title: Programming biological models in Python using PySB.
abstract: 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.
authors: Department of Cancer Biology, Center for Quantitative Sciences,                     Vanderbilt University School of Medicine, Nashville,                     TN, USA.
authors: Carlos F
authors: CF
authors: Lopez
authors: Jeremy L
authors: JL
authors: Muhlich
authors: John A
authors: JA
authors: Bachman
authors: Peter K
authors: PK
authors: Sorger
mesh_terms: D017209:Apoptosis / Q000502:physiology; D003198:Computer Simulation; D008928:Mitochondria / Q000502:physiology; D008954:Models, Biological; D011381:Programming Languages; D019253:Proto-Oncogene Proteins c-bcl-2 / Q000502:physiology; D012984:Software
chemical_list: D019253:Proto-Oncogene Proteins c-bcl-2