Modeling Framework for Cellular Communities in their Environments

Can be used for simulation of organisms living in communities. Each organism is represented individually and genome scale metabolic models determine the uptake and release of compounds. Biological processes such as movement, diffusion, chemotaxis and kinetics are available along with data analysis techniques.


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
  • Install the latest release:

install.packages("BacArena")

 
- Install the development version:
  ```r
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
library("BacArena")
openArena()

A tutorial is available: Introduction

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

News

BacArena v1.5.1 (Release date: 2016-07-20)

Changes:

  • improved vignette

  • gut community example data set

  • improved plotting

  • github reference: https://github.com/euba/BacArena/commit/67957d833e91d8ba4d118f69f5c3bbe8353ee548

BacArena v1.5 (Release date: 2016-07-13)

Changes:

  • parallel support

  • methods for evaluation of replicates

  • fixed numerical bugs

  • fixed growth model

  • findInArena(), getSubHist()

  • advances plotting using ggplot2:

    • plotSubCurve(), plotGrowthCurve(), plotPhenCurve()
    • plotAbundances(), plotSpecActivity(), plotSubUsages()
  • integration of shadow prices

  • addDefaultMed() and addEssentialMed()

  • imporved cross feeding detection

  • alternative objectives integration

  • lots of smaller bugfixes...

  • github reference: https://github.com/euba/BacArena/commit/5416fb09d82cbe87bcd701cc7bf389c6116e57ee

BacArena v1.0.1 (Release date: 2016-01-06)

Changes:

  • new method statSpec()

  • fixed bug in addSubs()

  • new method findFeeding()

  • fixed bug in addEval()

  • new method openArena()

  • corrected vignette

  • github reference: https://github.com/euba/BacArena/tree/8ce106f1351af95d387cc70ed2bd1fd18669ed84

BacArena v1.0 (Release date: 2015-12-08)

initial cran release

  • github reference: https://github.com/euba/BacArena/tree/8bf7459530c4a8eda9040e8feb2fa416dea55ab2

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("BacArena")

1.5.1 by Johannes Zimmermann, 7 months ago


https://github.com/euba/BacArena


Report a bug at https://github.com/euba/BacArena/issues


Browse source code at https://github.com/cran/BacArena


Authors: Eugen Bauer [aut], Johannes Zimmermann [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports igraph, methods, utils, stats, graphics, ggplot2, reshape2, glpkAPI, Rcpp

Depends on sybil, ReacTran, deSolve, Matrix

Suggests sybilSBML, knitr, rmarkdown

Linking to Rcpp, RcppArmadillo, RcppEigen


See at CRAN