ReactionNetworks : Index

• clusterModelCellDeath -- an example of a chemical reaction
• clusterModelCellDeath() -- an example of a chemical reaction
• Complexes -- a mutable hash table, stores information about a reaction network
• ConcentrationRates -- a mutable hash table, stores information about a reaction network
• conservationEquations -- creates the conservation equations of a reaction network
• conservationEquations(ReactionNetwork) -- creates the conservation equations of a reaction network
• conservationEquations(ReactionNetwork,Ring) -- creates the conservation equations of a reaction network
• createConcentrationRates -- used in creating reaction network ring
• createInitialValues -- used in creating reaction network ring
• createReactionRates -- used in creating reaction network ring
• createRing -- creates a ring with generators species concentrations, reaction rates, initial values
• createRing(ReactionNetwork) -- creates a ring with generators species concentrations, reaction rates, initial values
• createRing(ReactionNetwork,Ring) -- creates a ring with generators species concentrations, reaction rates, initial values
• crossLinkingModelCelldeath (missing documentation)
• displayComplexes (missing documentation)
• FullEdges (missing documentation)
• glue -- combine two networks
• glue(List,ReactionNetwork) -- combine two networks
• glue(ReactionNetwork,List) -- combine two networks
• glue(ReactionNetwork,ReactionNetwork) -- combine two networks
• InitialValues -- a mutable hash table, stores information about a reaction network
• Input (missing documentation)
• isDeficient -- determines deficiency of a network
• isWeaklyReversible -- determines if a network is weakly reversible
• modificationOfTwoSubstratesH -- an example chemical reaction motif
• modificationOfTwoSubstratesH() -- an example chemical reaction motif
• modificationOfTwoSubstratesI -- an example chemical reaction motif
• modificationOfTwoSubstratesI() -- an example chemical reaction motif
• negativeLaplacian -- Computes the negative of the Laplacian matrix of a Reaction Network.
• negativeLaplacian(ReactionNetwork) -- Computes the negative of the Laplacian matrix of a Reaction Network.
• negativeUndirectedLaplacian -- Computes the negative of the Laplacian matrix of an undirected graph associated with a Reaction Network.
• negativeUndirectedLaplacian(ReactionNetwork) -- Computes the negative of the Laplacian matrix of an undirected graph associated with a Reaction Network.
• negativeWeightedLaplacian -- Computes the negative of the weighted Laplacian matrix of a Reaction Network.
• negativeWeightedLaplacian(ReactionNetwork) -- Computes the negative of the weighted Laplacian matrix of a Reaction Network.
• nSiteAutocatalytic -- A motif for autocatalytic networks
• nSiteAutocatalytic(ZZ) -- A motif for autocatalytic networks
• nSiteDiffusion -- an example for a diffusion network
• nSiteDiffusion(ZZ) -- an example for a diffusion network
• nSiteDistributiveModification -- A motif for purely distributive phosphorylation
• nSiteDistributiveModification(ZZ) -- A motif for purely distributive phosphorylation
• nSiteImmuneReaction -- A motif for an immune response network
• nSiteImmuneReaction(ZZ) -- A motif for an immune response network
• nSitePoreForming -- an example for a pore forming network
• nSitePoreForming(ZZ) -- an example for a pore forming network
• nSiteProcessiveModification -- A motif for purely processive phosphorylation
• nSiteProcessiveModification(ZZ) -- A motif for purely processive phosphorylation
• nSiteSequestration -- A motif for sequestration networks
• nSiteSequestration(ZZ) -- A motif for sequestration networks
• NullEdges (missing documentation)
• NullIndex -- a mutable hash table, stores information about a reaction network
• NullSymbol -- a mutable hash table, stores information about a reaction network
• oneSiteModificationA -- an example for chemical reaction motif
• oneSiteModificationA() -- an example for chemical reaction motif
• oneSiteModificationB -- an example for chemical reaction motif
• oneSiteModificationB() -- an example for chemical reaction motif
• oneSiteModificationC -- an example for chemical reaction motif
• oneSiteModificationC() -- an example for chemical reaction motif
• oneSiteModificationD -- an example for chemical reaction motif
• oneSiteModificationD() -- an example for chemical reaction motif
• reactantMatrix -- Computes the reactants matrix of a Reaction Network.
• reactantMatrix(ReactionNetwork) -- Computes the reactants matrix of a Reaction Network.
• ReactionGraph -- a mutable hash table, stores information about a reaction network
• reactionMatrix (missing documentation)
• ReactionNetwork -- a mutable hash table, stores information about a reaction network
• reactionNetwork -- creates a reaction network
• reactionNetwork(Ideal) -- creates a reaction network
• reactionNetwork(List) -- creates a reaction network
• reactionNetwork(String) -- creates a reaction network
• ReactionNetworks -- create chemical reaction networks and corresponding steady-state and conservation equations
• ReactionRates -- a mutable hash table, stores information about a reaction network
• ReactionRing -- a mutable hash table, stores information about a reaction network
• Species -- a mutable hash table, stores information about a reaction network
• steadyStateEquations -- creates steady-state equations of a reaction network
• steadyStateEquations(ReactionNetwork) -- creates steady-state equations of a reaction network
• steadyStateEquations(ReactionNetwork,Ring) -- creates steady-state equations of a reaction network
• stoichiometricConeKer -- Computes a matrix whose columns are the rays of the cone non-negative kernel of the stoichiometric matrix of a Reaction Network.
• stoichiometricConeKer(ReactionNetwork) -- Computes a matrix whose columns are the rays of the cone non-negative kernel of the stoichiometric matrix of a Reaction Network.
• stoichiometricMatrix -- Computes the stoichiometric matrix of a Reaction Network.
• stoichiometricMatrix(ReactionNetwork) -- Computes the stoichiometric matrix of a Reaction Network.
• stoichiometricSubspace -- Computes the stoichiometric space of a Reaction Network.
• stoichiometricSubspace(ReactionNetwork) -- Computes the stoichiometric space of a Reaction Network.
• stoichSubspaceKer -- Computes the kernel of the stoichiometric matrix of a Reaction Network.
• stoichSubspaceKer(ReactionNetwork) -- Computes the kernel of the stoichiometric matrix of a Reaction Network.
• subRandomInitVals (missing documentation)
• subRandomReactionRates (missing documentation)
• substitute(ReactionNetwork,List) -- substitute species names in reaction network
• twoLayerCascadeJ -- an example chemical reaction motif
• twoLayerCascadeJ() -- an example chemical reaction motif
• twoLayerCascadeK -- an example chemical reaction motif
• twoLayerCascadeK() -- an example chemical reaction motif
• twoLayerCascadeL -- an example for chemical reaction motif
• twoLayerCascadeL() -- an example for chemical reaction motif
• twoSiteModificationE -- an example for chemical rection motif
• twoSiteModificationE() -- an example for chemical rection motif
• twoSiteModificationF -- an example for chemical reaction motif
• twoSiteModificationF() -- an example for chemical reaction motif
• twoSiteModificationG -- an example chemical reaction motif
• twoSiteModificationG() -- an example chemical reaction motif
• wnt -- shuttle model for Wnt signaling pathway
• wnt() -- shuttle model for Wnt signaling pathway