The ReactionNetworks package provides functions for creating the steady-state and conservation equations corresponding to a given reaction network. Included are some basic building-block motifs, which can be joined together to create specific reaction network. Examples are provided illustrating elimination and degeneration with removal of a species or a reaction and the corresponding effect on the solutions of the system.
Basic Functions: reactionNetwork, isDeficient, isWeaklyReversible, steadyStateEquations conservationEquations, glue
Motifs: oneSiteModificationA, oneSiteModificationB, oneSiteModificationC, oneSiteModificationD, twoSiteModificationE, twoSiteModificationF, twoSiteModificationG, modificationOfTwoSubstratesH, modificationOfTwoSubstratesI, twoLayerCascadeJ, twoLayerCascadeK, twoLayerCascadeL, crossLinkingModelCelldeath (missing documentation) , clusterModelCellDeath, wnt, nSiteProcessiveModification, nSiteDistributiveModification, nSiteImmuneReaction, nSiteDiffusion, nSitePoreForming, nSiteSequestration, nSiteAutocatalytic
Examples
The following example demonstrates how to compute the degree and dimension of the ideal cut out by the steady-state and conservation equations.
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After creating the reaction network and the corresponding ring, we create the steady state equations and substitute random values for the reaction rates; this will allows us to compute the degree of the ideal.
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Next, we create the conservation equations and assume there is no translation, i.e., the initial conditions are all zero.
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Finally, we join the two sets of equations and create an ideal. Thus, the degree and dimension can be computed.
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This documentation describes version 1.0 of ReactionNetworks.
If you have used this package in your research, please cite it as follows:
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The object ReactionNetworks is a package, defined in ReactionNetworks.m2, with auxiliary files in ReactionNetworks/.
The source of this document is in ReactionNetworks/DocReactionNetworks.m2:88:0.