Title: BacArena: Agent based modeling framework for cellular communities
Author: Eugen Bauer and Johannes Zimmermann
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")
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
- glpk header files needed, e.g. for debian install package:
-
Special hints for windows user:
Quick start
library("BacArena")
openArena()
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