{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "c6194f89",
   "metadata": {},
   "source": [
    "Create the repressilator step by step.\n",
    "\n",
    "See on biomodels.\n",
    "\n",
    "https://github.com/sbmlteam/libsbml"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "02e33d32",
   "metadata": {
    "collapsed": false,
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [],
   "source": [
    "from pathlib import Path\n",
    "\n",
    "import libsbml\n",
    "\n",
    "from combine_notebooks.validation.validation_sbml import validate_sbml"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "87a15b98",
   "metadata": {
    "collapsed": false,
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [],
   "source": [
    "def create_repressilator(sbml_path: Path) -> libsbml.SBMLDocument:\n",
    "    \"\"\"Create repressilator.\"\"\"\n",
    "    print(\"Create SBML model\")\n",
    "    # create a new document\n",
    "\n",
    "    doc: libsbml.SBMLDocument = libsbml.SBMLDocument(3, 2)\n",
    "    model: libsbml.Model = doc.createModel()\n",
    "\n",
    "    # --- compartments ---\n",
    "    # add compartment\n",
    "    c1: libsbml.Compartment = model.createCompartment()\n",
    "    c1.setId(\"cell\")\n",
    "    c1.setSize(1.0)\n",
    "    c1.setMetaId(\"meta_cell\")\n",
    "    c1.setSBOTerm(\"SBO:0000290\")\n",
    "    # set annotation\n",
    "    c1_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    c1_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    c1_cv.setBiologicalQualifierType(libsbml.BQB_IS)\n",
    "    c1_cv.addResource(\"http://identifiers.org/GO:0005623\")\n",
    "    c1.addCVTerm(c1_cv)\n",
    "\n",
    "    # --- species ---\n",
    "    # add species for the 3 mRNAs and 3 Proteins\n",
    "    s1: libsbml.Species = model.createSpecies()\n",
    "    s1.setId(\"PX\")\n",
    "    s1.setMetaId(\"PX\")\n",
    "    s1.setCompartment(\"cell\")\n",
    "    s1.setName(\"LacI protein\")\n",
    "    s1.setSBOTerm(\"SBO:0000252\")\n",
    "    s1.setInitialAmount(0)\n",
    "    s1.setHasOnlySubstanceUnits(True)\n",
    "    # set annotation\n",
    "    s1_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    s1_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    s1_cv.setBiologicalQualifierType(libsbml.BQB_IS)\n",
    "    s1_cv.addResource(\"http://identifiers.org/uniprot/P03023\")\n",
    "    s1.addCVTerm(s1_cv)\n",
    "\n",
    "    s2: libsbml.Species = model.createSpecies()\n",
    "    s2.setId(\"PY\")\n",
    "    s2.setMetaId(\"PY\")\n",
    "    s2.setCompartment(\"cell\")\n",
    "    s2.setName(\"TetR protein\")\n",
    "    s2.setSBOTerm(\"SBO:0000252\")\n",
    "    s2.setInitialAmount(0)\n",
    "    s2.setHasOnlySubstanceUnits(True)\n",
    "    # set annotation\n",
    "    s2_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    s2_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    s2_cv.setBiologicalQualifierType(libsbml.BQB_IS)\n",
    "    s2_cv.addResource(\"http://identifiers.org/uniprot/P04483\")\n",
    "    s2.addCVTerm(s2_cv)\n",
    "\n",
    "    s3: libsbml.Species = model.createSpecies()\n",
    "    s3.setId(\"PZ\")\n",
    "    s3.setMetaId(\"PZ\")\n",
    "    s3.setCompartment(\"cell\")\n",
    "    s3.setName(\"cI protein\")\n",
    "    s3.setSBOTerm(\"SBO:0000252\")\n",
    "    s3.setInitialAmount(0)\n",
    "    s3.setHasOnlySubstanceUnits(True)\n",
    "    # set annotation\n",
    "    s3_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    s3_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    s3_cv.setBiologicalQualifierType(libsbml.BQB_IS)\n",
    "    # example setting a model qualifier\n",
    "    # s3_cv.setQualifierType(libsbml.MODEL_QUALIFIER)\n",
    "    # s3_cv.setBiologicalQualifierType(libsbml.BQM_IS)\n",
    "    s3_cv.addResource(\"http://identifiers.org/uniprot/P03034\")\n",
    "    s3.addCVTerm(s3_cv)\n",
    "\n",
    "    s4: libsbml.Species = model.createSpecies()\n",
    "    s4.setId(\"X\")\n",
    "    s4.setMetaId(\"meta_X\")\n",
    "    s4.setCompartment(\"cell\")\n",
    "    s4.setName(\"LacI mRNA\")\n",
    "    s4.setSBOTerm(\"SBO:0000250\")\n",
    "    s4.setInitialAmount(0)\n",
    "    s4.setHasOnlySubstanceUnits(True)\n",
    "    # set annotation\n",
    "    s4_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    s4_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    s4_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    s4_cv.addResource(\"http://identifiers.org/CHEBI:33699\")\n",
