Lattice Microbes

Lattice Microbes is a software package for efficiently sampling trajectories from the chemical and reaction-diffusion master equations (CME/RDME) on high performance computing (HPC) infrastructure using both exact and approximate methods.

Our recent publication provides an overview of the software. In any publication of scientific results based completely or in part on the use of Lattice Microbes, please reference:

Elijah Roberts, John E Stone, and Zaida Luthey-Schulten.
Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation, J. Comput. Chem., 34(3):245-255, 2013.

Other publications describing and/or using the software:

E. Roberts, A. Magis, J.O. Ortiz, W. Baumeister, and Z. Luthey-Schulten
Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study
PLoS. Comput. Biol., 7(3):e1002010, 2011

E. Roberts, J.E. Stone, L. Sepulveda, W.W. Hwu, and Z. Luthey-Schulten
Long time-scale simulations of in vivo diffusion using GPU hardware
In Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing, 2009

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Documentation

Source Code

Binaries-LINUX

Binaries-MacOSX

Binaries-VMD Plugins

Old Versions

  • Old versions can be found here.

Support

Please visit our support forums at http://sourceforge.net/projects/latticemicrobes/forums for assistance with installing and using the software.

Cloud Computing

A Lattice Microbes virtual machine is available for Amazon EC2 under the public AMI name "LatticeMicrobes".

Funding

This work was partially supported by the Department of Energy Office of Science (BER) [DE-FG02-10ER6510], the National Institutes of Health through the Center for Macromolecular Modeling and Bioinformatics [NIH-RR005969], and the National Science Foundation [MCB08-44670].