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<!DOCTYPE html> <html lang="en"> <head> <title>ReactionNetworks : Table of Contents</title> <meta content="text/html; charset=utf-8" http-equiv="Content-Type"> <link type="text/css" rel="stylesheet" href="../../../../Macaulay2/Style/doc.css"> <link rel="stylesheet" href="../../../../Macaulay2/Style/katex/katex.min.css"> <script defer="defer" src="../../../../Macaulay2/Style/katex/katex.min.js"></script> <script defer="defer" src="../../../../Macaulay2/Style/katex/contrib/auto-render.min.js"></script> <script> var macros = { "\\break": "\\\\", "\\ZZ": "\\mathbb{Z}", "\\NN": "\\mathbb{N}", "\\QQ": "\\mathbb{Q}", "\\RR": "\\mathbb{R}", "\\CC": "\\mathbb{C}", "\\PP": "\\mathbb{P}" }, delimiters = [ { left: "$$", right: "$$", display: true}, { left: "\\[", right: "\\]", display: true}, { left: "$", right: "$", display: false}, { left: "\\(", right: "\\)", display: false} ], ignoredTags = [ "kbd", "var", "samp", "script", "noscript", "style", "textarea", "pre", "code", "option" ]; document.addEventListener("DOMContentLoaded", function() { renderMathInElement(document.body, { delimiters: delimiters, macros: macros, ignoredTags: ignoredTags, trust: true }); }); </script> <style>.katex { font-size: 1em; }</style> <script defer="defer" src="../../../../Macaulay2/Style/katex/contrib/copy-tex.min.js"></script> <script defer="defer" src="../../../../Macaulay2/Style/katex/contrib/render-a11y-string.min.js"></script> <script src="../../../../Macaulay2/Style/prism.js"></script> <script>var current_version = '1.25.06';</script> <script src="../../../../Macaulay2/Style/version-select.js"></script> <link type="image/x-icon" rel="icon" href="../../../../Macaulay2/Style/icon.gif"> </head> <body> <div id="buttons"> <div> <a href="https://macaulay2.com/">Macaulay2</a> <span id="version-select-container"></span> » <a title="Macaulay2 documentation" href="../../Macaulay2Doc/html/index.html">Documentation </a> <br><a href="../../Macaulay2Doc/html/_packages_spprovided_spwith_sp__Macaulay2.html">Packages</a> » <span><a title="create chemical reaction networks and corresponding steady-state and conservation equations" href="index.html">ReactionNetworks</a> :: <a href="toc.html">Table of Contents</a></span> </div> <div class="right"> <form method="get" action="https://www.google.com/search"> <input placeholder="Search" type="text" name="q" value=""> <input type="hidden" name="q" value="site:macaulay2.com/doc"> </form> next | previous | forward | backward | up | <a href="master.html">index</a> | <a href="toc.html">toc</a> </div> </div> <hr> <h1>ReactionNetworks : Table of Contents</h1> <ul> <li><span><a title="create chemical reaction networks and corresponding steady-state and conservation equations" href="index.html">ReactionNetworks</a> -- create chemical reaction networks and corresponding steady-state and conservation equations</span></li> <li><span><a title="an example of a chemical reaction" href="_cluster__Model__Cell__Death.html">clusterModelCellDeath</a> -- an example of a chemical reaction</span></li> <li><span><a title="creates the conservation equations of a reaction network" href="_conservation__Equations.html">conservationEquations</a> -- creates the conservation equations of a reaction network</span></li> <li><span><a title="used in creating reaction network ring" href="_create__Concentration__Rates.html">createConcentrationRates</a> -- used in creating reaction network ring</span></li> <li><span><a title="used in creating reaction network ring" href="_create__Initial__Values.html">createInitialValues</a> -- used in creating reaction network ring</span></li> <li><span><a title="used in creating reaction network ring" href="_create__Reaction__Rates.html">createReactionRates</a> -- used in creating reaction network ring</span></li> <li><span><a title="creates a ring with generators species concentrations, reaction rates, initial values" href="_create__Ring.html">createRing</a> -- creates a ring with generators species concentrations, reaction rates, initial values</span></li> <li><span><span class="tt">crossLinkingModelCelldeath</span> (missing documentation)<!