BacArena is an agent based modeling framework for cellular communities.
Existing genome-scale metabolic models can be used to simulate growth and interactions in time and space. In BacArena two well established methods are merged: a) Flux balance analysis to predict the activity of metabolic reactions and b) Agent based modelling in order to provide an environment.
It has been efficiently implemented in R language (with some C++ routines) and is freely available CRAN.
Features: - Each organism is represented individually - Simulation of >10 different species and thousands of organisms on your desktop computer - Diffusion of substances - Screening of phenotypes - Detection of crossfeeding - Chemotaxis - Kinetics of reactions - Separation of simulation and evaluation - Rich evaluation methods (data mining) - Reproducible simulations - Object oriented implementation - Easily expandable due to rule based approach
- Install the development version: ```r library(devtools) install_github("euba/bacarena")
glpk header files needed, e.g. for debian install package: libglpk-dev
Special hints for windows user:
A tutorial is available: Introduction
Please report bugs, disorders or features you would like to see: Issues
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