Python framework for Systems Biology modeling
Python Other
Latest commit f09a049 Jan 11, 2017 @jmuhlich jmuhlich committed on GitHub Fix SBML export species id mismatch with leading underscores (#237)
The SBML exporter makes some assumptions about how PySB names species,
and this changed in the BNG interface code which creates the species
but wasn't updated to match here.



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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:

For full instructions, see the Installation chapter of the manual at


The manual is available online at 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.