Modeling

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Modeling software

Copasi

http://www.copasi.org/tiki-view_articles.php
COmplex PAthway SImulator, for the simulation and analysis of biochemical reaction networks

MCell

http://mcell.org/
spatial Monte-Carlo simulator; integrates with blender to allow visualisation and animation

Model repositories

BioModels Database

http://www.ebi.ac.uk/biomodels-main/
A repository of computational models of biological processes.


Standards

Systems Biology Markup Language (SBML)

http://sbml.org/Main_Page
A community-developed language for encoding biological models; allows sharing of models across tools and platforms

Systems Biology Graphical Notation (SBGN)

http://www.sbgn.org/Main_Page
Standard for graphically representing biological processes


Modeling theory

Multi-state modeling of biomolecules

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003844
Melanie I. Stefan , Thomas M. Bartol, Terrence J. Sejnowski, Mary B. Kennedy
PLoS Comput Biol 10(9): e1003844, 2014