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biological_systems:sim [Wednesday, 11 March 2009 : 11:26:22]
s040995 created
biological_systems:sim [Wednesday, 11 March 2009 : 13:21:14] (current)
s040995
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 +====== Simulators ​ ======
 +  * [[Chi:​start|Chi]]
 +    *[[:​vanbeek:​jlap05|Syntax and consistent equation semantics (article published in JLAP, 2006)]] ​
 +    * Timed Chi
 +      * {{:​chi:​chi10_refman1689.pdf|Chi 1.0 reference manual}} (23 aug 2007)
 +      * {{:​chi:​learningchi_main.pdf|Learning timed chi}} - Chi user manual (August 2007)
 +    * Hybrid Chi
 +      * {{:​chi:​thesis_ramon.pdf|Formal specification and analysis of hybrid systems (PhD thesis K.L. Man and R.R.H. Schiffelers,​ 2006)}}
 +      * {{:​4c650:​simhchi.pdf|Analysis of hybrid systems using Chi (lecture notes 4C650, D.A. van Beek and J.E. Rooda, 2007)}}
 +  ​
 +  * [[http://​www.copasi.org/​tiki-index.php|COPASI]]:​ Complex Pathway Simulator ​
 +    *[[http://​ieeexplore.ieee.org/​stamp/​stamp.jsp?​arnumber=04117803|PDF]]:​Simulation of biochemical networks using COPASI - a complex pathway simulator
 +    *[[http://​www.copasi.org/​tiki-download_file.php?​fileId=103|User Guide]]
 +    *[[http://​projects.eml.org/​downloads/​copasi/​CopasiTutorial.pdf |Tutorial]]
  
 +  * MATLAB ​
 +    * [[http://​www.sbtoolbox2.org/​|SBTOOLBOX2]]:​ System Biology Toolbox for MATLAB
 +      *[[http://​www.sbtoolbox2.org/​main.php?​display=tutorials|Tutorial]]
 +      *[[http://​www.sbtoolbox2.org/​main.php?​display=documentationSBT&​menu=overview|Documentation]]
 +      *[[http://​www.sbtoolbox2.org/​main.php?​display=download|Download]]
 +
 +  * [[http://​www.molsci.org/​~lok/​moleculizer/​ |MOLECULIZER]]:​ Simulating Cellular Reaction Networks
 +    *[[http://​www.molsci.org/​~lok/​moleculizer/​moleculizer-doc/​index.html|Documentation]]
 +    *[[http://​www.molsci.org/​~lok/​moleculizer/​demo/​demos.html|Demo gallery]]
 +    *[[http://​www.molsci.org/​~lok/​moleculizer/​downloads/​index.html|Downloads]]
 +
 +  * [[http://​www.pdn.cam.ac.uk/​groups/​comp-cell/​StochSim.html|STOCHSIM]]:​ A stochastic simulator of (bio)chemical reactions ​
 +    * [[http://​bioinformatics.oxfordjournals.org/​cgi/​reprint/​17/​6/​575|PDF]]
 +    * [[http://​sourceforge.net/​projects/​stochsim/​|Download]]
 +   
biological_systems/sim.txt · Last modified: Wednesday, 11 March 2009 : 13:21:14 by s040995