--tag: crossLinkingModelCelldeath--> </span></li> <li><span><span class="tt">displayComplexes</span> (missing documentation)<!--tag: displayComplexes--> </span></li> <li><span><span class="tt">FullEdges</span> (missing documentation)<!--tag: FullEdges--> </span></li> <li><span><a title="combine two networks" href="_glue.html">glue</a> -- combine two networks</span></li> <li><span><span class="tt">Input</span> (missing documentation)<!--tag: Input--> </span></li> <li><span><a title="determines deficiency of a network" href="_is__Deficient.html">isDeficient</a> -- determines deficiency of a network</span></li> <li><span><a title="determines if a network is weakly reversible" href="_is__Weakly__Reversible.html">isWeaklyReversible</a> -- determines if a network is weakly reversible</span></li> <li><span><a title="an example chemical reaction motif" href="_modification__Of__Two__Substrates__H.html">modificationOfTwoSubstratesH</a> -- an example chemical reaction motif</span></li> <li><span><a title="an example chemical reaction motif" href="_modification__Of__Two__Substrates__I.html">modificationOfTwoSubstratesI</a> -- an example chemical reaction motif</span></li> <li><span><a title="Computes the negative of the Laplacian matrix of a Reaction Network." href="_negative__Laplacian.html">negativeLaplacian</a> -- Computes the negative of the Laplacian matrix of a Reaction Network.</span></li> <li><span><a title="Computes the negative of the Laplacian matrix of an undirected graph associated with a Reaction Network." href="_negative__Undirected__Laplacian.html">negativeUndirectedLaplacian</a> -- Computes the negative of the Laplacian matrix of an undirected graph associated with a Reaction Network.</span></li> <li><span><a title="Computes the negative of the weighted Laplacian matrix of a Reaction Network." href="_negative__Weighted__Laplacian.html">negativeWeightedLaplacian</a> -- Computes the negative of the weighted Laplacian matrix of a Reaction Network.</span></li> <li><span><a title="A motif for autocatalytic networks" href="_n__Site__Autocatalytic.html">nSiteAutocatalytic</a> -- A motif for autocatalytic networks</span></li> <li><span><a title="an example for a diffusion network" href="_n__Site__Diffusion.html">nSiteDiffusion</a> -- an example for a diffusion network</span></li> <li><span><a title="A motif for purely distributive phosphorylation" href="_n__Site__Distributive__Modification.html">nSiteDistributiveModification</a> -- A motif for purely distributive phosphorylation</span></li> <li><span><a title="A motif for an immune response network" href="_n__Site__Immune__Reaction.html">nSiteImmuneReaction</a> -- A motif for an immune response network</span></li> <li><span><a title="an example for a pore forming network" href="_n__Site__Pore__Forming.html">nSitePoreForming</a> -- an example for a pore forming network</span></li> <li><span><a title="A motif for purely processive phosphorylation" href="_n__Site__Processive__Modification.html">nSiteProcessiveModification</a> -- A motif for purely processive phosphorylation</span></li> <li><span><a title="A motif for sequestration networks" href="_n__Site__Sequestration.html">nSiteSequestration</a> -- A motif for sequestration networks</span></li> <li><span><span class="tt">NullEdges</span> (missing documentation)<!