Lattice Microbes is a program used to simulate stochastic reaction-diffusions dynamics. It consists of implementations of both the well-stirred chemical master equation (CME) and spatailly-resolved reaction-diffusion master equation (RDME).
jLM is a python/jupyter notebook interface used for constructing cell geomtries and defining reaction and diffusion rules for a RDME simualtion. Experimental data, such as cell organization from cryo-electron tomograms, can be incorporated into simulation cell geometry also using region builder functions.
pyLM is a python interface used to define well-stirred reaction systems without diffusion to be simulated using the CME.
GillespieDSolver is the Gillespie direct chemical master equation solver for well-stirred simulations
MpdRdmeSolver is the base version of the multi-particle diffusion reaction-diffusion master equation solver for spatial simulations
IntMpdRdmeSolver is the MpdRdmeSolver, but particle indexes are stored as 32-bit numbers rather than 8-bit. This is used for systems with many types of molecules and intermediates.
MGPUMpdRdmeSolver is the multi-GPU MpdRdmeSolver which is used to divide the simulation space for one spatial simulation across multiple GPUs.
- Installation guide: Instructions for installing Lattice Microbes.
- User Guide: Tutorial, full Python API description, and usage information.
- Citing Lattice Microbes: How to cite the code.