Modelling the structure and dynamics of biological pathways

Laura O'Hara, Alessandra Livigni, Thanos Theocharidis, Benjamin Boyer, Tim Angus, Derek Wright, Sz-Hau Chen, Sobia Raza, Mark Barnett, Paul Digard, Lee B. Smith, Thomas Freeman

Research output: Contribution to journalArticlepeer-review


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 accessible biological information, a stochastic flow algorithm that simulates the dynamics of pathway activity, and a 3D visualization 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.
Original languageEnglish
Pages (from-to)1-16
JournalPLoS Biology
Issue number8
Publication statusPublished - 10 Aug 2016


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