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Title: BacArena: Agent based modeling framework for cellular communities
Author: Eugen Bauer and Johannes Zimmermann

BacArena

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:

Each organism is represented individually
Simulation of >10 different species and thousands of organisms on your desktop computer
Diffusion of substances
Screening of phenotypes
Detection of crossfeeding
Chemotaxis
Kinetics of reactions
Separation of simulation and evaluation
Rich evaluation methods (data mining)
Reproducible simulations
Object oriented implementation
Easily expandable due to rule based approach

Installation

Install the latest CRAN release:

install.packages("BacArena")

Install the development version:

library(devtools)
install_github("euba/bacarena")

Special hints for linux user:
- glpk header files needed, e.g. for debian install package: libglpk-dev
Special hints for windows user:
- Besides R you need to install Rtools

Quick start

library("BacArena")
openArena()

matlab models

cobra matlab model files can be imported
tutorial

readMATmod("model.mat")

SBML support

sybilSBML is needed for SBML input
currently sybilSBML is not available on CRAN because the CRAN test servers do not have the latest version of libsbml yet
manual installation of sybilSBML (for linux):

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

Documentation

A tutorial is available: Introduction
Short tutorials are on github gist

Issues

Please report bugs, disorders or features you would like to see: Issues

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Version

Install

install.packages('BacArena')

Monthly Downloads

111

Version

1.8.2

License

GPL-3 | file LICENSE

Maintainer

Johannes Zimmermann

Last Published

May 20th, 2020

Functions in BacArena (1.8.2)

Structure of the S4 class "Arena"

Human-constructor

Constructor of the S4 class Human-class

BacArena: An Agent-Based Modeling Framework for Cellular Communities

Function to check if the there is a free place in the Moore neighbourhood

Bac-Constructor

Constructor of the S4 class Bac-class

Structure of the S4 class "Bac"

Arena-constructor

Constructor of the S4 class Arena-class

Structure of the S4 class "Human"

Eval-constructor

Constructor of the S4 class Eval-class

Substance-constructor

Constructor of the S4 class Substance

Add default medium of an organism to arena.

Function to show correlations of a simulated organism or substrate

Function for re-constructing an Arena object from a simulation step

Function for diffusion

Function for checking phenotypes in the environment

Function for diffusion of the Substance matrix

Function to compute and return correlation matrix

addEssentialMed

Add minimal medium of an organism to arena.

Function implementing a growth model of a human cell

Add substances to the environment

Function for adding a simulation step

Change organisms in the environment

Change substances in the environment

Function to get timeline of a substance

Function for investigation of feeding between phenotypes

Function for re-constructing a medium concentrations from simulations

Function for investigation of feeding between phenotypes

Lysis function of organismal cells by adding biomass_compounds to the medium

Function for calculated the substrate concentration for every organism

Add individuals to the environment

Function for mining/analyzing phenotypes which occured on the arena

Substance-class

Structure of the S4 class "Substance"

Change substance concentration patterns in the environment according to a gradient

Structure of the S4 class "Eval"

Structure of the S4 class "Organism"

Plot growth curve for several simulations

Organism-constructor

Constructor of the S4 class Organism-class

Plot number of phenotypes curve for several simulations

Change substance concentration patterns in the environment

Function for plotting the overall change in reaction activity

Function for transforming the organism data frame to a presence/absence matrix of organisms

Read matlab model

Function for changing the objective function of the model

Function for searching a keyword in arena organisms and media

Function implementing a growth model of a bacterium

findFeeding3rep

Function for investigation of cross feeding patterns of replicate simulations

Function for chemotaxis of bacteria to their prefered substrate

Function for checking phenotypes in the environment

Computer standard deviation lower bound

Function for plotting the overall change as curves

Function for plotting the overall change as curves with maximally distinct colors

Remove substances

Function to account for the consumption and production of substances

Function for plotting spatial and temporal change of populations and/or concentrations

Function to check if the there is a free place in the Moore neighbourhood

Function for constraining the models based on metabolite concentrations

Find biomass reaction in model

Function for parallelzied diffusion

Function for random movement of organisms

Function for naive diffusion (neighbourhood) of the Substance matrix

Function to get all reactions fluxes that are associated with the metabolite of a given exchange reactions

Function for investigation of feeding between phenotypes

Start simulation

Function for letting organisms grow linearly

Function to compute flux variability analysis on an simulation object to get min/max of substance usage

Remove all substances in the environment

Function for selecting phenotypes which occured on the arena from specific iterations and species

Plot number of variation in number of interactions for several simulations

Function to get varying substances

plotGrowthCurve

Plot growth curve for several simulations

Plot substance variations

Function to plot usage of substances species wise

Function for letting organisms grow exponentially

Function for computing the linear programming according to the model structure

Function for one simulation iteration for objects of Bac class

Function to overview the spatial distribution of a substance over time.

Function implementing a growth model of a bacterium

Function to overview the spatial distribution of a substance over time.

Function to set Michaelis-Menten kinetics for uptake of a substance

Function to extract the phenotype of an organism object

Plot abundances of species

Plot population flux variations

Function to plot population level minimum and maximum flux from alternative optimal solutions obtained by FVA

Function for getting a matrix of phenotypes from the dataset

plotSpecActivity

Function to plot substance usage for every species

Plot substance curve for several simulations

plotReaActivity

Function to plot reaction activity for every species

Function to plot substance shadow costs for a specie

Function for reducing the size of an Eval object by collapsing the medium concentrations

Reset plotting screen

Function for stirring/mixing the complete evironment

Function for investigating a specific phenotype of an organism

Function for one simulation iteration for objects of Human class

Multi-species test data set

Function for one simulation iteration for objects of Bac class

Computer standard deviation upper bound

Main function for simulating in parallel all processes in the environment

Main function for simulating all processes in the environment

unit_conversion

Function for unit conversion