An increasing number of research studies are combining experimental measurements of a particular process or phenomenon with mathematical models of it, frequently toggling between the two to yield a detailed quantitative understanding. Such models are typically written as equations, which can be difficult and tedious to modify without error or to share. Lopez et al. now describe an open-source framework, PySB, in which the biological models are Python programs. PySB is interoperable with the rule-based languages BioNetGen and Kappa. The resulting models will benefit from popular Python tools for documentation, analysis, visualization and sharing.
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Biological models in Python. Nat Methods 10, 384 (2013). https://doi.org/10.1038/nmeth.2460
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DOI: https://doi.org/10.1038/nmeth.2460