    "    s4_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    s4_cv.addResource(\"http://identifiers.org/kegg.compound/C00046\")\n",
    "    s4.addCVTerm(s4_cv)\n",
    "    s4_cv.setBiologicalQualifierType(libsbml.BQB_ENCODES)\n",
    "    s4_cv.addResource(\"http://identifiers.org/uniprot/P03023\")\n",
    "    s4.addCVTerm(s4_cv)\n",
    "\n",
    "    s5: libsbml.Species = model.createSpecies()\n",
    "    s5.setId(\"Y\")\n",
    "    s5.setMetaId(\"meta_Y\")\n",
    "    s5.setCompartment(\"cell\")\n",
    "    s5.setName(\"TetR mRNA\")\n",
    "    s5.setSBOTerm(\"SBO:0000250\")\n",
    "    s5.setInitialAmount(20)\n",
    "    s5.setHasOnlySubstanceUnits(True)\n",
    "    # set annotation\n",
    "    s5_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    s5_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    s5_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    s5_cv.addResource(\"http://identifiers.org/CHEBI:33699\")\n",
    "    s5_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    s5_cv.addResource(\"http://identifiers.org/kegg.compound/C00046\")\n",
    "    s5.addCVTerm(s5_cv)\n",
    "    s5_cv.setBiologicalQualifierType(libsbml.BQB_ENCODES)\n",
    "    s5_cv.addResource(\"http://identifiers.org/uniprot/P04483\")\n",
    "    s5.addCVTerm(s5_cv)\n",
    "\n",
    "    s6: libsbml.Species = model.createSpecies()\n",
    "    s6.setId(\"Z\")\n",
    "    s6.setMetaId(\"meta_Z\")\n",
    "    s6.setCompartment(\"cell\")\n",
    "    s6.setName(\"cl mRNA\")\n",
    "    s6.setSBOTerm(\"SBO:0000250\")\n",
    "    s6.setInitialAmount(0)\n",
    "    s6.setHasOnlySubstanceUnits(True)\n",
    "    # set annotation\n",
    "    s6_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    s6_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    s6_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    s6_cv.addResource(\"http://identifiers.org/CHEBI:33699\")\n",
    "    s6_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    s6_cv.addResource(\"http://identifiers.org/kegg.compound/C00046\")\n",
    "    s6.addCVTerm(s6_cv)\n",
    "    s6_cv.setBiologicalQualifierType(libsbml.BQB_ENCODES)\n",
    "    s6_cv.addResource(\"http://identifiers.org/uniprot/P03034\")\n",
    "    s6.addCVTerm(s6_cv)\n",
    "\n",
    "    # --- parameters ---\n",
    "    # <parameter id=\"kd_mRNA\" constant=\"false\" name=\"kd_mRNA\" sboTerm=\"SBO:0000356\">\n",
    "    p1: libsbml.Parameter = model.createParameter()\n",
    "    p1.setId(\"tau_mRNA\")\n",
    "    p1.setName(\"mRNA half life\")\n",
    "    p1.setConstant(True)\n",
    "    p1.setValue(2.0)\n",
    "\n",
    "    # <parameter id=\"kd_mRNA\" constant=\"false\" name=\"kd_mRNA\" sboTerm=\"SBO:0000356\">\n",
    "    p2: libsbml.Parameter = model.createParameter()\n",
    "    p2.setId(\"kd_mRNA\")\n",
    "    p2.setName(\"kd_mRNA\")\n",
    "    p2.setSBOTerm(\"SBO:0000356\")\n",
    "    p2.setConstant(False)\n",
    "\n",
    "    # <parameter metaid=\"metaid_0000233\" sboTerm=\"SBO:0000016\" id=\"k_tl\" name=\"k_tl\" constant=\"false\">\n",
    "    p3: libsbml.Parameter = model.createParameter()\n",
    "    p3.setId(\"k_tl\")\n",
    "    p3.setName(\"k_tl\")\n",
    "    p3.setSBOTerm(\"SBO:0000016\")\n",
    "    p3.setConstant(False)\n",
    "\n",
    "    # <parameter metaid=\"metaid_0000025\" id=\"eff\" name=\"translation efficiency\" value=\"20\">\n",
    "    p4: libsbml.Parameter = model.createParameter()\n",
    "    p4.setId(\"eff\")\n",
    "    p4.setName(\"translation efficiency\")\n",
    "    p4.setConstant(True)\n",
    "    p4.setValue(20)\n",
    "\n",
    "    # <parameter metaid=\"metaid_0000032\" sboTerm=\"SBO:0000348\" id=\"t_ave\" name=\"average mRNA life time\" constant=\"false\"/>\n",
    "    p5: libsbml.Parameter = model.createParameter()\n",
    "    p5.setId(\"t_ave\")\n",
    "    p5.setName(\"average mRNA life time\")\n",
    "    p5.setSBOTerm(\"SBO:0000348\")\n",
    "    p5.setConstant(False)\n",
    "\n",
    "    # <parameter metaid=\"metaid_0000133\" sboTerm=\"SBO:0000356\" id=\"kd_prot\" name=\"kd_prot\" constant=\"false\">\n",
    "    p6: libsbml.Parameter = model.createParameter()\n",
    "    p6.setId(\"kd_prot\")\n",
    "    p6.setName(\"kd_prot\")\n",
    "    p6.setSBOTerm(\"SBO:0000356\")\n",
    "    p6.setConstant(False)\n",
    "\n",
    "    # <parameter metaid=\"metaid_0000128\" sboTerm=\"SBO:0000332\" id=\"tau_prot\" name=\"protein half life\" value=\"10\"/>\n",
