Title: BacArena: Agent based modeling framework for cellular communities
Author: Eugen Bauer and Johannes Zimmermann

BacArena

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

Installation

• Install the latest CRAN release (currently not available):

  install.packages("BacArena")

• Install the development version:

  library(devtools)
  install_github("SysBioChalmers/sybil")
  install_github("euba/bacarena")

• 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

library("BacArena")
openArena()

matlab models

• cobra matlab model files can be imported
• tutorial

  readMATmod("model.mat")

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):

  wget https://www.cs.hhu.de/fileadmin/redaktion/Oeffentliche_Medien/Fakultaeten/Mathematisch-Naturwissenschaftliche_Fakultaet/Informatik/Bioinformatik/sybilSBML_3.0.5.tar.gz
  R CMD INSTALL  sybilSBML_3.0.5.tar.gz

Documentation

• A tutorial is available: Introduction
• Short tutorials are on github gist

Issues

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