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

SUBMITTER: Lopez CF 

PROVIDER: S-EPMC3588907 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature