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:

install.packages("BacArena")

Install the development version:

library(devtools)
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

Sivasan / BacArena