Modelling the Structure and Dynamics of Biological Pathways

Laura O’Hara, Alessandra Livigni, Thanos Theo, Benjamin Boyer, Tim Angus, Derek Wright, Sz-Hau Chen, Sobia Raza, Mark W Barnett, Paul Digard, Lee B Smith and Tom C Freeman

PLOS Biology, 2016, vol. 14, issue 8, 1-16

Abstract: There is a need for formalised diagrams that both summarise current biological pathway knowledge and support modelling approaches that explain and predict their behaviour. Here, we present a new, freely available modelling framework that includes a biologist-friendly pathway modelling language (mEPN), a simple but sophisticated method to support model parameterisation using available biological information; a stochastic flow algorithm that simulates the dynamics of pathway activity; and a 3-D visualisation engine that aids understanding of the complexities of a system’s dynamics. We present example pathway models that illustrate of the power of approach to depict a diverse range of systems.This Community Page presents a biologist-friendly method for compiling detailed graphical models of biological pathways from the literature, including their subsequent parameterization for use in dynamic simulations of their activity.

Date: 2016
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pbio00:1002530

DOI: 10.1371/journal.pbio.1002530

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