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.
- Install the development version:```rlibrary(devtools)install_github("euba/bacarena")
Special hints for linux user:
Special hints for windows user:
A tutorial is available: Introduction
Please report bugs, disorders or features you would like to see: Issues
gut community example data set
github reference: https://github.com/euba/BacArena/commit/67957d833e91d8ba4d118f69f5c3bbe8353ee548
methods for evaluation of replicates
fixed numerical bugs
fixed growth model
advances plotting using ggplot2:
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
new method statSpec()
fixed bug in addSubs()
new method findFeeding()
fixed bug in addEval()
new method openArena()
github reference: https://github.com/euba/BacArena/tree/8ce106f1351af95d387cc70ed2bd1fd18669ed84
initial cran release