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agent based modelling
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R improved plotting May 23, 2019
data updated examples and vignette Sep 20, 2018
man improved plotting May 23, 2019
model example update+new poa model Apr 24, 2016
src changed unit of diffusion constant Aug 23, 2017
vignettes updated examples and vignette Sep 20, 2018
.Rbuildignore updated R.buildignore Jan 8, 2016
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DESCRIPTION changed igraph to suggest packages Jun 12, 2019
LICENSE Create LICENSE May 11, 2018
NEWS bacarena 1.8 cran release Feb 15, 2019 Update May 22, 2019


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.


  • 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 latest CRAN release:
  • Install the development version:
  • Special hints for linux user:

    • glpk header files needed, e.g. for debian install package: libglpk-dev
  • Special hints for windows user:

    • Besides R you need to install Rtools

Quick start


matlab models

  • cobra matlab model files can be imported
  • tutorial

SBML support

  • sybilSBML is needed for SBML input
  • currently sybilSBML is not available on CRAN because the CRAN test servers do not have the latest version of libsbml yet
  • manual installation of sybilSBML (for linux):
R CMD INSTALL  sybilSBML_3.0.5.tar.gz



Please report bugs, disorders or features you would like to see: Issues

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