--tag: NullEdges--> </span></li> <li><span><a title="an example for chemical reaction motif" href="_one__Site__Modification__A.html">oneSiteModificationA</a> -- an example for chemical reaction motif</span></li> <li><span><a title="an example for chemical reaction motif" href="_one__Site__Modification__B.html">oneSiteModificationB</a> -- an example for chemical reaction motif</span></li> <li><span><a title="an example for chemical reaction motif" href="_one__Site__Modification__C.html">oneSiteModificationC</a> -- an example for chemical reaction motif</span></li> <li><span><a title="an example for chemical reaction motif" href="_one__Site__Modification__D.html">oneSiteModificationD</a> -- an example for chemical reaction motif</span></li> <li><span><a title="Computes the reactants matrix of a Reaction Network." href="_reactant__Matrix.html">reactantMatrix</a> -- Computes the reactants matrix of a Reaction Network.</span></li> <li><span><span class="tt">reactionMatrix</span> (missing documentation)<!--tag: reactionMatrix--> </span></li> <li><span><a title="a mutable hash table, stores information about a reaction network" href="___Reaction__Network.html">ReactionNetwork</a> -- a mutable hash table, stores information about a reaction network</span></li> <li><span><a title="creates a reaction network" href="_reaction__Network.html">reactionNetwork</a> -- creates a reaction network</span></li> <li><span><a title="creates steady-state equations of a reaction network" href="_steady__State__Equations.html">steadyStateEquations</a> -- creates steady-state equations of a reaction network</span></li> <li><span><a title="Computes a matrix whose columns are the rays of the cone non-negative kernel of the stoichiometric matrix of a Reaction Network." href="_stoichiometric__Cone__Ker.html">stoichiometricConeKer</a> -- Computes a matrix whose columns are the rays of the cone non-negative kernel of the stoichiometric matrix of a Reaction Network.</span></li> <li><span><a title="Computes the stoichiometric matrix of a Reaction Network." href="_stoichiometric__Matrix.html">stoichiometricMatrix</a> -- Computes the stoichiometric matrix of a Reaction Network.</span></li> <li><span><a title="Computes the stoichiometric space of a Reaction Network." href="_stoichiometric__Subspace.html">stoichiometricSubspace</a> -- Computes the stoichiometric space of a Reaction Network.</span></li> <li><span><a title="Computes the kernel of the stoichiometric matrix of a Reaction Network." href="_stoich__Subspace__Ker.html">stoichSubspaceKer</a> -- Computes the kernel of the stoichiometric matrix of a Reaction Network.</span></li> <li><span><span class="tt">subRandomInitVals</span> (missing documentation)<!--tag: subRandomInitVals--> </span></li> <li><span><span class="tt">subRandomReactionRates</span> (missing documentation)<!--tag: subRandomReactionRates--> </span></li> <li><span><a title="substitute species names in reaction network" href="_substitute_lp__Reaction__Network_cm__List_rp.html">substitute(ReactionNetwork,List)</a> -- substitute species names in reaction network</span></li> <li><span><a title="an example chemical reaction motif" href="_two__Layer__Cascade__J.html">twoLayerCascadeJ</a> -- an example chemical reaction motif</span></li> <li><span><a title="an example chemical reaction motif" href="_two__Layer__Cascade__K.html">twoLayerCascadeK</a> -- an example chemical reaction motif</span></li> <li><span><a title="an example for chemical reaction motif" href="_two__Layer__Cascade__L.html">twoLayerCascadeL</a> -- an example for chemical reaction motif</span></li> <li><span><a title="an example for chemical reaction motif" href="_two__Site__Modification__E.html">twoSiteModificationE</a> -- an example for chemical reaction motif</span></li> <li><span><a title="an example for chemical reaction motif" href="_two__Site__Modification__F.html">twoSiteModificationF</a> -- an example for chemical reaction motif</span></li> <li><span><a title="an example chemical reaction motif" href="_two__Site__Modification__G.html">twoSiteModificationG</a> -- an example chemical reaction motif</span></li> <li><span><a title="shuttle model for Wnt signaling pathway" href="_wnt.html">wnt</a> -- shuttle model for Wnt signaling pathway</span></li> </ul> </body> </html>