    "    p7: libsbml.Parameter = model.createParameter()\n",
    "    p7.setId(\"tau_prot\")\n",
    "    p7.setName(\"protien half life\")\n",
    "    p7.setConstant(True)\n",
    "    p7.setValue(10)\n",
    "\n",
    "    # <parameter metaid=\"metaid_0000234\" sboTerm=\"SBO:0000485\" id=\"a0_tr\" name=\"a0_tr\" constant=\"false\">\n",
    "    p8: libsbml.Parameter = model.createParameter()\n",
    "    p8.setId(\"a0_tr\")\n",
    "    p8.setName(\"a0_tr\")\n",
    "    p8.setSBOTerm(\"SBO:0000485\")\n",
    "    p8.setConstant(False)\n",
    "\n",
    "    # <parameter metaid=\"metaid_0500235\" sboTerm=\"SBO:0000485\" id=\"ps_0\" name=\"tps_repr\" value=\"0.0005\">\n",
    "    p9: libsbml.Parameter = model.createParameter()\n",
    "    p9.setId(\"ps_0\")\n",
    "    p9.setName(\"tps_repr\")\n",
    "    p9.setConstant(True)\n",
    "    p9.setValue(0.0005)\n",
    "\n",
    "    # <parameter metaid=\"metaid_0900235\" sboTerm=\"SBO:0000186\" id=\"a_tr\" name=\"a_tr\" constant=\"false\">\n",
    "    p10: libsbml.Parameter = model.createParameter()\n",
    "    p10.setId(\"a_tr\")\n",
    "    p10.setName(\"a_tr\")\n",
    "    p10.setSBOTerm(\"SBO:0000186\")\n",
    "    p10.setConstant(False)\n",
    "\n",
    "    # <parameter metaid=\"metaid_0800235\" sboTerm=\"SBO:0000186\" id=\"ps_a\" name=\"tps_active\" value=\"0.5\">\n",
    "    p11: libsbml.Parameter = model.createParameter()\n",
    "    p11.setId(\"ps_a\")\n",
    "    p11.setName(\"tps_active\")\n",
    "    p11.setConstant(True)\n",
    "    p11.setValue(0.5)\n",
    "\n",
    "    # <parameter metaid=\"metaid_0000027\" sboTerm=\"SBO:0000288\" id=\"KM\" name=\"KM\" value=\"40\">\n",
    "    p12: libsbml.Parameter = model.createParameter()\n",
    "    p12.setId(\"KM\")\n",
    "    p12.setName(\"KM\")\n",
    "    p12.setConstant(True)\n",
    "    p12.setValue(40)\n",
    "\n",
    "    # <parameter metaid=\"metaid_0000026\" sboTerm=\"SBO:0000190\" id=\"n\" name=\"n\" value=\"2\">\n",
    "    p13: libsbml.Parameter = model.createParameter()\n",
    "    p13.setId(\"n\")\n",
    "    p13.setName(\"n\")\n",
    "    p13.setConstant(True)\n",
    "    p13.setValue(2.0)\n",
    "\n",
    "    # TODO: a0_tr, a_tr, n, KM\n",
    "\n",
    "    # --- rules ---\n",
    "    a1: libsbml.AssignmentRule = model.createAssignmentRule()\n",
    "    a1.setVariable(\"kd_mRNA\")\n",
    "    math_ast1: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\n",
    "        \"ln(2) / tau_mRNA\", model\n",
    "    )\n",
    "    a1.setMath(math_ast1)\n",
    "\n",
    "    a2: libsbml.AssignmentRule = model.createAssignmentRule()\n",
    "    a2.setVariable(\"t_ave\")\n",
    "    math_ast2: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\n",
    "        \"tau_mRNA / ln(2)\", model\n",
    "    )\n",
    "    a2.setMath(math_ast2)\n",
    "\n",
    "    a3: libsbml.AssignmentRule = model.createAssignmentRule()\n",
    "    a3.setVariable(\"k_tl\")\n",
    "    math_ast3: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\"eff / t_ave\", model)\n",
    "    a3.setMath(math_ast3)\n",
    "\n",
    "    a4: libsbml.AssignmentRule = model.createAssignmentRule()\n",
    "    a4.setVariable(\"kd_prot\")\n",
    "    math_ast4: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\n",
    "        \"ln(2) / tau_prot\", model\n",
    "    )\n",
    "    a4.setMath(math_ast4)\n",
    "\n",
    "    a5: libsbml.AssignmentRule = model.createAssignmentRule()\n",
    "    a5.setVariable(\"a0_tr\")\n",
    "    math_ast5: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\"ps_0 * 60\", model)\n",
    "    a5.setMath(math_ast5)\n",
    "\n",
    "    a6: libsbml.AssignmentRule = model.createAssignmentRule()\n",
    "    a6.setVariable(\"a_tr\")\n",
    "    math_ast6: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\n",
    "        \"(ps_a - ps_0) * 60\", model\n",
    "    )\n",
    "    a6.setMath(math_ast6)\n",
    "\n",
    "    # --- reaction ---\n",
    "    # X -> None\n",
    "    r1: libsbml.Reaction = model.createReaction()\n",
    "    r1.setId(\"Reaction1\"),  # set reaction id\n",
    "    r1.setMetaId(\"meta_Reaction1\")\n",
    "    r1.setSBOTerm(\"SBO:0000179\")\n",
    "    r1.setName(\"degradation of LacI transcripts\")\n",
    "    r1.setReversible(False)\n",
    "    # set annotation\n",
