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

BacArena

DOI:10.1371/journal.pcbi.1005544
CRAN version CRAN downloads CRAN downloads/month twitter

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

Issues

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