{"action":"created","issue":{"url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/issues/67","labels_url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/issues/67/labels{/name}","comments_url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/issues/67/comments","events_url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/issues/67/events","html_url":"https://github.com/matthiaskoenig/cy3sbml/issues/67","id":120207443,"number":67,"title":"SBMLValidator output \"<\" \">\" have to be escaped","user":{"login":"matthiaskoenig","id":900538,"avatar_url":"https://avatars.githubusercontent.com/u/900538?v=3","gravatar_id":"","url":"https://api.github.com/users/matthiaskoenig","html_url":"https://github.com/matthiaskoenig","followers_url":"https://api.github.com/users/matthiaskoenig/followers","following_url":"https://api.github.com/users/matthiaskoenig/following{/other_user}","gists_url":"https://api.github.com/users/matthiaskoenig/gists{/gist_id}","starred_url":"https://api.github.com/users/matthiaskoenig/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthiaskoenig/subscriptions","organizations_url":"https://api.github.com/users/matthiaskoenig/orgs","repos_url":"https://api.github.com/users/matthiaskoenig/repos","events_url":"https://api.github.com/users/matthiaskoenig/events{/privacy}","received_events_url":"https://api.github.com/users/matthiaskoenig/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-12-03T16:07:39Z","updated_at":"2015-12-04T08:21:51Z","closed_at":null,"body":"When displaying the warnings and errors tags have to be escaped like <model>, so that these are displayed properly.\r\n```\r\nMessage [lang=en_US, messageContent=(SBML Validation Rule #10701) Invalid 'sboTerm' attribute value for a Model object] Line: 3 (SBML Validation Rule #10701) \r\nThe value of the 'sboTerm' attribute on a   is ....\r\n```\r\nIn addition check why the JSBML validator results are different than the 5.12.0 validation results (is JSBML validator using the latest libSBML?)\r\nCertain units consistency checks are not warnings any more in 5.12.0, like\r\n```\r\nE2 Units consistency (Warning)\r\nMessage [lang=en_US, messageContent=(LibSBML Check #99505) Missing unit declarations on \r\nparameters or literal numbers in expression] Line: 403 (LibSBML Check #99505) In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the     expression 'scale_f * (Vmax_bA / Km_A) * (e__A - c__A) / (1 + e__A / Km_A + c__A / Km_A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n```\r\nbut still warnings in JSBML?\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/issues/comments/161906504","html_url":"https://github.com/matthiaskoenig/cy3sbml/issues/67#issuecomment-161906504","issue_url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/issues/67","id":161906504,"user":{"login":"matthiaskoenig","id":900538,"avatar_url":"https://avatars.githubusercontent.com/u/900538?v=3","gravatar_id":"","url":"https://api.github.com/users/matthiaskoenig","html_url":"https://github.com/matthiaskoenig","followers_url":"https://api.github.com/users/matthiaskoenig/followers","following_url":"https://api.github.com/users/matthiaskoenig/following{/other_user}","gists_url":"https://api.github.com/users/matthiaskoenig/gists{/gist_id}","starred_url":"https://api.github.com/users/matthiaskoenig/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthiaskoenig/subscriptions","organizations_url":"https://api.github.com/users/matthiaskoenig/orgs","repos_url":"https://api.github.com/users/matthiaskoenig/repos","events_url":"https://api.github.com/users/matthiaskoenig/events{/privacy}","received_events_url":"https://api.github.com/users/matthiaskoenig/received_events","type":"User","site_admin":false},"created_at":"2015-12-04T08:21:51Z","updated_at":"2015-12-04T08:21:51Z","body":"Hi Niko and @draeger ,\r\n\r\nSeems to be some problem with JSBML and the validator. I think there is an issue on using the units for constants in the math formula. I.e. something like\r\n```\r\n<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:sbml=\"http://www.sbml.org/sbml/level3/version1/core\">\r\n        <apply>\r\n          <times/>\r\n          <apply>\r\n            <divide/>\r\n            <apply>\r\n              <times/>\r\n              <ci> scale_f </ci>\r\n              <ci> Vmax_v1 </ci>\r\n            </apply>\r\n            <ci> Km_A </ci>\r\n          </apply>\r\n          <apply>\r\n            <minus/>\r\n            <ci> c__A </ci>\r\n            <apply>\r\n              <times/>\r\n              <apply>\r\n                <divide/>\r\n                <cn sbml:units=\"dimensionless\" type=\"integer\"> 1 </cn>\r\n                <ci> Keq_v1 </ci>\r\n              </apply>\r\n              <ci> c__B </ci>\r\n            </apply>\r\n          </apply>\r\n        </apply>\r\n      </math>\r\n```\r\n\r\n\r\n\r\nThe example model (attached) validates without warnings via libsbml 5.12.0 (python bindings) and the online validation on sbml.org/validator but gives unit consistency warnings via JSBML (see below).\r\nI can only imagine that the xml you send via JSBML to the validator is not exactly the xml of the file, but the parsed xml, so that the units on the constants get somehow lost.\r\nI just udated to the latest revision of JSBML 2432 and can reproduce the problem on two computers.\r\n\r\nCould you try to validate the file via JSBML to reproduce the problem?\r\nThe best \r\nMatthias\r\n\r\n```\r\nE1 Units consistency (Warning)\r\nMessage [lang=en_US, messageContent=(LibSBML Check #99505) Missing unit declarations on parameters or literal numbers in expression] Line: 128 (LibSBML Check #99505) In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the     expression 'scale_f * (Vmax_bA / Km_A) * (e__A - c__A) / (1 + e__A / Km_A + c__A / Km_A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\nE2 Units consistency (Warning)\r\nMessage [lang=en_US, messageContent=(LibSBML Check #99505) Missing unit declarations on parameters or literal numbers in expression] Line: 171 (LibSBML Check #99505) In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the     expression 'scale_f * (Vmax_bB / Km_B) * (c__B - e__B) / (1 + e__B / Km_B + c__B / Km_B)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\nE3 Units consistency (Warning)\r\nMessage [lang=en_US, messageContent=(LibSBML Check #99505) Missing unit declarations on parameters or literal numbers in expression] Line: 214 (LibSBML Check #99505) In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the     expression 'scale_f * (Vmax_bC / Km_C) * (c__C - e__C) / (1 + e__C / Km_C + c__C / Km_C)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\nE4 Units consistency (Warning)\r\nMessage [lang=en_US, messageContent=(LibSBML Check #99505) Missing unit declarations on parameters or literal numbers in expression] Line: 257 (LibSBML Check #99505) In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the     expression 'scale_f * Vmax_v1 / Km_A * (c__A - 1 / Keq_v1 * c__B)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\nE5 Units consistency (Warning)\r\nMessage [lang=en_US, messageContent=(LibSBML Check #99505) Missing unit declarations on parameters or literal numbers in expression] Line: 344 (LibSBML Check #99505) In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the     expression 'scale_f * Vmax_v4 / Km_A * (c__C - 1 / Keq_v4 * c__B)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n```\r\nCannot attach xml, so here the SBML:\r\n\r\n```\r\n<?xml version=\"1.0\" encoding=\"UTF-8\"?