    "    r1_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    r1_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    r1_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    r1_cv.addResource(\"http://identifiers.org/GO:0006402\")\n",
    "    r1.addCVTerm(r1_cv)\n",
    "\n",
    "    species_ref1: libsbml.SpeciesReference = r1.createReactant()\n",
    "    species_ref1.setSpecies(\"X\")  # assign reactant species\n",
    "\n",
    "    math_ast7: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\"kd_mRNA * X\", model)\n",
    "    kinetic_law = r1.createKineticLaw()\n",
    "    kinetic_law.setSBOTerm(\"SBO:0000049\")\n",
    "    kinetic_law.setMath(math_ast7)\n",
    "\n",
    "    r2 = model.createReaction()\n",
    "    r2.setId(\"Reaction2\"),  # set reaction id\n",
    "    r2.setMetaId(\"meta_Reaction2\")\n",
    "    r2.setSBOTerm(\"SBO:0000179\")\n",
    "    r2.setName(\"degradation of TetR transcripts\")\n",
    "    r2.setReversible(False)\n",
    "\n",
    "    r2_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    r2_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    r2_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    r2_cv.addResource(\"http://identifiers.org/GO:0006402\")\n",
    "    r2.addCVTerm(r1_cv)\n",
    "\n",
    "    species_ref2 = r2.createReactant()\n",
    "    species_ref2.setSpecies(\"Y\")  # assign reactant species\n",
    "\n",
    "    math_ast8: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\"kd_mRNA * Y\", model)\n",
    "    kinetic_law = r2.createKineticLaw()\n",
    "    kinetic_law.setSBOTerm(\"SBO:0000049\")\n",
    "    kinetic_law.setMath(math_ast8)\n",
    "\n",
    "    r3 = model.createReaction()\n",
    "    r3.setId(\"Reaction3\"),  # set reaction id\n",
    "    r3.setMetaId(\"meta_Reaction3\")\n",
    "    r3.setSBOTerm(\"SBO:0000179\")\n",
    "    r3.setName(\"degradation of CI transcripts\")\n",
    "    r3.setReversible(False)\n",
    "    # set annotation\n",
    "    r3_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    r3_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    r3_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    r3_cv.addResource(\"http://identifiers.org/GO:0006402\")\n",
    "    r3.addCVTerm(r3_cv)\n",
    "\n",
    "    species_ref3 = r3.createReactant()\n",
    "    species_ref3.setSpecies(\"Z\")  # assign reactant species\n",
    "\n",
    "    math_ast9: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\"kd_mRNA * Z\", model)\n",
    "    kinetic_law = r3.createKineticLaw()\n",
    "    kinetic_law.setSBOTerm(\"SBO:0000049\")\n",
    "    kinetic_law.setMath(math_ast9)\n",
    "\n",
    "    r4 = model.createReaction()\n",
    "    r4.setId(\"Reaction4\"),  # set reaction id\n",
    "    r4.setMetaId(\"meta_Reaction4\")\n",
    "    r4.setSBOTerm(\"SBO:0000184\")\n",
    "    r4.setName(\"translation of LacI\")\n",
    "    r4.setReversible(False)\n",
    "    # set annotation\n",
    "    r4_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    r4_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    r4_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    r4_cv.addResource(\"http://identifiers.org/GO:0006412\")\n",
    "    r4.addCVTerm(r4_cv)\n",
    "\n",
    "    species_ref4 = r4.createProduct()\n",
    "    species_ref4.setSpecies(\"PX\")  # assign product species\n",
    "\n",
    "    species_ref_4 = r4.createModifier()\n",
    "    species_ref_4.setSpecies(\"X\")\n",
    "    species_ref_4.setSBOTerm(\"SBO:0000461\")\n",
    "\n",
    "    math_ast10: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\"k_tl * X\", model)\n",
    "    kinetic_law = r4.createKineticLaw()\n",
    "    kinetic_law.setSBOTerm(\"SBO:0000049\")\n",
    "    kinetic_law.setMath(math_ast10)\n",
    "\n",
    "    r5 = model.createReaction()\n",
    "    r5.setId(\"Reaction5\"),  # set reaction id\n",
    "    r5.setMetaId(\"meta_Reaction5\")\n",
    "    r5.setSBOTerm(\"SBO:0000184\")\n",
    "    r5.setName(\"translation of TetR\")\n",
    "    r5.setReversible(False)\n",
    "    s3_cv = libsbml.CVTerm()\n",
    "    # set annotation\n",
    "    r5_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    r5_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    r5_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    r5_cv.addResource(\"http://identifiers.org/GO:0006412\")\n",
    "    r5.addCVTerm(r5_cv)\n",
    "\n",
    "    species_ref5 = r5.createProduct()\n",
    "    species_ref5.setSpecies(\"PY\")  # assign product species\n",
