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.packages("BacArena")
library(devtools)
install_github("euba/bacarena")

Quick start

library("BacArena")
openArena()

matlab models

readMATmod("model.mat")

SBML support

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