>\r\n<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\">\r\n  <model metaid=\"meta_demo_9\" id=\"demo_9\" name=\"demo_9\" substanceUnits=\"mole\" timeUnits=\"s\" volumeUnits=\"m3\" areaUnits=\"m2\" lengthUnits=\"m\" extentUnits=\"mole\">\r\n    <notes>\r\n      <body xmlns=\"http://www.w3.org/1999/xhtml\">\r\n        <h1>Koenig Demo Metabolism</h1>\r\n        <h2>Description</h2>\r\n        <p>This is a demonstration model in\r\n    <a href=\"http://sbml.org\" target=\"_blank\" title=\"Access the definition of the SBML file format.\">\r\n    SBML</a> format.\r\n    </p>\r\n      <div class=\"dc:provenance\">The content of this model has been carefully created in a manual research effort.</div>\r\n      <div class=\"dc:publisher\">This file has been produced by\r\n      <a href=\"https://livermetabolism.com/contact.html\" title=\"Matthias Koenig\" target=\"_blank\">Matthias Koenig</a>.\r\n      </div>\r\n    <h2>Terms of use</h2>\r\n    <div class=\"dc:rightsHolder\">Copyright © 2015 Matthias Koenig.</div>\r\n    <div class=\"dc:license\">\r\n      <p>Redistribution and use of any part of this model, with or without modification, are permitted provided that\r\n      the following conditions are met:\r\n        <ol>\r\n        <li>Redistributions of this SBML file must retain the above copyright notice, this list of conditions\r\n              and the following disclaimer.</li>\r\n        <li>Redistributions in a different form must reproduce the above copyright notice, this list of\r\n              conditions and the following disclaimer in the documentation and/or other materials provided\r\n          with the distribution.</li>\r\n      </ol>\r\n        This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even\r\n             the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</p>\r\n  </div>\r\n</body>\r\n</notes><annotation>\r\n  <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\r\n    <rdf:Description rdf:about=\"#meta_demo_9\">\r\n      <dc:creator>\r\n        <rdf:Bag>\r\n          <rdf:li rdf:parseType=\"Resource\">\r\n            <vCard:N rdf:parseType=\"Resource\">\r\n              <vCard:Family>Koenig</vCard:Family>\r\n              <vCard:Given>Matthias</vCard:Given>\r\n            </vCard:N>\r\n            <vCard:EMAIL>konigmatt@googlemail.com</vCard:EMAIL>\r\n            <vCard:ORG rdf:parseType=\"Resource\">\r\n              <vCard:Orgname>Charite Berlin</vCard:Orgname>\r\n            </vCard:ORG>\r\n          </rdf:li>\r\n        </rdf:Bag>\r\n      </dc:creator>\r\n      <dcterms:created rdf:parseType=\"Resource\">\r\n        <dcterms:W3CDTF>2015-12-03T15:54:56Z</dcterms:W3CDTF>\r\n      </dcterms:created>\r\n      <dcterms:modified rdf:parseType=\"Resource\">\r\n        <dcterms:W3CDTF>2015-12-03T15:54:56Z</dcterms:W3CDTF>\r\n      </dcterms:modified>\r\n    </rdf:Description>\r\n  </rdf:RDF>\r\n</annotation><listOfUnitDefinitions>\r\n  <unitDefinition id=\"kg\">\r\n    <listOfUnits>\r\n      <unit kind=\"kilogram\" exponent=\"1\" scale=\"0\" multiplier=\"1\"/>\r\n    </listOfUnits>\r\n  </unitDefinition>\r\n  <unitDefinition id=\"mM\">\r\n    <listOfUnits>\r\n      <unit kind=\"mole\" exponent=\"1\" scale=\"0\" multiplier=\"1\"/>\r\n      <unit kind=\"metre\" exponent=\"-3\" scale=\"0\" multiplier=\"1\"/>\r\n    </listOfUnits>\r\n  </unitDefinition>\r\n  <unitDefinition id=\"m\">\r\n    <listOfUnits>\r\n      <unit kind=\"metre\" exponent=\"1\" scale=\"0\" multiplier=\"1\"/>\r\n    </listOfUnits>\r\n  </unitDefinition>\r\n  <unitDefinition id=\"s\">\r\n    <listOfUnits>\r\n      <unit kind=\"second\" exponent=\"1\" scale=\"0\" multiplier=\"1\"/>\r\n    </listOfUnits>\r\n  </unitDefinition>\r\n  <unitDefinition id=\"m3\">\r\n    <listOfUnits>\r\n      <unit kind=\"metre\" exponent=\"3\" scale=\"0\" multiplier=\"1\"/>\r\n    </listOfUnits>\r\n  </unitDefinition>\r\n  <unitDefinition id=\"m2\">\r\n    <listOfUnits>\r\n      <unit