Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

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    Debian-Med Project

    3rd September 2008

    There’s a Debian-Med project, aiming to

    develop Debian into an operating system that is particularly well fit for the requirements for medical practice and research

    Debian-Med has several web sites/pages: one at (descriptive), and the actual project’s website at There’s also debian-med wiki (for developers).

    As of nowadays, Debian-Med has released a number of Debian packages, which are grouped into respective Debian Med Tasks. The Biology-dev task, for example, contains MCL and libsbml packages (among many others).

    Check this project out – you might find that the software you need is already available as Debian package.

    This post was stimulated by Steffen’s comment.


    Posted in *nix, Links, Science, Software | No Comments »

    Installing libsbml on Debian (to make iBioSim start)

    30th August 2008

    There’s a troubleshooter for Ubuntu, which (expectedly) works quite the same for Debian (lenny in my case).

    I’m installing libsbml to make the iBioSim tool work under Debian GNU/Linux. First thing I had to do was to make Sun’s java interpreter do all the java interpretation work instead of gcj: sudo update-java-alternatives -s java-6-sun (this assumes you do have java-6-sun installed).

    Installing libsbml moved me one step further, now I’m getting another error from iBioSim:

    Exception in thread "main" java.lang.NoClassDefFoundError: biomodelsim/BioSim
    Caused by: java.lang.ClassNotFoundException: biomodelsim.BioSim
            at Method)
            at java.lang.ClassLoader.loadClass(
            at sun.misc.Launcher$AppClassLoader.loadClass(
            at java.lang.ClassLoader.loadClass(
            at java.lang.ClassLoader.loadClassInternal(

    This yet has to be fixed somehow.

    If Zhou Xin’s blog becomes for any reason inaccessible (or moves to his own domain), below is the extract of the instructions from his post on how to install libsbml on Debian/Ubuntu Linux:
    Read the rest of this entry »


    Posted in *nix, Links, Science, Software, Systems Biology | 3 Comments » universal Ukrainian Debian mirror

    15th July 2008 and

    What is on offer (mirrors):

    • cygwin
    • debian – stable, testing, sid
    • debian-archive (starting from 1.1!)
    • debian-multimedia
    • installation media (CDs/DVDs)
    • debian-security
    • even debian-volatile is here!

    All this goodness is only 3 hops away from my DSL modem…. (ISP UkrTelecom)

    Gone editing /etc/apt/sources.list :)

    P.S. For non-ukrainian IPs, access might be slow/bandwidth-limited; for Ukrainian IPs, speed might be up to 100MBit/sec.

    Update: some time after publishing this post, was down for some reason. When it was up, it was serving me packages with a mere 3 kb/sec :( . I found that mirror is faster at the moment.


    Posted in *nix, Links | No Comments »

    Concise guide to CPU frequency scaling in Linux

    11th July 2008

    Debian HOW-TO: CPU power management / frequency scaling

    Also as a PDF: Debian how-to: CPU frequency scaling and power management.


    Posted in *nix, how-to, Links | No Comments »

    Fresh install of Debian Etch 4.0r1 hangs/freezes dead after boot: solution

    24th October 2007

    Recently, I installed Debian Etch 4.0r1 onto my laptop. However, after the first boot into plain console, computer was dead-frozen after some console usage. I rebooted using the Power button – this time to gdm; and again, after some keyboard input system was hanging dead.

    I found the reason at forums. Basically, it’s the PC speaker module (pcspr) not functioning correctly. I suspect this problem manifests itself only on some types of laptops. The solution is either to somehow reconfigure the pcspkr module, or just disable it. More on how to disable the module below.
    Read the rest of this entry »


    Posted in *nix, Links | 1 Comment »

    Topologilinux 6.0.0 BSOD (Blue Screen Of Death) fix

    1st September 2006

    Topologilinux ‘BSOD at launch’ problem solution is at the end of this post.

    Topologilinux is a special linux flavour, which is especially fit for the newcomers to the *nix world. The motto of Topologilunux is ‘Running Linux inside Windows’ – and that is what it does. Even more – you can run it inside windows, or you can boot into it and work Linux-only – in both cases the system is the same.
    Personally, I consider this kind of setup extremely useful for users who are strongly used to working in Windows (or just stuck with windows for too long), but at the same time are inclined to script a bit (be it bash, Perl, PHP or Python), to run server applications, write cross-platform programs, to test something or just play with software. With Topologilunux, it’s perfectly fine to work in DreamWeaver on your windows machine, and launch Topologilinux with apache+php+mysql to serve as a testing server – on that same machine. You can easily replicate the needed server config, and play with it the way you wouldn’t if that was the production server.
    Read the rest of this entry »


    Posted in *nix, OS | 1 Comment »