PySB

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Python Systems Biology modeling framework

http://pysb.org/

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.

Installation

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 at http://docs.pysb.org/en/latest/installation.html

Documentation

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.