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.
Special hints for linux user:
Special hints for windows user:
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
Please report bugs, disorders or features you would like to see: Issues
BacArena v.1.8 (Release data: 2019-02-15) Changes:
redefined growth model
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
renamed growth to biomass in [email protected]
gut community example data set
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...
new method statSpec()
fixed bug in addSubs()
new method findFeeding()
fixed bug in addEval()
new method openArena()
initial cran release