Python Systems Biology modeling framework
PySB (pronounced "Pie Ess Bee") is a framework for building rule-based mathematical models of biochemical systems. It works nicely with scientific Python libraries such as NumPy, SciPy and SymPy for model simulation and analysis.
PySB depends on the following:
- numpy
- scipy
- sympy
- Perl - http://www.perl.org/get.html
- BioNetGen - http://bionetgen.org/
For full instructions, see the Installation chapter of the manual.
The manual is available online at http://docs.pysb.org/. You can also generate the documentation locally by installing Sphinx and running the following commands:
$ cd doc $ make html
Then open _build/html/index.html in your web browser.