Eutropia

Agent-based metabolic modelling of microbial communities in time and continuous µ-meter-scale space

What is Eutropia

Eutropia is a R-package for cell agent-based metabolic modelling of microbial communities. It allows dynamic simulations of two-dimensional surface-attached cell communities. A few features of Eutropia, that you might find interesting:

Complex polygons (also non-convex) as growth environment
Extracellular enzymes
Nutrient regimes
Chemotaxis (attracting and repelling)
Direct calculations of community assortment and segregation (see e.g. Yanni et al. (2015) Current Biology)

Installation

Eutropia is in its development phase. The current development version can be installed using:

# install.packages("devtools")
devtools::install_github("Waschina/Eutropia")

If you have not installed devtools yet, just uncomment the first line.

Getting started

For an example simulation, please have a look at the package's vignette.

Some tricks to increase performance

For the individual Flux-Balance-Analysis steps, Eutropia requires a LP-solver. Ideally, the GLPK (GNU Linear Programming Kit) together with the R-interface-package glpkAPI should work. If you like to speed up the simulations, you could consider installing IBM's ILOG CPLEX Optimization Studio along with the R-interface-package cplexAPI. If you are in academia, make sure to check out IBM's academic initiative. Installing the R-package cplexAPI can sometimes be a bit tricky, so we'd suggest to get the latest version here and following the install instructions.

A big Thank You 💐

To the developers and maintainers of the sybil-universe (sybil, glpkAPI, cplexAPI, and sybilSBML). R is a better place with those packages. If you use Eutropia, please make sure to give credits to sybil by citing: Gelius-Dietrich, G., Desouki, A.A., Fritzemeier, C.J., Lercher, M.J. sybil – Efficient constraint-based modelling in R. BMC Syst Biol 7, 125 (2013). https://doi.org/10.1186/1752-0509-7-125
To everyone behind GLPK (GNU Linear Programming Kit)