MASS Toolbox
Abstract ...
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
Model attributes
getAttributes get a list of available model attributes
InitialConditions  ▪ Parameters  ▪ ID  ▪ CustomRateLaws  ▪ ...
getInitialConditions get initial conditions of model
getParameters  ▪ getReactions  ▪ getID  ▪ getCustomRateLaws  ▪ getRates  ▪ ...
setInitialConditions set initial conditions of model
setParameters  ▪ setID  ▪ setCustomRateLaws  ▪ setIgnore  ▪ ...
updateInitialConditions update initial conditions of model
Overloaded functions
Union unify models
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
Length  ▪ RowReduce  ▪ Equal  ▪ SameQ
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
minspan  ▪ gimme
Modeling types
species represent a species
metabolite represent a small compound
reaction represent a reaction
Keq represent an equilibrium constant
rateconst represent an elementary rate constant
enzyme  ▪ gene  ▪ protein  ▪ parameter  ▪ vmax  ▪ Km
Import & Export
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
Graph theory
model2bipartite construct a bipartite representation