Model construction and manipulation
constructModel — construct models
addReactions — add reactions to a model
deleteReactions — delete reactions from a model
deleteGenes — delete genes from a model
splitReversible — split all reversible reactions into separate irreversible reactions
getAttributes — get a list of available model attributes
getInitialConditions — get initial conditions of model
setInitialConditions — set initial conditions of model
updateInitialConditions — update initial conditions of model
Intersection — get intersecting parts of multiple models
Complement — get unique part of a model that cannout be found in a series of other models
MatrixRank — rank of model stoichiometry matrix
Transpose — transpose of model stoichiometry matrix
NullSpace — null space of a model stoichiometry matrix
Dot — Dot product of model stoichiometry matrix and vector
ToString — textual representation of types
ReplaceAll (/.) — use a model as a replacement list
Simulation and Visualization
simulate — integrate ODEs
plotSimulation — plot concentration and flux profiles
plotPhasePortrait — plot phase portraits of concentration and flux profiles
Constraint-based modeling
fba — perform flux-balance analysis
fva — perform flux-variability analysis
reduceModel — remove reaction that cannot carry steady-state flux
species — represent a species
metabolite — represent a small compound
reaction — represent a reaction
Keq — represent an equilibrium constant
rateconst — represent an elementary rate constant
importModel — import a model
sbml2model — import a model defined in SBML format
mat2model — import COBRA toolbox models from a Matlab file
biomodel2model — import a model from biomodels.net
model2bipartite — construct a bipartite representation
