notebooks/example_sbml_libsbml.ipynb

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   "source": [
    "Create the repressilator step by step.\n",
    "\n",
    "See on biomodels.\n",
    "\n",
    "\n",
    "https://github.com/sbmlteam/libsbml"
   ]
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   "source": [
    "import os\n",
    "from pathlib import Path\n",
    "\n",
    "import libsbml\n",
    "\n",
    "from combine_notebooks.helper_functions.utils import *\n",
    "from combine_notebooks.validation.validation_sbml import validate_sbml"
   ]
  },
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   "source": [
    "\n",
    "\n",
    "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 and set annotation\n",
    "    c1 = add_compartment(model, \"cell\", 1.0, \"meta_cell\", \"SBO:0000290\")\n",
    "    c1_cv = create_annotation(\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS,\n",
    "        \"http://identifiers.org/GO:0005623\",\n",
    "    )\n",
    "    c1.addCVTerm(c1_cv)\n",
    "\n",
    "    # --- species ---\n",
    "    # add species for the 3 mRNAs and 3 Proteins and set annotations\n",
    "    s1 = add_species(model, \"PX\", \"PX\", \"cell\", \"LacI protein\", \"SBO:0000252\", 0, True)\n",
    "    s1_cv = create_annotation(\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS,\n",
    "        \"http://identifiers.org/uniprot/P03023\",\n",
    "    )\n",
    "    s1.addCVTerm(s1_cv)\n",
    "\n",
    "    s2 = add_species(model, \"PY\", \"PY\", \"cell\", \"TetR protein\", \"SBO:0000252\", 0, True)\n",
    "    s2_cv = create_annotation(\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS,\n",
    "        \"http://identifiers.org/uniprot/P04483\",\n",
    "    )\n",
    "    s2.addCVTerm(s2_cv)\n",
    "\n",
    "    s3 = add_species(model, \"PZ\", \"PZ\", \"cell\", \"cI protein\", \"SBO:0000252\", 0, True)\n",
    "    s3_cv = create_annotation(\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS,\n",
    "        \"http://identifiers.org/uniprot/P03034\",\n",
    "    )\n",
    "    # example setting a model qualifier\n",
    "    # s3_cv.setQualifierType(libsbml.MODEL_QUALIFIER)\n",
    "    # s3_cv.setBiologicalQualifierType(libsbml.BQM_IS)\n",
    "    s3.addCVTerm(s3_cv)\n",
    "\n",
    "    s4 = add_species(model, \"X\", \"meta_X\", \"cell\", \"LacI mRNA\", \"SBO:0000250\", 0, True)\n",
    "    s4_cv = create_annotation(\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/CHEBI:33699\",\n",
    "    )\n",
    "    s4_cv = add_annotation_resource(\n",
    "        s4_cv, libsbml.BQB_IS_VERSION_OF, \"http://identifiers.org/kegg.compound/C00046\"\n",
    "    )\n",
    "    s4.addCVTerm(s4_cv)\n",
    "    s4_cv = add_annotation_resource(\n",
    "        s4_cv, libsbml.BQB_ENCODES, \"http://identifiers.org/uniprot/P03023\"\n",
    "    )\n",
    "    s4.addCVTerm(s4_cv)\n",
    "\n",
    "    s5 = add_species(model, \"Y\", \"meta_Y\", \"cell\", \"TetR mRNA\", \"SBO:0000250\", 20, True)\n",
    "    s5_cv = create_annotation(\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/CHEBI:33699\",\n",
    "    )\n",
    "    s5_cv = add_annotation_resource(\n",
    "        s5_cv, libsbml.BQB_IS_VERSION_OF, \"http://identifiers.org/kegg.compound/C00046\"\n",
    "    )\n",
    "    s5.addCVTerm(s5_cv)\n",
    "    s5_cv = add_annotation_resource(\n",
    "        s5_cv, libsbml.BQB_ENCODES, \"http://identifiers.org/uniprot/P04483\"\n",
    "    )\n",
    "    s5.addCVTerm(s5_cv)\n",
    "\n",
    "    s6 = add_species(model, \"Z\", \"meta_Z\", \"cell\", \"cl mRNA\", \"SBO:0000250\", 0, True)\n",
