BacArena

Structure of the S4 class "Arena"

Constructor of the S4 class Arena-class

Structure of the S4 class "Bac"

Constructor of the S4 class Bac-class

BacArena: An Agent-Based Modeling Framework for Cellular Communities

Structure of the S4 class "Eval"

Constructor of the S4 class Eval-class

Structure of the S4 class "Human"

Constructor of the S4 class Human-class

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

Structure of the S4 class "Organism"

Constructor of the S4 class Organism-class

Structure of the S4 class "Substance"

Constructor of the S4 class Substance

Add default medium of an organism to arena.

Add minimal medium of an organism to arena.

Function for adding a simulation step

Add individuals to the environment

Add substances to the environment

Function implementing a growth model of a human cell

Change substance concentration patterns in the environment

Function for changing the objective function of the model

Change organisms in the environment

Change substances in the environment

Function to show correlations of a simulated organism or substrate

Function for checking phenotypes in the environment

Function for checking phenotypes in the environment

Function for chemotaxis of bacteria to their prefered substrate

Color palette

Color palette

Color palette

Color palette

Color palette

Color palette

Function for constraining the models based on metabolite concentrations

Function to account for the consumption and production of substances

Change substance concentration patterns in the environment according to a gradient

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

Function for diffusion

Function for diffusion of the Substance matrix

Function for naive diffusion (neighbourhood) of the Substance matrix

Function for parallelzied diffusion

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

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

Function for re-constructing a medium concentrations from simulations

Function for investigation of feeding between phenotypes

Function for investigation of feeding between phenotypes

Function for investigation of feeding between phenotypes

Function for investigation of cross feeding patterns of replicate simulations

Function for searching a keyword in arena organisms and media

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

Find biomass reaction in model

Remove all substances in the environment

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

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

Function to compute and return correlation matrix

Function for getting a matrix of phenotypes from the dataset

Function to extract the phenotype of an organism object

Function to get timeline of a substance

Function for calculated the substrate concentration for every organism

Function to get varying substances

Function for letting organisms grow exponentially

Function for letting organisms grow linearly

Function implementing a growth model of a bacterium

Function implementing a growth model of a bacterium

Computer standard deviation lower bound

Lysis function of organismal cells by adding biomass_compounds to the medium

Function for mining/analyzing phenotypes which occured on the arena

Function for random movement of organisms

Start simulation

Function for computing the linear programming according to the model structure

Plot abundances of species

Function for plotting the overall change as curves

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

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

Plot population flux variations

Plot growth curve for several simulations

Plot number of variation in number of interactions for several simulations

Plot growth curve for several simulations

Plot number of phenotypes curve for several simulations

Function to plot reaction activity for every species

Function to plot substance shadow costs for a specie

Function to plot substance usage for every species

Plot substance curve for several simulations

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

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

Function to plot usage of substances species wise

Plot substance variations

Function for plotting the overall change in reaction activity

Read matlab model

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

Reset plotting screen

Remove substances

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

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

Multi-species test data set

Function for one simulation iteration for objects of Bac class

Function for one simulation iteration for objects of Bac class

Main function for simulating all processes in the environment

Main function for simulating in parallel all processes in the environment

Function for one simulation iteration for objects of Human class

Function for investigating a specific phenotype of an organism

Function for stirring/mixing the complete evironment

Function for unit conversion

Computer standard deviation upper bound