Autarchy of the Private Cave » java

Using Python in a Java project

Bogdan — Tue, 17 May 2011 11:33:52 +0000

If you are a Python zealot, and Java doesn’t feel right, but the project you are working on is a Java project – try

Jython – Python for the Java platform, compile your python scripts into Java bytecode
Groovy – not Python, but still a scripting language which compiles to jars

CLANS: CLuster ANalysis of Sequences

Bogdan — Fri, 24 Oct 2008 23:20:39 +0000

CLANS (CLuster ANalysis of Sequences).

Found via Freelancing science:

CLANS runs (PSI)BLAST on your sequences, all vs all, and clusters them in 2D or 3D according to their similarity. This method allows for rapid classification of huge datasets and has the advantage over, lets say, phylogenetic tree, that one can quickly assess results of the clustering in a visual way (I cannot imagine making any sense of looking at phylogenetic tree with 1500 branches, while the graphical output, as on the animation below, is pretty easy to read).

Installing libsbml on Debian (to make iBioSim start)

Bogdan — Sat, 30 Aug 2008 21:38:26 +0000

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:

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