Modelling the Structure and Dynamics of Biological Pathways

Modelling the Structure and Dynamics of Biological Pathways

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...

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Bibliographic Details
Main Authors: O’Hara, Laura, Livigni, Alessandra, Theo, Thanos, Boyer, Benjamin, Angus, Tim, Wright, Derek, Chen, Sz-Hau, Raza, Sobia, Barnett, Mark W., Digard, Paul, Smith, Lee B., Freeman, Tom C.
Format: Online
Language:English
Published: Public Library of Science 2016
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980033/
Description
Summary: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.

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