    "    s6_cv = create_annotation(\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/CHEBI:33699\",\n",
    "    )\n",
    "    s6_cv = add_annotation_resource(\n",
    "        s6_cv, libsbml.BQB_IS_VERSION_OF, \"http://identifiers.org/kegg.compound/C00046\"\n",
    "    )\n",
    "    s6.addCVTerm(s6_cv)\n",
    "    s6_cv = add_annotation_resource(\n",
    "        s6_cv, libsbml.BQB_ENCODES, \"http://identifiers.org/uniprot/P03034\"\n",
    "    )\n",
    "    s6.addCVTerm(s6_cv)\n",
    "\n",
    "    # --- parameters ---\n",
    "    # <parameter id=\"tau_mRNA\" name=\"mRNA half life\" value=\"2\" constant=\"true\"/>\n",
    "    add_parameters(model, \"tau_mRNA\", \"mRNA half life\", True, value=2.0)\n",
    "    # <parameter id=\"kd_mRNA\" constant=\"false\" name=\"kd_mRNA\" sboTerm=\"SBO:0000356\">\n",
    "    add_parameters(model, \"kd_mRNA\", \"kd_mRNA\", False, sbo_term=\"SBO:0000356\")\n",
    "    # <parameter metaid=\"metaid_0000233\" sboTerm=\"SBO:0000016\" id=\"k_tl\" name=\"k_tl\" constant=\"false\">\n",
    "    add_parameters(model, \"k_tl\", \"k_tl\", False, sbo_term=\"SBO:0000016\")\n",
    "    # <parameter metaid=\"metaid_0000025\" id=\"eff\" name=\"translation efficiency\" value=\"20\">\n",
    "    add_parameters(model, \"eff\", \"translation efficiency\", True, value=20)\n",
    "    # <parameter metaid=\"metaid_0000032\" sboTerm=\"SBO:0000348\" id=\"t_ave\" name=\"average mRNA life time\" constant=\"false\"/>\n",
    "    add_parameters(\n",
    "        model, \"t_ave\", \"average mRNA life time\", False, sbo_term=\"SBO:0000348\"\n",
    "    )\n",
    "    # <parameter metaid=\"metaid_0000133\" sboTerm=\"SBO:0000356\" id=\"kd_prot\" name=\"kd_prot\" constant=\"false\">\n",
    "    add_parameters(model, \"kd_prot\", \"kd_prot\", False, sbo_term=\"SBO:0000356\")\n",
    "    # <parameter metaid=\"metaid_0000128\" sboTerm=\"SBO:0000332\" id=\"tau_prot\" name=\"protein half life\" value=\"10\"/>\n",
    "    add_parameters(model, \"tau_prot\", \"protien half life\", True, value=10)\n",
    "    # <parameter metaid=\"metaid_0000234\" sboTerm=\"SBO:0000485\" id=\"a0_tr\" name=\"a0_tr\" constant=\"false\">\n",
    "    add_parameters(model, \"a0_tr\", \"a0_tr\", False, sbo_term=\"SBO:0000485\")\n",
    "    # <parameter metaid=\"metaid_0500235\" sboTerm=\"SBO:0000485\" id=\"ps_0\" name=\"tps_repr\" value=\"0.0005\">\n",
    "    add_parameters(model, \"ps_0\", \"tps_repr\", True, value=0.0005)\n",
    "    # <parameter metaid=\"metaid_0900235\" sboTerm=\"SBO:0000186\" id=\"a_tr\" name=\"a_tr\" constant=\"false\">\n",
    "    add_parameters(model, \"a_tr\", \"a_tr\", False, sbo_term=\"SBO:0000186\")\n",
    "    # <parameter metaid=\"metaid_0800235\" sboTerm=\"SBO:0000186\" id=\"ps_a\" name=\"tps_active\" value=\"0.5\">\n",
    "    add_parameters(model, \"ps_a\", \"tps_active\", True, value=0.5)\n",
    "    # <parameter metaid=\"metaid_0000027\" sboTerm=\"SBO:0000288\" id=\"KM\" name=\"KM\" value=\"40\">\n",
    "    add_parameters(model, \"KM\", \"KM\", True, value=40)\n",
    "    # <parameter metaid=\"metaid_0000026\" sboTerm=\"SBO:0000190\" id=\"n\" name=\"n\" value=\"2\">\n",
    "    add_parameters(model, \"n\", \"n\", True, value=2.0)\n",
    "\n",
    "    # TODO: a0_tr, a_tr, n, KM\n",
    "\n",
    "    # --- rules ---\n",
    "    add_assignment_rule(model, \"kd_mRNA\", \"ln(2) / tau_mRNA\")\n",
    "    add_assignment_rule(model, \"t_ave\", \"tau_mRNA / ln(2)\")\n",
    "    add_assignment_rule(model, \"k_tl\", \"eff / t_ave\")\n",
    "    add_assignment_rule(model, \"kd_prot\", \"ln(2) / tau_prot\")\n",
