Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Archive for the 'Systems Biology' Category

    R tutorial links

    29th March 2010

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    Posted in Bioinformatics, Links, Science, Systems Biology | 1 Comment »

    The 9th ICSB-2008 in Gothenburg, Sweden

    12th September 2008

    It has been quite a time since my last serious and long post. On the one hand, summer is vacations time – so I’ve been to one in Turkey; on the other hand – the long-awaited ICSB-2008 conference finally took place in Gothenburg, Sweden, on August 23-27 (or 22-28, counting in tutorials and workshops).

    Update: it appears that conference domain name http://www.icsb-2008.org/ was not maintained after the conference, so I had to remove all the links to that website (which now appears to be owned by someone not related to ICSB). However, there seems to be a mirror of ICSB-2008 at http://www.gmm.gu.se/groups/icsb08test/.

    Synopsis: in this post I present a personal-perspective report on the 9th ICSB (with a condensed ICSB-2008 photo-report in my gallery).

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