BacArena: Modeling Framework for Cellular Communities in their Environments

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Can be used for simulation of organisms living in communities. Each organism is represented individually and genome scale metabolic models determine the uptake and release of compounds. Biological processes such as movement, diffusion, chemotaxis and kinetics are available along with data analysis techniques.

Author
Eugen Bauer [aut], Johannes Zimmermann [aut, cre]
Date of publication
2016-12-05 18:28:46
Maintainer
Johannes Zimmermann <j.zimmermann@iem.uni-kiel.de>
License
GPL-3
Version
1.5.1
URLs

View on CRAN

Man pages

addDefaultMed
Add default medium of an organism to arena.
addEssentialMed
Add minimal medium of an organism to arena.
addEval
Function for adding a simulation step
addOrg
Add individuals to the environment
addSubs
Add substances to the environment
Arena-class
Structure of the S4 class "Arena"
Arena-constructor
Constructor of the S4 class 'Arena-class'
Bac
Structure of the S4 class "Bac"
BacArena
BacArena: An Agent-Based Modeling Framework for Cellular...
Bac-Constructor
Constructor of the S4 class 'Bac-class'
cellgrowth
Function implementing a growth model of a human cell
changeDiff
Change substance concentration patterns in the environment
changeFobj
Function for changing the objective function of the model
changeOrg
Change organisms in the environment
changeSub
Change substances in the environment
checkCorr
Function to show correlations of a simulated organism or...
checkPhen
Function for checking phenotypes in the environment
checkPhen_par
Function for checking phenotypes in the environment
chemotaxis
Function for chemotaxis of bacteria to their prefered...
colpal1
Color palette
colpal2
Color palette
colpal3
Color palette
colpal4
Color palette
colpal5
Color palette
colpal6
Color palette
constrain
Function for constraining the models based on metabolite...
consume
Function to account for the consumption and production of...
createGradient
Change substance concentration patterns in the environment...
dat2mat
Function for transforming the organism data frame to a...
diffuse
Function for diffusion
diffuse_par
Function for parallelzied diffusion
diffusePDE
Function for diffusion of the Substance matrix
diffuseR
Function for naive diffusion (neighbourhood) of the Substance...
emptyHood
Function to check if the there is a free place in the Moore...
evalArena
Function for plotting spatial and temporal change of...
Eval-class
Structure of the S4 class "Eval"
Eval-constructor
Constructor of the S4 class 'Eval-class'
extractMed
Function for re-constructing a medium concentrations from...
findFeeding
Function for investigation of feeding between phenotypes
findFeeding2
Function for investigation of feeding between phenotypes
findFeeding3
Function for investigation of feeding between phenotypes
findInArena
Function for searching a keyword in arena organisms and media
flushSubs
Remove all substances in the environment
getArena
Function for re-constructing an Arena object from a...
getCorrM
Function to compute and return correlation matrix
getPhenoMat
Function for getting a matrix of phenotypes from the dataset
getPhenotype
Function to extract the phenotype of an organism object
getSubHist
Function to get timeline of a substance
getSublb
Function for calculated the substrate concentration for every...
getVarSubs
Function to get varying substances
growExp
Function for letting organisms grow exponentially
growLin
Function for letting organisms grow linearly
growth
Function implementing a growth model of a bacterium
growth_par
Function implementing a growth model of a bacterium
Human
Structure of the S4 class "Human"
Human-constructor
Constructor of the S4 class 'Human-class'
lsd
Computer standard deviation lower bound
lysis
Lysis function of organismal cells by adding...
minePheno
Function for mining/analyzing phenotypes which occured on the...
move
Function for random movement of organisms
NemptyHood
Function to check if the there is a free place in the Moore...
openArena
Start simulation
optimizeLP
Function for computing the linear programming according to...
Organism-class
Structure of the S4 class "Organism"
Organism-constructor
Constructor of the S4 class 'Organism'
plotAbundance
Plot abundances of species
plotCurves
Function for plotting the overall change as curves
plotCurves2
Function for plotting the overall change as curves with...
plotFluxVar
Plot population flux variations
plotGrowthCurve
Plot growth curve for several simulations
plotInterNum
Plot number of variation in number of interactions for...
plotPhenCurve
Plot growth curve for several simulations
plotPhenNum
Plot number of phenotypes curve for several simulations
plotShadowCost
Function to plot substance shadow costs for a specie
plotSpecActivity
Function to plot substance usage for every species
plotSubCurve
Plot substance curve for several simulations
plotSubUsage
Function to plot usage of substances species wise
plotSubVar
Plot substance variations
plotTotFlux
Function for plotting the overall change in reaction activity
redEval
Function for reducing the size of an Eval object by...
reset_screen
Reset plotting screen
rmSubs
Remove substances
selPheno
Function for selecting phenotypes which occured on the arena...
setKinetics
Function to set Michaelis-Menten kinetics for uptake of a...
sihumi_test
Multi-species test data set
simBac
Function for one simulation iteration for objects of Bac...
simBac_par
Function for one simulation iteration for objects of Bac...
simEnv
Main function for simulating all processes in the environment
simEnv_par
Main function for simulating in parallel all processes in the...
simHum
Function for one simulation iteration for objects of Human...
statPheno
Function for investigating a specific phenotype of an...
stirEnv
Function for stirring/mixing the complete evironment
Substance
Structure of the S4 class "Substance"
Substance-constructor
Constructor of the S4 class 'Substance'
usd
Computer standard deviation upper bound

