![]() Download 3DdFBA_Tools (continuumColony v 1.1).This download also contains useful MATLAB files for generating input FBA tables and viewing simulation data, as well as a user guide. (2015) Spatially-Resolved Metabolic Cooperativity Within Dense Bacterial Colonies. Note: This script requires the use of the COBRA toolbox, which is freely available here:ĬontinuumColony for 3DdFBA colony simulationsĬontinuumColony Includes a compressed directory containing source code for simulating the growth of a colony using the 3DdFBA methodology described in:Ĭole JA, Kohler L, Hedhli J, and Luthey-Schulten Z. Please download both the script (populationFBA_ZLS.m) and data (populationFBA_ZLS_Data.mat) files: Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population. A detailed description of this methodology can be found in: coli, and uses them to set constraints on reaction fluxes throughout a comprehensive model of metabolism. PopulationFBA includes a Matlab script and data file which, when run, samples the copy number distributions of over 350 metabolic proteins in E. In Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing, 2009 Long time-scale simulations of in vivo diffusion using GPU hardware Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation StudyĮ. Lattice Microbes: high-performance stochastic simulations of the reaction-diffusion master equationĮ. ![]() Representative papers related to Lattice Microbes/pyLM :Įlijah Roberts, John E Stone, and Zaida Luthey-Schulten. Along with it, the pyLM problem solving environment allows for customizable simulations.įor more information, see the Lattice Microbes/pyLM home page. 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. ![]()
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