    "    species_ref_5 = r5.createModifier()\n",
    "    species_ref_5.setSpecies(\"Y\")\n",
    "    species_ref_5.setSBOTerm(\"SBO:0000461\")\n",
    "\n",
    "    math_ast11: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\"k_tl * Y\", model)\n",
    "    kinetic_law = r5.createKineticLaw()\n",
    "    kinetic_law.setSBOTerm(\"SBO:0000049\")\n",
    "    kinetic_law.setMath(math_ast11)\n",
    "\n",
    "    r6 = model.createReaction()\n",
    "    r6.setId(\"Reaction6\"),  # set reaction id\n",
    "    r6.setMetaId(\"meta_Reaction6\")\n",
    "    r6.setSBOTerm(\"SBO:0000184\")\n",
    "    r6.setName(\"translation of CI\")\n",
    "    r6.setReversible(False)\n",
    "    # set annotation\n",
    "    r6_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    r6_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    r6_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    r6_cv.addResource(\"http://identifiers.org/GO:0006412\")\n",
    "    r6.addCVTerm(r6_cv)\n",
    "\n",
    "    species_ref6 = r6.createProduct()\n",
    "    species_ref6.setSpecies(\"PZ\")  # assign product species\n",
    "    species_ref_6 = r6.createModifier()\n",
    "    species_ref_6.setSpecies(\"Z\")\n",
    "    species_ref_6.setSBOTerm(\"SBO:0000461\")\n",
    "\n",
    "    math_ast12: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\"k_tl * Z\", model)\n",
    "    kinetic_law = r6.createKineticLaw()\n",
    "    kinetic_law.setSBOTerm(\"SBO:0000049\")\n",
    "    kinetic_law.setMath(math_ast12)\n",
    "\n",
    "    r7 = model.createReaction()\n",
    "    r7.setId(\"Reaction7\"),  # set reaction id\n",
    "    r7.setMetaId(\"meta_Reaction7\")\n",
    "    r7.setSBOTerm(\"SBO:0000179\")\n",
    "    r7.setName(\"degradation of LacI\")\n",
    "    r7.setReversible(False)\n",
    "    # set annotation\n",
    "    r7_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    r7_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    r7_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    r7_cv.addResource(\"http://identifiers.org/GO:0030163\")\n",
    "    r7.addCVTerm(r7_cv)\n",
    "\n",
    "    species_ref7 = r7.createReactant()\n",
    "    species_ref7.setSpecies(\"PX\")  # assign reactant species\n",
    "\n",
    "    math_ast13: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\"kd_prot * PX\", model)\n",
    "    kinetic_law = r7.createKineticLaw()\n",
    "    kinetic_law.setSBOTerm(\"SBO:0000049\")\n",
    "    kinetic_law.setMath(math_ast13)\n",
    "\n",
    "    r8 = model.createReaction()\n",
    "    r8.setId(\"Reaction8\"),  # set reaction id\n",
    "    r8.setMetaId(\"meta_Reaction8\")\n",
    "    r8.setSBOTerm(\"SBO:0000179\")\n",
    "    r8.setName(\"degradation of TetR\")\n",
    "    r8.setReversible(False)\n",
    "    # set annotation\n",
    "    r8_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    r8_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    r8_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    r8_cv.addResource(\"http://identifiers.org/GO:0030163\")\n",
    "    r8.addCVTerm(r8_cv)\n",
    "\n",
    "    species_ref8 = r8.createReactant()\n",
    "    species_ref8.setSpecies(\"PY\")  # assign reactant species\n",
    "\n",
    "    math_ast14: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\"kd_prot * PY\", model)\n",
    "    kinetic_law = r8.createKineticLaw()\n",
    "    kinetic_law.setSBOTerm(\"SBO:0000049\")\n",
    "    kinetic_law.setMath(math_ast14)\n",
    "\n",
    "    r9 = model.createReaction()\n",
    "    r9.setId(\"Reaction9\"),  # set reaction id\n",
    "    r9.setMetaId(\"meta_Reaction9\")\n",
    "    r9.setSBOTerm(\"SBO:0000179\")\n",
    "    r9.setName(\"degradation of CI\")\n",
    "    r9.setReversible(False)\n",
    "    # set annotation\n",
    "    r9_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    r9_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    r9_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    r9_cv.addResource(\"http://identifiers.org/GO:0030163\")\n",
    "    r9.addCVTerm(r9_cv)\n",
    "\n",
    "    species_ref9 = r9.createReactant()\n",
    "    species_ref9.setSpecies(\"PZ\")  # assign reactant species\n",
    "\n",
    "    math_ast15: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\"kd_prot * PZ\", model)\n",
    "    kinetic_law = r9.createKineticLaw()\n",
    "    kinetic_law.setSBOTerm(\"SBO:0000049\")\n",
    "    kinetic_law.setMath(math_ast15)\n",
    "\n",
