Modeling Framework for Cellular Communities in their Environments

Can be used for simulation of organisms living in communities (Bauer and Zimmermann (2017) ). 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

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()

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

News

BacArena v.1.8 (Release data: 2019-02-15) Changes:

improved detection of limiting substances (shadow costs)
shadow costs analysis now possible with cplex, too
support for non-default objective functions
fixed interaction finding in findfeeding3()
occupied arena cells valid also for human cells (bug in emptyHood)

github reference: https://github.com/euba/BacArena/releases/tag/v1.8

BacArena v.1.7 (Release date: 2018-05-09)

Changes:

fine-tuning on growth model
- several duplications per time step
- fixed no growth bug for very high accumulated biomass
improved handling of non-biomass objectives
better status printing
more then one compound in chemotaxis
wrong unit of diffusion constant
several small updated in plotting methods

github reference: https://github.com/euba/BacArena/releases/tag/v1.7

BacArena v.1.6 (Release date: 2017-03-21)

Changes:

redefined growth model
- max cell weight value is used as upper bound for biomass reaction to avoid biomass accumulation in case of overcrowding
- deathrate is now scaled according to time steps
fixed several issues related to grid geometry (relevant for non-square grids)
handling of alternative solutions with flux variability analysis
diffusion and advection can be blocked for occupied cells
corrected bugs related to continuing of simulations
expanded tutorial
renamed growth to biomass in [email protected]
fast stiring
vectorized addOrg
new reactions
- plotReaActivity (plot reaction activity)
- findRxnFlux (find usage of metabolite in reactions)
- plotSubDist, plotSubDist2 (plot spatial distribution for substances)

github reference: https://github.com/euba/BacArena/tree/v1.6

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