BNSim is an open-source, parallel, stochastic, and multi-scale modeling platform which integrates various simulation algorithms, together with chemotaixs, quorum sensing, and biofilm models in a 3D environment.
BNSim is developed by CMU SLD Group, and released under GPLv2 license Please check http://www.ece.cmu.edu/~sld/ for more information
BNSim is developed using C++ and pthread under Linux and Mac OS
If you use it or part of it for your work, please cite Wei, Guopeng, Paul Bogdan, and Radu Marculescu. "Efficient Modeling and Simulation of Bacteria-Based Nanonetworks with BNSim." Selected Areas in Communications, IEEE Journal on 31.12 (2013): 868-878. Note that if you use Eclipse, please mannually add the link to pthread library, and use -std=c++11 for compilation.
You can build the program easily by importing the source files into Xcode or Eclipse or any other IDE you like.
The simulator is fully extensible, you can add regulatory networks in the library, and different cell types in the zoo.