    "    r10 = model.createReaction()\n",
    "    r10.setId(\"Reaction10\"),  # set reaction id\n",
    "    r10.setMetaId(\"meta_Reaction10\")\n",
    "    r10.setSBOTerm(\"SBO:0000183\")\n",
    "    r10.setName(\"transcription of LacI\")\n",
    "    r10.setReversible(False)\n",
    "    # set annotation\n",
    "    r10_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    r10_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    r10_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    r10_cv.addResource(\"http://identifiers.org/GO:0006351\")\n",
    "    r10.addCVTerm(r10_cv)\n",
    "\n",
    "    species_ref10 = r10.createProduct()\n",
    "    species_ref10.setSpecies(\"X\")  # assign product species\n",
    "    species_ref_10 = r10.createModifier()\n",
    "    species_ref_10.setSpecies(\"PZ\")\n",
    "    species_ref_10.setSBOTerm(\"SBO:0000536\")\n",
    "\n",
    "    math_ast16: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\n",
    "        \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PZ, n))\", model\n",
    "    )\n",
    "    kinetic_law = r10.createKineticLaw()\n",
    "    kinetic_law.setMath(math_ast16)\n",
    "\n",
    "    r11 = model.createReaction()\n",
    "    r11.setId(\"Reaction11\"),  # set reaction id\n",
    "    r11.setMetaId(\"meta_Reaction11\")\n",
    "    r11.setSBOTerm(\"SBO:0000183\")\n",
    "    r11.setName(\"transcription of TetR\")\n",
    "    r11.setReversible(False)\n",
    "    # set annotation\n",
    "    r11_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    r11_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    r11_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    r11_cv.addResource(\"http://identifiers.org/GO:0006351\")\n",
    "    r11.addCVTerm(r11_cv)\n",
    "\n",
    "    species_ref11 = r11.createProduct()\n",
    "    species_ref11.setSpecies(\"Y\")  # assign product species\n",
    "    species_ref_11 = r11.createModifier()\n",
    "    species_ref_11.setSpecies(\"PX\")\n",
    "    species_ref_11.setSBOTerm(\"SBO:0000536\")\n",
    "\n",
    "    math_ast17: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\n",
    "        \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PX, n))\", model\n",
    "    )\n",
    "    kinetic_law = r11.createKineticLaw()\n",
    "    kinetic_law.setMath(math_ast17)\n",
    "\n",
    "    r12 = model.createReaction()\n",
    "    r12.setId(\"Reaction12\"),  # set reaction id\n",
    "    r12.setMetaId(\"meta_Reaction12\")\n",
    "    r12.setSBOTerm(\"SBO:0000183\")\n",
    "    r12.setName(\"transcription of CI\")\n",
    "    r12.setReversible(False)\n",
    "    # set annotation\n",
    "    r12_cv: libsbml.CVTerm = libsbml.CVTerm()\n",
    "    r12_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    r12_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)\n",
    "    r12_cv.addResource(\"http://identifiers.org/GO:0006351\")\n",
    "    r12.addCVTerm(r12_cv)\n",
    "\n",
    "    species_ref12 = r12.createProduct()\n",
    "    species_ref12.setSpecies(\"Z\")  # assign product species\n",
    "    species_ref_12 = r12.createModifier()\n",
    "    species_ref_12.setSpecies(\"PY\")\n",
    "    species_ref_12.setSBOTerm(\"SBO:0000536\")\n",
    "\n",
    "    math_ast18: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(\n",
    "        \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PY, n))\", model\n",
    "    )\n",
    "    kinetic_law = r12.createKineticLaw()\n",
    "    kinetic_law.setMath(math_ast18)\n",
    "\n",
    "    print(\"-\" * 80)\n",
    "    print(libsbml.writeSBMLToString(doc))\n",
    "    print(\"-\" * 80)\n",
    "\n",
    "    # write to file\n",
    "    libsbml.writeSBMLToFile(doc, str(sbml_path))\n",
    "\n",
    "    # validate file\n",
    "    validate_sbml(doc, units_consistency=False)\n",
    "\n",
    "    return doc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "0a18aa9a",
   "metadata": {
    "collapsed": false,
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Create SBML model\n",
      "--------------------------------------------------------------------------------\n",
      "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
      "<sbml xmlns=\"http://www.sbml.org/sbml/level3/version2/core\" level=\"3\" version=\"2\">\n",
      "  <model>\n",
      "    <listOfCompartments>\n",
      "      <compartment metaid=\"meta_cell\" sboTerm=\"SBO:0000290\" id=\"cell\" size=\"1\">\n",
