28 August 2014

Installing libSBML Python bindings on Ubuntu 14.04 LTS

Now that Ubuntu 14.04 has been around a bit now and I have started upgrading my development machines.

One of the first things that always gets installed is the libSBML and its Python bindings which then gives me access to the best library for reading/writing/manipulating Systems Biology Markup Language (SBML) files out there and is critical for my work.

Thanks to the fantastic work done by the development team installation is this easy:

# Python development packages and Pip install system
sudo apt-get install python-dev python-pip

# libSBML dependencies and development libraries
sudo apt-get install libxml2 libxml2-dev
sudo apt-get install zlib1g zlib1g-dev
sudo apt-get install bzip2 libbz2-dev

# libSBML
sudo pip install python-libsbml

That's it, happy modelling (please look up the above packages, before installing them, if you don't know what they are)!

01 August 2014

Modelling with Python

I rediscovered this paper the other day, as far as I know, one of the first published uses of Python/SciPy for modelling cellular metabolism (a.k.a systems biology). Today it looks trivial but considering the time it was written/published it's not too bad.

Modelling cellular processes with Python and Scipy
BG Olivier, JM Rohwer, JHS Hofmeyr - Molecular biology reports, 2002

Unfortunately, the PDF was published as a bitmap so the next step is to transcribe the code contained in the paper and see if it still works ... reproducible research in the life sciences with a paper over 10 years old? Watch this space ...