    "    add_assignment_rule(model, \"a0_tr\", \"ps_0 * 60\")\n",
    "    add_assignment_rule(model, \"a_tr\", \"(ps_a - ps_0) * 60\")\n",
    "\n",
    "    # --- reaction ---\n",
    "    # X -> None\n",
    "    r1 = add_reactions(\n",
    "        model,\n",
    "        \"Reaction1\",\n",
    "        \"meta_Reaction1\",\n",
    "        \"SBO:0000179\",\n",
    "        \"degradation of LacI transcripts\",\n",
    "        False,\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/GO:0006402\",\n",
    "        \"kd_mRNA * X\",\n",
    "        \"SBO:0000049\",\n",
    "    )\n",
    "    add_reactant_to_reaction(r1, \"X\")\n",
    "\n",
    "    r2 = add_reactions(\n",
    "        model,\n",
    "        \"Reaction2\",\n",
    "        \"meta_Reaction2\",\n",
    "        \"SBO:0000179\",\n",
    "        \"degradation of TetR transcripts\",\n",
    "        False,\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/GO:0006402\",\n",
    "        \"kd_mRNA * Y\",\n",
    "        \"SBO:0000049\",\n",
    "    )\n",
    "    add_reactant_to_reaction(r2, \"Y\")\n",
    "\n",
    "    r3 = add_reactions(\n",
    "        model,\n",
    "        \"Reaction3\",\n",
    "        \"meta_Reaction3\",\n",
    "        \"SBO:0000179\",\n",
    "        \"degradation of CI transcripts\",\n",
    "        False,\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/GO:0006402\",\n",
    "        \"kd_mRNA * Z\",\n",
    "        \"SBO:0000049\",\n",
    "    )\n",
    "    add_reactant_to_reaction(r3, \"Z\")\n",
    "\n",
    "    r4 = add_reactions(\n",
    "        model,\n",
    "        \"Reaction4\",\n",
    "        \"meta_Reaction4\",\n",
    "        \"SBO:0000184\",\n",
    "        \"translation of LacI\",\n",
    "        False,\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/GO:0006412\",\n",
    "        \"k_tl * X\",\n",
    "        \"SBO:0000049\",\n",
    "    )\n",
    "    add_product_to_reaction(r4, \"PX\")\n",
    "    add_modifier_to_reaction(r4, \"X\", \"SBO:0000461\")\n",
    "\n",
    "    r5 = add_reactions(\n",
    "        model,\n",
    "        \"Reaction5\",\n",
    "        \"meta_Reaction5\",\n",
    "        \"SBO:0000184\",\n",
    "        \"translation of TetR\",\n",
    "        False,\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/GO:0006412\",\n",
    "        \"k_tl * Y\",\n",
    "        \"SBO:0000049\",\n",
    "    )\n",
    "    add_product_to_reaction(r5, \"PY\")\n",
    "    add_modifier_to_reaction(r5, \"Y\", \"SBO:0000461\")\n",
    "\n",
    "    r6 = add_reactions(\n",
    "        model,\n",
    "        \"Reaction6\",\n",
    "        \"meta_Reaction6\",\n",
    "        \"SBO:0000184\",\n",
    "        \"translation of CI\",\n",
    "        False,\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/GO:0006412\",\n",
    "        \"k_tl * Z\",\n",
    "        \"SBO:0000049\",\n",
    "    )\n",
    "    add_product_to_reaction(r6, \"PZ\")\n",
    "    add_modifier_to_reaction(r6, \"Z\", \"SBO:0000461\")\n",
    "\n",
    "    r7 = add_reactions(\n",
    "        model,\n",
    "        \"Reaction7\",\n",
    "        \"meta_Reaction7\",\n",
    "        \"SBO:0000179\",\n",
    "        \"degradation of LacI\",\n",
    "        False,\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/GO:0030163\",\n",
    "        \"kd_prot * PX\",\n",
    "        \"SBO:0000049\",\n",
    "    )\n",
    "    add_reactant_to_reaction(r7, \"PX\")\n",
    "\n",
    "    r8 = add_reactions(\n",
    "        model,\n",
    "        \"Reaction8\",\n",
    "        \"meta_Reaction8\",\n",
