Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    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:

    - first, install all the necessary packages:
    aptitude install build-essential libxml2 libxml2-dev python-dev

    - then configure, make and install libsbml:
    ./configure ––with-python (execute from the directory where the downloaded libsbml archive was extracted to)
    make install

    - then check if installation was successful:
    and when the python prompt >>> appears, run from libsbml import * – if there are no warnings/errors, then you are done!


    3 Responses to “Installing libsbml on Debian (to make iBioSim start)”

    1. Steffen Moeller Says:

      Hi, nice blog! There is a Debian package for libSBML more or less ready. You can inspect it on the subversion repository accompanying and have packages to download on



    2. Bogdan Says:


      thanks a lot for the links! I’ll consider using the libsbml2/3 libraries from E-cell’s Lenny repository.

      However, it’s even more exciting for me to learn that Debian has a bio-medical software task force! The least I can do right now is to write a post about the Debian Med project, what I’m already doing…

      Frankly speaking, I was somewhat surprised at the ICSB-2008 to see that some software tutorials explicitly stated that Windows will be the “tutorial OS” (for the sake of completeness, it must be mentioned that presented software did have Linux version). Also, given some problems I’m trying to overcome with other pieces of systems biology tools, it appears that Linux isn’t (yet!) that popular among systems biology software developers, even despite the fact that most of the software is written either in Java (which is cross-platform, as well as Eclipse), or in C++ (which, to the best of my knowledge, is also highly portable, given that cross-platform GUI toolkit is used).

      To conclude: thanks for your efforts in helping Debian become the truly versatile and popular OS, also for bio/med applications.

    3. Debian-Med Project » Autarchy of the Private Cave Says:

      [...] post was stimulated by Steffen’s comment [...]

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