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From 2011.igem.org

CellDesigner is graphical simulation package that can model simple cellular mechanics that is pretty but not very usefull. While it has a superb graph and network drawing options. It has relativly limited visualisation options for simulations. It biggest shortcomming is that the mathematics that can be used to define the reaction speeds are rather limited. There are no options for stogastic implementations so checking the robustness of your circiut will be a tedious process.