kind=\"metre\" exponent=\"2\" scale=\"0\" multiplier=\"1\"/>\r\n    </listOfUnits>\r\n  </unitDefinition>\r\n  <unitDefinition id=\"mole_per_s\">\r\n    <listOfUnits>\r\n      <unit kind=\"mole\" exponent=\"1\" scale=\"0\" multiplier=\"1\"/>\r\n      <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\r\n    </listOfUnits>\r\n  </unitDefinition>\r\n</listOfUnitDefinitions><listOfCompartments>\r\n  <compartment id=\"e\" name=\"external compartment\" spatialDimensions=\"3\" size=\"1e-06\" units=\"m3\" constant=\"false\"/>\r\n  <compartment id=\"c\" name=\"cell compartment\" spatialDimensions=\"3\" size=\"1e-06\" units=\"m3\" constant=\"false\"/>\r\n  <compartment id=\"m\" name=\"plasma membrane\" spatialDimensions=\"2\" size=\"1\" units=\"m2\" constant=\"false\"/>\r\n</listOfCompartments><listOfSpecies>\r\n  <species id=\"e__A\" name=\"A\" compartment=\"e\" initialConcentration=\"10\" substanceUnits=\"mole\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\r\n  <species id=\"e__C\" name=\"C\" compartment=\"e\" initialConcentration=\"0\" substanceUnits=\"mole\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\r\n  <species id=\"e__B\" name=\"B\" compartment=\"e\" initialConcentration=\"0\" substanceUnits=\"mole\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\r\n  <species id=\"c__C\" name=\"C\" compartment=\"c\" initialConcentration=\"0\" substanceUnits=\"mole\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\r\n  <species id=\"c__B\" name=\"B\" compartment=\"c\" initialConcentration=\"0\" substanceUnits=\"mole\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\r\n  <species id=\"c__A\" name=\"A\" compartment=\"c\" initialConcentration=\"0\" substanceUnits=\"mole\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\r\n</listOfSpecies><listOfParameters>\r\n  <parameter id=\"Km_C\" value=\"3\" units=\"mM\" constant=\"true\"/>\r\n  <parameter id=\"scale_f\" name=\"metabolic scaling factor\" value=\"1e-06\" units=\"dimensionless\" constant=\"true\"/>\r\n  <parameter id=\"Vmax_bB\" value=\"2\" units=\"mole_per_s\" constant=\"true\"/>\r\n  <parameter id=\"Vmax_bC\" value=\"2\" units=\"mole_per_s\" constant=\"true\"/>\r\n  <parameter id=\"Vmax_bA\" value=\"5\" units=\"mole_per_s\" constant=\"true\"/>\r\n  <parameter id=\"Vmax_v2\" value=\"0.5\" units=\"mole_per_s\" constant=\"true\"/>\r\n  <parameter id=\"Vmax_v3\" value=\"0.5\" units=\"mole_per_s\" constant=\"true\"/>\r\n  <parameter id=\"Vmax_v1\" value=\"1\" units=\"mole_per_s\" constant=\"true\"/>\r\n  <parameter id=\"Km_A\" value=\"1\" units=\"mM\" constant=\"true\"/>\r\n  <parameter id=\"Vmax_v4\" value=\"0.5\" units=\"mole_per_s\" constant=\"true\"/>\r\n  <parameter id=\"Km_B\" value=\"0.5\" units=\"mM\" constant=\"true\"/>\r\n  <parameter id=\"Keq_v4\" value=\"2\" units=\"dimensionless\" constant=\"true\"/>\r\n  <parameter id=\"Keq_v1\" value=\"10\" units=\"dimensionless\" constant=\"true\"/>\r\n</listOfParameters><listOfReactions>\r\n  <reaction id=\"bA\" name=\"bA (A import)\" reversible=\"false\" fast=\"false\" compartment=\"m\">\r\n    <listOfReactants>\r\n      <speciesReference species=\"e__A\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfReactants>\r\n    <listOfProducts>\r\n      <speciesReference species=\"c__A\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfProducts>\r\n    <kineticLaw>\r\n      <math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:sbml=\"http://www.sbml.org/sbml/level3/version1/core\">\r\n        <apply>\r\n          <divide/>\r\n          <apply>\r\n            <times/>\r\n            <ci> scale_f </ci>\r\n            <apply>\r\n              <divide/>\r\n              <ci> Vmax_bA </ci>\r\n              <ci> Km_A </ci>\r\n            </apply>\r\n            <apply>\r\n              <minus/>\r\n              <ci> e__A </ci>\r\n              <ci> c__A </ci>\r\n            </apply>\r\n          </apply>\r\n          <apply>\r\n            <plus/>\r\n            <cn sbml:units=\"dimensionless\" type=\"integer\"> 1 </cn>\r\n            <apply>\r\n              <divide/>\r\n              <ci> e__A </ci>\r\n              <ci> Km_A </ci>\r\n            </apply>\r\n            <apply>\r\n              <divide/>\r\n              <ci> c__A </ci>\r\n              <ci> Km_A </ci>\r\n            </apply>\r\n          </apply>\r\n        </apply>\r\n      </math>\r\n    </kineticLaw>\r\n  </reaction>\r\n  <reaction id=\"bB\" name=\"bB (B export)\" reversible=\"false\" fast=\"false\" compartment=\"m\">\r\n    <listOfReactants>\r\n      <speciesReference species=\"c__B\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfReactants>\r\n    <listOfProducts>\r\n      <speciesReference species=\"e__B\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfProducts>\r\n    <kineticLaw>\r\n      <math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:sbml=\"http://www.sbml.org/sbml/level3/version1/core\">\r\n        <apply>\r\n          <divide/>\r\n          <apply>\r\n            <times/>\r\n            <ci> scale_f </ci>\r\n            <apply>\r\n              <divide/>\r\n              <ci> Vmax_bB </ci>\r\n              <ci> Km_B </ci>\r\n            </apply>\r\n            <apply>\r\n              <minus/>\r\n              <ci> c__B </ci>\r\n              <ci> e__B </ci>\r\n            </apply>\r\n          </apply>\r\n          <apply>\r\n            <plus/>\r\n            <cn sbml:units=\"dimensionless\" type=\"integer\"> 1 </cn>\r\n            <apply>\r\n              <divide/>\r\n              <ci> e__B </ci>\r\n              <ci> Km_B </ci>\r\n            </apply>\r\n            <apply>\r\n              <divide/>\r\n              <ci> c__B </ci>\r\n              <ci> Km_B </ci>\r\n            </apply>\r\n          </apply>\r\n        </apply>\r\n      </math>\r\n    </kineticLaw>\r\n  </reaction>\r\n  <reaction id=\"bC\" name=\"bC (C export)\" reversible=\"false\" fast=\"false\" compartment=\"m\">\r\n    <listOfReactants>\r\n      <speciesReference species=\"c__C\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfReactants>\r\n    <listOfProducts>\r\n      <speciesReference species=\"e__C\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfProducts>\r\n    <kineticLaw>\r\n      <math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:sbml=\"http://www.sbml.org/sbml/level3/version1/core\">\r\n        <apply>\r\n          <divide/>\r\n          <apply>\r\n            <times/>\r\n            <ci> scale_f </ci>\r\n            <apply>\r\n              <divide/>\r\n              <ci> Vmax_bC </ci>\r\n              <ci> Km_C </ci>\r\n            </apply>\r\n            <apply>\r\n              <minus/>\r\n              <ci> c__C </ci>\r\n              <ci> e__C </ci>\r\n            </apply>\r\n          </apply>\r\n          <apply>\r\n            <plus/>\r\n            <cn sbml:units=\"dimensionless\" type=\"integer\"> 1 </cn>\r\n            <apply>\r\n              <divide/>\r\n              <ci> e__C </ci>\r\n              <ci> Km_C </ci>\r\n            </apply>\r\n            <apply>\r\n              <divide/>\r\n              <ci> c__C </ci>\r\n              <ci> Km_C </ci>\r\n            </apply>\r\n          </apply>\r\n        </apply>\r\n      </math>\r\n    </kineticLaw>\r\n  </reaction>\r\n  <reaction id=\"v1\" name=\"v1 (A -&gt; B)\" reversible=\"false\" fast=\"false\" compartment=\"c\">\r\n    <listOfReactants>\r\n      <speciesReference species=\"c__A\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfReactants>\r\n    <listOfProducts>\r\n      <speciesReference species=\"c__B\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfProducts>\r\n    <kineticLaw>\r\n      <math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:sbml=\"http://www.sbml.org/sbml/level3/version1/core\">\r\n        <apply>\r\n          <times/>\r\n          <apply>\r\n            <divide/>\r\n            <apply>\r\n              <times/>\r\n              <ci> scale_f </ci>\r\n              <ci> Vmax_v1 </ci>\r\n            </apply>\r\n            <ci> Km_A </ci>\r\n          </apply>\r\n          <apply>\r\n            <minus/>\r\n            <ci> c__A </ci>\r\n            <apply>\r\n              <times/>\r\n              <apply>\r\n                <divide/>\r\n                <cn sbml:units=\"dimensionless\" type=\"integer\"> 1 </cn>\r\n                <ci> Keq_v1 </ci>\r\n              </apply>\r\n              <ci> c__B </ci>\r\n            </apply>\r\n          </apply>\r\n        </apply>\r\n      </math>\r\n    </kineticLaw>\r\n  </reaction>\r\n  <reaction id=\"v2\" name=\"v2 (A -&gt; C)\" reversible=\"false\" fast=\"false\" compartment=\"c\">\r\n    <listOfReactants>\r\n      <speciesReference species=\"c__A\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfReactants>\r\n    <listOfProducts>\r\n      <speciesReference species=\"c__C\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfProducts>\r\n    <kineticLaw>\r\n      <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\r\n        <apply>\r\n          <times/>\r\n          <apply>\r\n            <divide/>\r\n            <apply>\r\n              <times/>\r\n              <ci> scale_f </ci>\r\n              <ci> Vmax_v2 </ci>\r\n            </apply>\r\n            <ci> Km_A </ci>\r\n          </apply>\r\n          <ci> c__A </ci>\r\n        </apply>\r\n      </math>\r\n    </kineticLaw>\r\n  </reaction>\r\n  <reaction id=\"v3\" name=\"v3 (C -&gt; A)\" reversible=\"false\" fast=\"false\" compartment=\"c\">\r\n    <listOfReactants>\r\n      <speciesReference species=\"c__C\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfReactants>\r\n    <listOfProducts>\r\n      <speciesReference species=\"c__A\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfProducts>\r\n    <kineticLaw>\r\n      <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\r\n        <apply>\r\n          <times/>\r\n          <apply>\r\n            <divide/>\r\n            <apply>\r\n              <times/>\r\n              <ci> scale_f </ci>\r\n              <ci> Vmax_v3 </ci>\r\n            </apply>\r\n            <ci> Km_A </ci>\r\n          </apply>\r\n          <ci> c__C </ci>\r\n        </apply>\r\n      </math>\r\n    </kineticLaw>\r\n  </reaction>\r\n  <reaction id=\"v4\" name=\"v4 (C -&gt; B)\" reversible=\"false\" fast=\"false\" compartment=\"c\">\r\n    <listOfReactants>\r\n      <speciesReference species=\"c__C\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfReactants>\r\n    <listOfProducts>\r\n      <speciesReference species=\"c__B\" stoichiometry=\"1\" constant=\"true\"/>\r\n    </listOfProducts>\r\n    <kineticLaw>\r\n      <math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:sbml=\"http://www.sbml.org/sbml/level3/version1/core\">\r\n        <apply>\r\n          <times/>\r\n          <apply>\r\n            <divide/>\r\n            <apply>\r\n              <times/>\r\n              <ci> scale_f </ci>\r\n              <ci> Vmax_v4 </ci>\r\n            </apply>\r\n            <ci> Km_A </ci>\r\n          </apply>\r\n          <apply>\r\n            <minus/>\r\n            <ci> c__C </ci>\r\n            <apply>\r\n              <times/>\r\n              <apply>\r\n                <divide/>\r\n                <cn sbml:units=\"dimensionless\" type=\"integer\"> 1 </cn>\r\n                <ci> Keq_v4 </ci>\r\n              </apply>\r\n              <ci> c__B </ci>\r\n            </apply>\r\n          </apply>\r\n        </apply>\r\n      </math>\r\n    </kineticLaw>\r\n  </reaction>\r\n</listOfReactions>\r\n</model>\r\n</sbml>\r\n```\r\n\r\n\r\n"}}