pysb.org - Welcome to PySB: Systems biology modeling in Python

home > domains > pysb.org

Example domain paragraphs

PySB is a framework for building mathematical models of biochemical systems as Python programs. PySB abstracts the complex process of creating equations describing interactions among multiple proteins or other biomolecules into a simple and intuitive domain specific programming language (see example below), which is internally translated into BioNetGen or Kappa rules and from there into systems of equations. PySB makes it straightforward to divide models into modules and to call libraries of reusable elemen

For further information, please see the following publication:

Lopez, C. F., Muhlich, J. L., Bachman, J. A. & Sorger, P. K. Programming biological models in Python using PySB . Mol Syst Biol 9, (2013). doi: 10.1038/msb.2013.1

Links to pysb.org (3)

• indra.readthedocs.io INDRA documentation — INDRA 1.22.0 documentation
• earm.readthedocs.io Extrinsic Apoptosis Reaction Model (EARM) — EARM 2.0 documentation
• sorgerlab.org Sorger Lab