BacArena-package	BacArena
addDefaultMed	addDefaultMed
addDefaultMed,Arena-method	addDefaultMed
addEssentialMed	addEssentialMed
addEssentialMed,Arena-method	addEssentialMed
addEval	addEval
addEval,Eval-method	addEval
addOrg	addOrg
addOrg,Arena-method	addOrg
addSubs	addSubs
addSubs,Arena-method	addSubs
Arena	Arena-constructor
Arena-class	Arena-class
Arena-constructor	Arena-constructor
Bac	Bac-Constructor
Bac-class	Bac
Bac-Constructor	Bac-Constructor
BacArena	BacArena
cellgrowth	cellgrowth
cellgrowth,Human-method	cellgrowth
changeDiff	changeDiff
changeDiff,Arena-method	changeDiff
changeFobj	changeFobj
changeFobj,Human-method	changeFobj
changeOrg	changeOrg
changeOrg,Arena-method	changeOrg
changeSub	changeSub
changeSub,Arena-method	changeSub
checkCorr	checkCorr
checkCorr,Eval-method	checkCorr
checkPhen	checkPhen
checkPhen,Arena-method	checkPhen
checkPhen_par	checkPhen_par
checkPhen_par,Arena-method	checkPhen_par
chemotaxis	chemotaxis
chemotaxis,Bac-method	chemotaxis
colpal1	colpal1
colpal2	colpal2
colpal3	colpal3
colpal4	colpal4
colpal5	colpal5
colpal6	colpal6
constrain	constrain
constrain,Organism-method	constrain
consume	consume
consume,Organism-method	consume
createGradient	createGradient
createGradient,Arena-method	createGradient
dat2mat	dat2mat
dat2mat,Arena-method	dat2mat
diffuse	diffuse
diffuse,Arena-method	diffuse
diffusePDE	diffusePDE
diffusePDE,Substance-method	diffusePDE
diffuseR	diffuseR
diffuseR,Substance-method	diffuseR
diffuse_par	diffuse_par
diffuse_par,Arena-method	diffuse_par
emptyHood	emptyHood
emptyHood,Organism-method	emptyHood
Eval	Eval-constructor
Eval-class	Eval-class
Eval-constructor	Eval-constructor
evalArena	evalArena
evalArena,Eval-method	evalArena
extractMed	extractMed
extractMed,Eval-method	extractMed
findFeeding	findFeeding
findFeeding,Eval-method	findFeeding
findFeeding2	findFeeding2
findFeeding2,Eval-method	findFeeding2
findFeeding3	findFeeding3
findFeeding3,Eval-method	findFeeding3
findInArena	findInArena
findInArena,Arena-method	findInArena
flushSubs	flushSubs
flushSubs,Arena-method	flushSubs
getArena	getArena
getArena,Eval-method	getArena
getCorrM	getCorrM
getCorrM,Eval-method	getCorrM
getPhenoMat	getPhenoMat
getPhenoMat,Eval-method	getPhenoMat
getPhenotype	getPhenotype
getPhenotype,Organism-method	getPhenotype
getSubHist	getSubHist
getSubHist,Eval-method	getSubHist
getSublb	getSublb
getSublb,Arena-method	getSublb
getVarSubs	getVarSubs
getVarSubs,Eval-method	getVarSubs
growExp	growExp
growExp,Organism-method	growExp
growLin	growLin
growLin,Organism-method	growLin
growth	growth
growth,Bac-method	growth
growth_par	growth_par
growth_par,Bac-method	growth_par
Human	Human-constructor
Human-class	Human
Human-constructor	Human-constructor
lsd	lsd
lysis	lysis
lysis,Organism-method	lysis
minePheno	minePheno
minePheno,Eval-method	minePheno
move	move
move,Organism-method	move
NemptyHood	NemptyHood
NemptyHood,Organism-method	NemptyHood
openArena	openArena
optimizeLP	optimizeLP
optimizeLP,Organism-method	optimizeLP
Organism	Organism-constructor
Organism-class	Organism-class
Organism-constructor	Organism-constructor
plotAbundance	plotAbundance
plotCurves	plotCurves
plotCurves,Eval-method	plotCurves
plotCurves2	plotCurves2
plotCurves2,Eval-method	plotCurves2
plotFluxVar	plotFluxVar
plotGrowthCurve	plotGrowthCurve
plotInterNum	plotInterNum
plotPhenCurve	plotPhenCurve
plotPhenNum	plotPhenNum
plotShadowCost	plotShadowCost
plotShadowCost,Eval-method	plotShadowCost
plotSpecActivity	plotSpecActivity
plotSubCurve	plotSubCurve
plotSubUsage	plotSubUsage
plotSubVar	plotSubVar
plotTotFlux	plotTotFlux
plotTotFlux,Eval-method	plotTotFlux
redEval	redEval
redEval,Eval-method	redEval
reset_screen	reset_screen
rmSubs	rmSubs
rmSubs,Arena-method	rmSubs
selPheno	selPheno
selPheno,Eval-method	selPheno
setKinetics	setKinetics
setKinetics,Organism-method	setKinetics
sihumi_test	sihumi_test
simBac	simBac
simBac,Bac-method	simBac
simBac_par	simBac_par
simBac_par,Bac-method	simBac_par
simEnv	simEnv
simEnv,Arena-method	simEnv
simEnv_par	simEnv_par
simEnv_par,Arena-method	simEnv_par
simHum	simHum
simHum,Human-method	simHum
statPheno	statPheno
statPheno,Eval-method	statPheno
stirEnv	stirEnv
stirEnv,Arena-method	stirEnv
Substance	Substance-constructor
Substance-class	Substance
Substance-constructor	Substance-constructor
usd	usd
