README.md

In Waschina/Eutropia: Agent-based modelling of microbial communities in time and continuous µ-meter-scale space

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 :bouquet:

• 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)

Waschina/Eutropia documentation built on Jan. 4, 2023, 12:42 p.m.