    "        \"SBO:0000179\",\n",
    "        \"degradation of TetR\",\n",
    "        False,\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/GO:0030163\",\n",
    "        \"kd_prot * PY\",\n",
    "        \"SBO:0000049\",\n",
    "    )\n",
    "    add_reactant_to_reaction(r8, \"PY\")\n",
    "\n",
    "    r9 = add_reactions(\n",
    "        model,\n",
    "        \"Reaction9\",\n",
    "        \"meta_Reaction9\",\n",
    "        \"SBO:0000179\",\n",
    "        \"degradation of CI\",\n",
    "        False,\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/GO:0030163\",\n",
    "        \"kd_prot * PZ\",\n",
    "        \"SBO:0000049\",\n",
    "    )\n",
    "    add_reactant_to_reaction(r9, \"PZ\")\n",
    "\n",
    "    r10 = add_reactions(\n",
    "        model,\n",
    "        \"Reaction10\",\n",
    "        \"meta_Reaction10\",\n",
    "        \"SBO:0000183\",\n",
    "        \"transcription of LacI\",\n",
    "        False,\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/GO:0006351\",\n",
    "        \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PZ, n))\",\n",
    "        None,\n",
    "    )\n",
    "    add_product_to_reaction(r10, \"X\")\n",
    "    add_modifier_to_reaction(r10, \"PZ\", \"SBO:0000536\")\n",
    "\n",
    "    r11 = add_reactions(\n",
    "        model,\n",
    "        \"Reaction11\",\n",
    "        \"meta_Reaction11\",\n",
    "        \"SBO:0000183\",\n",
    "        \"transcription of TetR\",\n",
    "        False,\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/GO:0006351\",\n",
    "        \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PX, n))\",\n",
    "        None,\n",
    "    )\n",
    "    add_product_to_reaction(r11, \"Y\")\n",
    "    add_modifier_to_reaction(r11, \"PX\", \"SBO:0000536\")\n",
    "\n",
    "    r12 = add_reactions(\n",
    "        model,\n",
    "        \"Reaction12\",\n",
    "        \"meta_Reaction12\",\n",
    "        \"SBO:0000183\",\n",
    "        \"transcription of CI\",\n",
    "        False,\n",
    "        libsbml.BIOLOGICAL_QUALIFIER,\n",
    "        libsbml.BQB_IS_VERSION_OF,\n",
    "        \"http://identifiers.org/GO:0006351\",\n",
    "        \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PY, n))\",\n",
    "        None,\n",
    "    )\n",
    "    add_product_to_reaction(r12, \"Z\")\n",
    "    add_modifier_to_reaction(r12, \"PY\", \"SBO:0000536\")\n",
    "\n",
    "    print(\"-\" * 80)\n",
    "    print(libsbml.writeSBMLToString(doc))\n",
    "    print(\"-\" * 80)\n",
    "\n",
    "    # write to file\n",
    "    os.makedirs(os.path.dirname(str(sbml_path)), exist_ok=True)\n",
    "    libsbml.writeSBMLToFile(doc, str(sbml_path))\n",
    "\n",
    "    # validate file\n",
    "    validate_sbml(doc, units_consistency=False)\n",
    "\n",
    "    return doc"
   ]
  },
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   "id": "5842c5ae",
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    {
     "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",
      "      <assignmentRule variable=\"a0_tr\">\n",
      "        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "          <apply>\n",
      "            <times/>\n",
      "            <ci> ps_0 </ci>\n",
      "            <cn type=\"integer\"> 60 </cn>\n",
      "          </apply>\n",
      "        </math>\n",
      "      </assignmentRule>\n",
      "      <assignmentRule variable=\"a_tr\">\n",
      "        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "          <apply>\n",
      "            <times/>\n",
