Modelling the Structure and Dynamics of Biological Pathways

PLoS Biol. 2016 Aug 10;14(8):e1002530. doi: 10.1371/journal.pbio.1002530. eCollection 2016 Aug.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Computational Biology / methods*
  • Computer Simulation
  • Humans
  • Models, Biological*
  • Reproducibility of Results
  • Signal Transduction*