Files in this package

BacArena
BacArena/inst
BacArena/inst/doc
BacArena/inst/doc/BacArena-Introduction.R
BacArena/inst/doc/BacArena-Introduction.Rmd
BacArena/inst/doc/BacArena-Introduction.pdf
BacArena/src
BacArena/src/diff.cpp
BacArena/src/move.cpp
BacArena/src/addBac.cpp
BacArena/src/duplicate.cpp
BacArena/src/RcppExports.cpp
BacArena/NAMESPACE
BacArena/NEWS
BacArena/data
BacArena/data/colpal.rda
BacArena/data/sihumi_test.rda
BacArena/data/datalist
BacArena/R
BacArena/R/data.R
BacArena/R/BacArena.R
BacArena/R/Substance.R
BacArena/R/RcppExports.R
BacArena/R/Stuff.R
BacArena/R/Organism.R
BacArena/R/Arena.R
BacArena/vignettes
BacArena/vignettes/BacArena-Introduction.Rmd
BacArena/README.md
BacArena/MD5
BacArena/build
BacArena/build/vignette.rds
BacArena/DESCRIPTION
BacArena/man
BacArena/man/changeDiff.Rd
BacArena/man/checkPhen.Rd
BacArena/man/growExp.Rd
BacArena/man/getPhenoMat.Rd
BacArena/man/extractMed.Rd
BacArena/man/diffusePDE.Rd
BacArena/man/colpal1.Rd
BacArena/man/lsd.Rd
BacArena/man/Arena-constructor.Rd
BacArena/man/getVarSubs.Rd
BacArena/man/findFeeding.Rd
BacArena/man/Human.Rd
BacArena/man/addSubs.Rd
BacArena/man/Human-constructor.Rd
BacArena/man/createGradient.Rd
BacArena/man/setKinetics.Rd
BacArena/man/plotFluxVar.Rd
BacArena/man/growLin.Rd
BacArena/man/usd.Rd
BacArena/man/colpal5.Rd
BacArena/man/Eval-class.Rd
BacArena/man/simEnv_par.Rd
BacArena/man/plotAbundance.Rd
BacArena/man/emptyHood.Rd
BacArena/man/rmSubs.Rd
BacArena/man/minePheno.Rd
BacArena/man/plotCurves.Rd
BacArena/man/chemotaxis.Rd
BacArena/man/findInArena.Rd
BacArena/man/Substance-constructor.Rd
BacArena/man/colpal3.Rd
BacArena/man/dat2mat.Rd
BacArena/man/plotPhenNum.Rd
BacArena/man/getSublb.Rd
BacArena/man/flushSubs.Rd
BacArena/man/findFeeding3.Rd
BacArena/man/selPheno.Rd
BacArena/man/consume.Rd
BacArena/man/plotInterNum.Rd
BacArena/man/cellgrowth.Rd
BacArena/man/simEnv.Rd
BacArena/man/constrain.Rd
BacArena/man/Bac-Constructor.Rd
BacArena/man/optimizeLP.Rd
BacArena/man/checkPhen_par.Rd
BacArena/man/plotGrowthCurve.Rd
BacArena/man/plotSubCurve.Rd
BacArena/man/Organism-class.Rd
BacArena/man/plotTotFlux.Rd
BacArena/man/findFeeding2.Rd
BacArena/man/colpal2.Rd
BacArena/man/simHum.Rd
BacArena/man/lysis.Rd
BacArena/man/evalArena.Rd
BacArena/man/plotPhenCurve.Rd
BacArena/man/growth_par.Rd
BacArena/man/colpal4.Rd
BacArena/man/getPhenotype.Rd
BacArena/man/plotSpecActivity.Rd
BacArena/man/simBac.Rd
BacArena/man/addOrg.Rd
BacArena/man/getSubHist.Rd
BacArena/man/growth.Rd
BacArena/man/Organism-constructor.Rd
BacArena/man/changeFobj.Rd
BacArena/man/NemptyHood.Rd
BacArena/man/changeSub.Rd
BacArena/man/changeOrg.Rd
BacArena/man/plotSubVar.Rd
BacArena/man/addEssentialMed.Rd
BacArena/man/addDefaultMed.Rd
BacArena/man/checkCorr.Rd
BacArena/man/diffuse_par.Rd
BacArena/man/diffuse.Rd
BacArena/man/simBac_par.Rd
BacArena/man/statPheno.Rd
BacArena/man/diffuseR.Rd
BacArena/man/openArena.Rd
BacArena/man/redEval.Rd
BacArena/man/getCorrM.Rd
BacArena/man/colpal6.Rd
BacArena/man/plotShadowCost.Rd
BacArena/man/reset_screen.Rd
BacArena/man/move.Rd
BacArena/man/BacArena.Rd
BacArena/man/stirEnv.Rd
BacArena/man/getArena.Rd
BacArena/man/plotSubUsage.Rd
BacArena/man/Eval-constructor.Rd
BacArena/man/Substance.Rd
BacArena/man/plotCurves2.Rd
BacArena/man/sihumi_test.Rd
BacArena/man/Bac.Rd
BacArena/man/Arena-class.Rd
BacArena/man/addEval.Rd