Can be used for simulation of organisms living in
communities (Bauer and Zimmermann (2017)
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:
install.packages("BacArena")
library(devtools)install_github("euba/bacarena")
Special hints for linux user:
libglpk-dev
Special hints for windows user:
library("BacArena")openArena()
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:
Changes:
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
expanded tutorial
renamed growth to biomass in [email protected]
fast stiring
vectorized addOrg
new reactions
Changes:
improved vignette
gut community example data set
improved plotting
github reference: https://github.com/euba/BacArena/commit/67957d833e91d8ba4d118f69f5c3bbe8353ee548
Changes:
parallel support
methods for evaluation of replicates
fixed numerical bugs
fixed growth model
findInArena(), getSubHist()
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
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
initial cran release