Index

A

addDegradationSteps (buildNetworks.Settings attribute)

allowMassViolatingReactions (buildNetworks.Settings attribute)

B

buildNetworks module

G

getLinearChain() (in module buildNetworks) getODEsFromModel() (in module odePrint) getODEsFromSBMLFile() (in module odePrint)

getODEsFromSBMLString() (in module odePrint) getRandomNetwork() (in module buildNetworks) getRandomNetworkDataStructure() (in module buildNetworks)

M

module buildNetworks odePrint parameterScanning plotting prettyTabular

O

odePrint module

P

parameterScanning module plotArray() (in module plotting) plotArrayHeatMap() (in module plotting) plotAsciiConcentrationsBar() (in module plotting) plotAsciiReactionRatesBar() (in module plotting) plotConcentrationControlBar() (in module plotting) plotConcentrationControlHeatMap() (in module plotting) plotConcentrationControlIn3D() (in module plotting) plotFloatingSpecies() (in module plotting)

plotFluxControlBar() (in module plotting) plotFluxControlHeatMap() (in module plotting) plotFluxControlIn3D() (in module plotting) plotPhasePortraitGrid() (in module plotting) plotRandSimGrid() (in module plotting) plotReactionRates() (in module plotting) plotting module prettyTabular module

R

rateConstantScale (buildNetworks.Settings attribute) readCsvFile() (in module fileUtils)

removeBoundarySpecies (buildNetworks.Settings attribute) restoreDefaultProbabilities() (buildNetworks.Settings method)

S

Settings (class in buildNetworks)

Settings.ReactionProbabilities (class in buildNetworks) simpleTimeCourseScan() (in module parameterScanning)

T

tabulateConcentrations() (in module prettyTabular)

tabulateFluxes() (in module prettyTabular) testme() (in module plotting)