README.md

In euba/BacArena: Modeling Framework for Cellular Communities in their Environments

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

euba/BacArena documentation built on March 27, 2024, 2:33 p.m.