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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 release:

install.packages("BacArena")


- Install the development version:
  ```r
library(devtools)
install_github("euba/bacarena")

Special hints for windows user
- Besides R you need to install Rtools

Quick start

library("BacArena")
openArena()

Documentation

A tutorial is available: Introduction

Issues

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

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Version

Install

install.packages('BacArena')

Monthly Downloads

61

Version

1.0.1

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/euba/BacArena

Maintainer

Johannes Zimmermann

Last Published

January 6th, 2016

Functions in BacArena (1.0.1)

Function for one simulation iteration for objects of Bac class

Function for chemotaxis of bacteria to their prefered substrate

Function implementing a growth model of a bacterium

Structure of the S4 class "Human"

Function implementing a growth model of a human cell

Function for checking phenotypes in the environment

Function for getting a matrix of phenotypes from the dataset

Function for computing the linear programming according to the model structure

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

Function for adding a simulation step

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

Function for letting organisms grow linearly

Function for plotting the overall change as curves

Change substance concentration patterns in the environment according to a gradient

Function for stirring/mixing the complete evironment

Structure of the S4 class "Eval"

Change organisms in the environment

Substance-class

Structure of the S4 class "Substance"

Function for letting organisms grow exponentially

Function for diffusion of the Substance matrix

Function for mining/analyzing phenotypes which occured on the arena

Function for one simulation iteration for objects of Human class

Eval-constructor

Constructor of the S4 class Eval-class

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

Structure of the S4 class "Bac"

Remove all substances in the environment

Function to show correlations of a simulated organism or substrate

Change substances in the environment

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

Function for calculated the substrate concentration for every organism

Function for constraining the models based on metabolite concentrations

Function for investigating a specific phenotype of an organism

Add individuals to the environment

Function to extract the phenotype of an organism object

BacArena: An Agent-Based Modeling Framework for Cellular Communities

Function for plotting the overall change in reaction activity

Bac-Constructor

Constructor of the S4 class Bac-class

Function to account for the consumption and production of substances

Function for random movement of organisms

Function for re-constructing a medium concentrations from simulations

Structure of the S4 class "Arena"

Human-constructor

Constructor of the S4 class Human-class

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

Function for changing the objective function of the model

Structure of the S4 class "Organism"

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

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

Main function for simulating all processes in the environment

Start simulation

Function for naive diffusion (neighbourhood) of the Substance matrix

Change substance concentration patterns in the environment

Organism-constructor

Constructor of the S4 class Organism

Add substances to the environment

Function to compute and return correlation matrix

Arena-constructor

Constructor of the S4 class Arena-class

Substance-constructor

Constructor of the S4 class Substance

Function for investigation of feeding between phenotypes

Lysis function of organismal cells by adding biomass_compounds to the medium