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Modeling software

COmplex PAthway SImulator, for the simulation and analysis of biochemical reaction networks

spatial Monte-Carlo simulator; integrates with blender to allow visualisation and animation

Model repositories

BioModels Database
A repository of computational models of biological processes.


Systems Biology Markup Language (SBML)
A community-developed language for encoding biological models; allows sharing of models across tools and platforms

Systems Biology Graphical Notation (SBGN)
Standard for graphically representing biological processes

Modeling theory

Multi-state modeling of biomolecules
Melanie I. Stefan , Thomas M. Bartol, Terrence J. Sejnowski, Mary B. Kennedy
PLoS Comput Biol 10(9): e1003844, 2014