BacArena: 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.

Version: 1.8
Depends: R (≥ 3.0.0), sybil (≥ 1.3.0), ReacTran (≥ 1.4.2), deSolve (≥ 1.12), Matrix (≥ 1.2)
Imports: igraph, methods, utils, stats, graphics, ggplot2, reshape2, glpkAPI, plyr, Rcpp
LinkingTo: Rcpp, RcppArmadillo, RcppEigen
Suggests: parallel, knitr, rmarkdown
Published: 2019-02-15
Author: Eugen Bauer [aut], Johannes Zimmermann [aut, cre]
Maintainer: Johannes Zimmermann <j.zimmermann at>
License: GPL-3 | file LICENSE
NeedsCompilation: yes
Materials: README NEWS
CRAN checks: BacArena results


Reference manual: BacArena.pdf
Vignettes: BacArena-Introduction
Package source: BacArena_1.8.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X binaries: r-release: BacArena_1.8.tgz, r-oldrel: BacArena_1.8.tgz
Old sources: BacArena archive


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