DESCRIPTION

Cyto-Sim is a free downloadable software prototype for non commercial purposes (see below) upon acceptance of this licence. Cyto-Sim is a stochastic simulator of biochemical processes in hierarchical compartments. The compartments may be isolated or may communicate via peripheral and integral membrane proteins. The native syntax is designed to be a compact and intuitive way of describing chemical systems. Arbitrary kinetic rate functions are permitted, allowing seamless import and export to SBML. Export to Matlab is also facilitated.

Two versions of Cyto-Sim are available: an applet and a standalone version with greater functionality.

SCREENSHOTS

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ReleaseSelect VersionCyto-Sim for Java VM 1.6

 

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Other resources

• Cyto-Sim applet
• Cyto-Sim applet interface quick reference guide
• Example oscillatory models
• Technical report describing the Cyto-Sim model

REFERENCES

• Sean Sedwards & Tommaso Mazza
  Cyto-Sim: A formal language model and stochastic simulator of membrane-enclosed biochemical processes, Bioinformatics, 23:20 (Oct. 15 2007), 2800-2802.


• Matteo Cavaliere & Sean Sedwards
  Modelling cellular processes using Membrane Systems with peripheral and integral proteins, Lecture Notes in Computer Science, 4210 (Oct. 11 2006), 108-126.

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