Install libsbml on Ubuntu

I have changed OS to Ubuntu 8.04(hardy), so everything I installed and configured on my old FedoraCore4 were lost

>_< :-(

Now I'm installing libsbml.

./configure complained that C++ compiler cannot produce executables. So I installed "build-essential".

Then ./configure complained following:
*** Could not find 'xml2-config' in directory yes/bin/.
*** Please check that the PATH supplied to --with-libxml=PATH
*** is of the form '/usr/local' and not '/usr/local/lib'; in
*** other words, omit the 'lib' part of the name. The 'configure'
*** utility will append 'lib' to the given path automatically.

I googled, and installed "libxml2-dev".

Then I configured successfully.
./configure --with-python

But make produces a lot of errors. This is because Python developer tools has not been installed.
apt-get install python-dev

Compilation succeeded this time!

make
make install

ldconfig

After this, run python, run "from libsbml import *", command succeed!

Install Python API to libsbml

I installed Python API to libsbml, the famous SBML library.

First build libsbml with "--with-python" during configure, the libsbml library is installed on /usr/local/lib/ by default, and the Python API is installed on /usr/local/lib/python2.4/site-packages/libsbml;

Then add following line to .bashrc:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
export PYTHONPATH=/usr/local/lib/python2.4/site-packages/libsbml:/usr/local/lib/python2.4/site-packages

This way python can import libsbml!

Mourn the lives lost in earthquake

May 19, 2008. Chinese people all over the country and world wide mourned the lives lost in earthquake.

Following are screenshots of major Chinese websites at the moment. All were in black-and-white.

We Chinese people are one family!

Earthquake strike in Sichuan, China

Strong earthquake struck Sichuan Province, China on May 12th, ~14:00. What can I do to help??


Photo from Xinhua News Agency.

Be a blogger...

I hasten to add a few words to my Blog when I discovered something, so as to be a blogger...

In the coding morning, I ran into one strange problem which kept me scratch hair for an hour...

      file = 'tmp.ode'
      fout = open(file,'w')
      ... (write goodies) ...
      fout.write('done\n')
      subprocess.Popen(['xppaut %s -silent > out 2>err' % file], shell=True).wait()

Obviously I forgot to close the output file object. For me, this has the peculiar effect of disturbing the following system call: the xppaut interpreter simply refused to read the ODE file, which I have found to be readily there on the directory, and contents are all correct.