title: 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.
authors: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, Scotland, United Kingdom.|MRC Centre for Reproductive Health, University of Edinburgh, The Queen's Medical Research Institute, Edinburgh, United Kingdom.
authors: Laura
authors: L
authors: O'Hara
authors: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, Scotland, United Kingdom.
authors: Alessandra
authors: A
authors: Livigni
authors: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, Scotland, United Kingdom.
authors: Thanos
authors: 0000-0001-8421-8581
authors: T
authors: Theo
authors: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, Scotland, United Kingdom.
authors: Benjamin
authors: 0000-0003-2414-8731
authors: B
authors: Boyer
authors: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, Scotland, United Kingdom.
authors: Tim
authors: 0000-0003-1736-9456
authors: T
authors: Angus
authors: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, Scotland, United Kingdom.
authors: Derek
authors: 0000-0003-0411-4497
authors: D
authors: Wright
authors: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, Scotland, United Kingdom.
authors: Sz-Hau
authors: SH
authors: Chen
authors: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, Scotland, United Kingdom.
authors: Sobia
authors: S
authors: Raza
authors: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, Scotland, United Kingdom.
authors: Mark W
authors: 0000-0002-3066-9747
authors: MW
authors: Barnett
authors: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, Scotland, United Kingdom.
authors: Paul
authors: P
authors: Digard
authors: MRC Centre for Reproductive Health, University of Edinburgh, The Queen's Medical Research Institute, Edinburgh, United Kingdom.
authors: Lee B
authors: LB
authors: Smith
authors: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, Scotland, United Kingdom.
authors: Tom C
authors: TC
authors: Freeman
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D006801:Humans; D008954:Models, Biological; D015203:Reproducibility of Results; D015398:Signal Transduction