      "        <annotation>\n",
      "          <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:vCard4=\"http://www.w3.org/2006/vcard/ns#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n",
      "            <rdf:Description rdf:about=\"#meta_cell\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0005623\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </compartment>\n",
      "    </listOfCompartments>\n",
      "    <listOfSpecies>\n",
      "      <species metaid=\"PX\" sboTerm=\"SBO:0000252\" id=\"PX\" name=\"LacI protein\" compartment=\"cell\" initialAmount=\"0\" hasOnlySubstanceUnits=\"true\">\n",
      "        <annotation>\n",
      "          <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:vCard4=\"http://www.w3.org/2006/vcard/ns#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n",
      "            <rdf:Description rdf:about=\"#PX\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/uniprot/P03023\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </species>\n",
      "      <species metaid=\"PY\" sboTerm=\"SBO:0000252\" id=\"PY\" name=\"TetR protein\" compartment=\"cell\" initialAmount=\"0\" hasOnlySubstanceUnits=\"true\">\n",
      "        <annotation>\n",
      "          <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:vCard4=\"http://www.w3.org/2006/vcard/ns#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n",
      "            <rdf:Description rdf:about=\"#PY\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/uniprot/P04483\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </species>\n",
      "      <species metaid=\"PZ\" sboTerm=\"SBO:0000252\" id=\"PZ\" name=\"cI protein\" compartment=\"cell\" initialAmount=\"0\" hasOnlySubstanceUnits=\"true\">\n",
      "        <annotation>\n",
      "          <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:vCard4=\"http://www.w3.org/2006/vcard/ns#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n",
      "            <rdf:Description rdf:about=\"#PZ\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/uniprot/P03034\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </species>\n",
      "      <species metaid=\"meta_X\" sboTerm=\"SBO:0000250\" id=\"X\" name=\"LacI mRNA\" compartment=\"cell\" initialAmount=\"0\" hasOnlySubstanceUnits=\"true\">\n",
      "        <annotation>\n",
      "          <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:vCard4=\"http://www.w3.org/2006/vcard/ns#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n",
      "            <rdf:Description rdf:about=\"#meta_X\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/CHEBI:33699\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/kegg.compound/C00046\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "              <bqbiol:encodes>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/uniprot/P03023\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:encodes>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </species>\n",
      "      <species metaid=\"meta_Y\" sboTerm=\"SBO:0000250\" id=\"Y\" name=\"TetR mRNA\" compartment=\"cell\" initialAmount=\"20\" hasOnlySubstanceUnits=\"true\">\n",
      "        <annotation>\n",
      "          <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:vCard4=\"http://www.w3.org/2006/vcard/ns#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n",
      "            <rdf:Description rdf:about=\"#meta_Y\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/CHEBI:33699\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/kegg.compound/C00046\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "              <bqbiol:encodes>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/uniprot/P04483\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:encodes>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </species>\n",
      "      <species metaid=\"meta_Z\" sboTerm=\"SBO:0000250\" id=\"Z\" name=\"cl mRNA\" compartment=\"cell\" initialAmount=\"0\" hasOnlySubstanceUnits=\"true\">\n",
      "        <annotation>\n",
      "          <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:vCard4=\"http://www.w3.org/2006/vcard/ns#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n",
      "            <rdf:Description rdf:about=\"#meta_Z\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/CHEBI:33699\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/kegg.compound/C00046\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "              <bqbiol:encodes>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/uniprot/P03034\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:encodes>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </species>\n",
