For each model, the MASS toolbox provides a series of mutable and immutable attributes with associated
getter,
setter,
updater Functions (see
). In general, when working with model attributes it is very helpful to use
Mathematica's command completion capabilities (see
) to complete either the various getter, setter, updater functions or the attribute names directly.
ID — Model identifier (String)
Name — Model full name (String)
Constraints — Constraints on model fluxes ({
vID → {
lb,
ub}, ...})
InitialConditions — Model initial conditions ({
x1c →
val, ...})
Parameters — Model parameters ({
→
val,
→
val, ...})
GPR — Gene-protein-reaction associations ({"
RxnID" -> p["
ID"], p["
ID"] → g["
ID"], ...})
Ignore — Species that should be ignored under mass-action considerations (List of species)
BoundaryConditions — Boundary conditions for species (list of species)
Constant — Constant species (list of species)
ReversibleColumnIndices — Columns in stoichiometry matrix that correspond to reversible reactions (list of integer indices)
CustomRateLaws — Custom rate laws ({
vID -> equation, ...})
CustomODE — Additional algebraic or differential equations (list of equations)
ElementalComposition — Elemental composition of species ({
H2Oc → 2
"H" + "O", ...})
UnitChecking — If units should be checked (Boolean)
Objective — Objective that should be optimized in COBRA related methods (
vID or
vID + ...)
Stoichiometry — Stoichiometry matrix
SparseStoichiometry — Sparse stoichiometry matrix (SparseArray)
Reactions — Model reactions (List of reactions; same order as rows in stoichiometry matrix)
Exchanges — Exchanges reactions in model (List of reactions)
Variables — Time dependent variables in model ({v[t], ...})
Species — Model species (List of species; same order as rows in stoichiometry matrix)
Fluxes — Model fluxes (List of species; same order as columns in stoichiometry matrixrows)
ForwardRateConstants — All forward rate constants in model ({
, ...})
ReverseRateConstants — All reverse rate constants in model ({
, ...})
EquilibriumConstants — All equilibrium constants in model ({
, ...})
IrreversibleColumnIndices — Columns in stoichiometry matrix that correspond to irreversible reactions (list of integer indices)
Rates — overall rate laws of model (list of equations; same order as columns in stoichiometry matrix)
ODE — overall ordinary differential equations of model (list of equations)
Compartments — compartmens in model (list of compartments)
Genes — genes in model (list of genes)
GeneAssociations — reaction-gene associations ({"RxnID" -> g["ID"], ...})
Proteins — proteins in model (list of proteins)
ProteinAssociations — reaction-gene associations ({"RxnID" -> p["ID"], ...})
Enzymes — enzymes in model (list of enzymes)
