Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Archive for August, 2008

    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 java.net.URLClassLoader$1.run(URLClassLoader.java:200)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
            at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
            at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
            at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
            at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
    

    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 »

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    Posted in *nix, Links, Science, Software, Systems Biology | 3 Comments »