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Modelling the Structure and Dynamics of Biological Pathways.

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.

SUBMITTER: O'Hara L

PROVIDER: S-EPMC4980033 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Modelling the Structure and Dynamics of Biological Pathways.

O'Hara Laura L Livigni Alessandra A Theo Thanos T Boyer Benjamin B Angus Tim T Wright Derek D Chen Sz-Hau SH Raza Sobia S Barnett Mark W MW Digard Paul P Smith Lee B LB Freeman Tom C TC

PLoS biology 20160810 8

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 vi ...[more]

PMID: 27509052

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