      "    </listOfSpecies>\n",
      "    <listOfParameters>\n",
      "      <parameter id=\"tau_mRNA\" name=\"mRNA half life\" value=\"2\" constant=\"true\"/>\n",
      "      <parameter sboTerm=\"SBO:0000356\" id=\"kd_mRNA\" name=\"kd_mRNA\" constant=\"false\"/>\n",
      "      <parameter sboTerm=\"SBO:0000016\" id=\"k_tl\" name=\"k_tl\" constant=\"false\"/>\n",
      "      <parameter id=\"eff\" name=\"translation efficiency\" value=\"20\" constant=\"true\"/>\n",
      "      <parameter sboTerm=\"SBO:0000348\" id=\"t_ave\" name=\"average mRNA life time\" constant=\"false\"/>\n",
      "      <parameter sboTerm=\"SBO:0000356\" id=\"kd_prot\" name=\"kd_prot\" constant=\"false\"/>\n",
      "      <parameter id=\"tau_prot\" name=\"protien half life\" value=\"10\" constant=\"true\"/>\n",
      "      <parameter sboTerm=\"SBO:0000485\" id=\"a0_tr\" name=\"a0_tr\" constant=\"false\"/>\n",
      "      <parameter id=\"ps_0\" name=\"tps_repr\" value=\"0.0005\" constant=\"true\"/>\n",
      "      <parameter sboTerm=\"SBO:0000186\" id=\"a_tr\" name=\"a_tr\" constant=\"false\"/>\n",
      "      <parameter id=\"ps_a\" name=\"tps_active\" value=\"0.5\" constant=\"true\"/>\n",
      "      <parameter id=\"KM\" name=\"KM\" value=\"40\" constant=\"true\"/>\n",
      "      <parameter id=\"n\" name=\"n\" value=\"2\" constant=\"true\"/>\n",
      "    </listOfParameters>\n",
      "    <listOfRules>\n",
      "      <assignmentRule variable=\"kd_mRNA\">\n",
      "        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "          <apply>\n",
      "            <divide/>\n",
      "            <apply>\n",
      "              <ln/>\n",
      "              <cn type=\"integer\"> 2 </cn>\n",
      "            </apply>\n",
      "            <ci> tau_mRNA </ci>\n",
      "          </apply>\n",
      "        </math>\n",
      "      </assignmentRule>\n",
      "      <assignmentRule variable=\"t_ave\">\n",
      "        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "          <apply>\n",
      "            <divide/>\n",
      "            <ci> tau_mRNA </ci>\n",
      "            <apply>\n",
      "              <ln/>\n",
      "              <cn type=\"integer\"> 2 </cn>\n",
      "            </apply>\n",
      "          </apply>\n",
      "        </math>\n",
      "      </assignmentRule>\n",
      "      <assignmentRule variable=\"k_tl\">\n",
      "        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "          <apply>\n",
      "            <divide/>\n",
      "            <ci> eff </ci>\n",
      "            <ci> t_ave </ci>\n",
      "          </apply>\n",
      "        </math>\n",
      "      </assignmentRule>\n",
      "      <assignmentRule variable=\"kd_prot\">\n",
      "        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "          <apply>\n",
      "            <divide/>\n",
      "            <apply>\n",
      "              <ln/>\n",
      "              <cn type=\"integer\"> 2 </cn>\n",
      "            </apply>\n",
      "            <ci> tau_prot </ci>\n",
      "          </apply>\n",
      "        </math>\n",
      "      </assignmentRule>\n",
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      "--------------------------------------------------------------------------------\n",
      "--------------------------------------------------------------------------------\n",
      "validation error(s)      : 0\n",
      "validation warning(s)    : 0\n",
      "--------------------------------------------------------------------------------\n"
     ]
    }
   ],
   "source": [
    "if __name__ == \"__main__\":\n",
    "    from combine_notebooks import RESULTS_DIR\n",
    "\n",
    "    # RESOURCES_DIR: Path = Path(__file__).parent / \"resources\"\n",
    "    # RESULTS_DIR: Path = RESOURCES_DIR / \"results\"\n",
    "    doc: libsbml.SBMLDocument = create_repressilator(\n",
    "        sbml_path=RESULTS_DIR / \"repressilator_libsbml.xml\"\n",
    "    )\n",
    "\n",
    "        # <markdowncell>\n",
    "        "
   ]
  }
 ],
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   "display_name": "combine_notebooks",
   "language": "python",
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    "name": "ipython",
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