Open AccessProgramming biological models in Python using PySB
Author(s) -
Lopez Carlos F,
Muhlich Jeremy L,
Bachman John A,
Sorger Peter K
Publication year - 2013
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb.2013.1
Subject(s) - python (programming language) , computer science , software , software engineering , programming language , leverage (statistics) , extensibility , macro , biological network , biology , computational biology , artificial intelligence
Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule‐based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule‐based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high‐level, action‐oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open‐source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis.