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constructModel

constructModel[reactions]
constructs a model from reactions.
constructModel[S, species, rxnIDs]
constructs a model from the stoichiometry matrix, species and reaction identifiers.
  • The following options can be given:
InitialConditions{}Provide a list of initial conditions
Constraints{}Provide a list of constraints
Parameters{}Provide a list of parameters
Irreversible{}Provide a list of irreversible reaction identifiers (if a stoichiometry matrix is used for model construction)
GPR{}Provide a list of gene-protein-reaction relations
CustomRateLaws{}Provide custom rate laws if the default mass-action rate laws are not appropriate
CustomODE{}Provide additional differential and/or algebraic equations
Constant{}Provide a list of species to be treated as constants
BoundaryConditions{}Provide a list of species to be treated as x'[t] == 0
NameAutomaticProvide a full name for model
IDAutomaticProvide a shorter identifier for model
ElementalComposition{}Provide the elemental compositions for species
NotesAttach notes to model
Ignore{}Provide a list of species that should be ignored for mass-action considerations
ReorderStoichiometryTrueIf the stoichiometry matrix S should be reordered such that the first rank(S) rows are linearly independent
UnitCheckingFalseToggle unit checking
EXAMPLESCLOSE ALL
Basic Examples   (1)
Use a list of reactions
Use a stoichiometry matrix, a list of metabolites, and a list of reaction identifiers
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Use a list of reactions
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Use a stoichiometry matrix, a list of metabolites, and a list of reaction identifiers
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Click for copyable input
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