in the product itself (and/or on how it facilitates works or makes you make more money increasing the productivity) and not in a self-owned fancy site claiming “I MADE IT, I AM BIG, GIMME MORE MONEY”. Don’t you think so?

5 thoughts on “Bio-Linux: Ubuntu and bioinformatics

  1. Hey, I totally agree. I do bioinformatics but that doesn’t mean I’m a bioinformatician all day long. I also play games, write papers, do development. A specialized distro might be good for one purpose, but it will suck for other purposes. So I don’t care about that. I just want a generic distro, and make it so that it includes a lot of bioinformatics software as well/

    Luckily there are also efforts like the debian-med team (http://www.debian.org/devel/debian-med/) which focuses on packaging medical applications directly for Debian. Their effort is less flashy, but it ends up benefiting a larger population of Debian and Ubuntu users.

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    1. Hello, Martijn.

      I think that Bio-Linux *is* just a generic distro that includes a lot of bioinformatics software as well🙂

      Bye,

      Tony.

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    1. Well, it’s the kind of distro you search when you want your need quickly fulfilled … like ubuntu for netbooks, ubuntu studio, Linux Mint and such … in this case one could want a ready to go bio-informatic desktop / server (it comes also with some apache+mysql, apache+postgresql services preconfigured).

      Got it ?

      Like

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