      "            <apply>\n",
      "              <minus/>\n",
      "              <ci> ps_a </ci>\n",
      "              <ci> ps_0 </ci>\n",
      "            </apply>\n",
      "            <cn type=\"integer\"> 60 </cn>\n",
      "          </apply>\n",
      "        </math>\n",
      "      </assignmentRule>\n",
      "    </listOfRules>\n",
      "    <listOfReactions>\n",
      "      <reaction metaid=\"meta_Reaction1\" sboTerm=\"SBO:0000179\" id=\"Reaction1\" name=\"degradation of LacI transcripts\" reversible=\"false\">\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_Reaction1\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006402\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfReactants>\n",
      "          <speciesReference species=\"X\"/>\n",
      "        </listOfReactants>\n",
      "        <kineticLaw sboTerm=\"SBO:0000049\">\n",
      "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <ci> kd_mRNA </ci>\n",
      "              <ci> X </ci>\n",
      "            </apply>\n",
      "          </math>\n",
      "        </kineticLaw>\n",
      "      </reaction>\n",
      "      <reaction metaid=\"meta_Reaction2\" sboTerm=\"SBO:0000179\" id=\"Reaction2\" name=\"degradation of TetR transcripts\" reversible=\"false\">\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_Reaction2\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006402\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfReactants>\n",
      "          <speciesReference species=\"Y\"/>\n",
      "        </listOfReactants>\n",
      "        <kineticLaw sboTerm=\"SBO:0000049\">\n",
      "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <ci> kd_mRNA </ci>\n",
      "              <ci> Y </ci>\n",
      "            </apply>\n",
      "          </math>\n",
      "        </kineticLaw>\n",
      "      </reaction>\n",
      "      <reaction metaid=\"meta_Reaction3\" sboTerm=\"SBO:0000179\" id=\"Reaction3\" name=\"degradation of CI transcripts\" reversible=\"false\">\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_Reaction3\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006402\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfReactants>\n",
      "          <speciesReference species=\"Z\"/>\n",
      "        </listOfReactants>\n",
      "        <kineticLaw sboTerm=\"SBO:0000049\">\n",
      "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <ci> kd_mRNA </ci>\n",
      "              <ci> Z </ci>\n",
      "            </apply>\n",
      "          </math>\n",
      "        </kineticLaw>\n",
      "      </reaction>\n",
      "      <reaction metaid=\"meta_Reaction4\" sboTerm=\"SBO:0000184\" id=\"Reaction4\" name=\"translation of LacI\" reversible=\"false\">\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_Reaction4\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006412\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfProducts>\n",
      "          <speciesReference species=\"PX\"/>\n",
      "        </listOfProducts>\n",
      "        <listOfModifiers>\n",
      "          <modifierSpeciesReference sboTerm=\"SBO:0000461\" species=\"X\"/>\n",
      "        </listOfModifiers>\n",
      "        <kineticLaw sboTerm=\"SBO:0000049\">\n",
      "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <ci> k_tl </ci>\n",
      "              <ci> X </ci>\n",
      "            </apply>\n",
      "          </math>\n",
      "        </kineticLaw>\n",
      "      </reaction>\n",
      "      <reaction metaid=\"meta_Reaction5\" sboTerm=\"SBO:0000184\" id=\"Reaction5\" name=\"translation of TetR\" reversible=\"false\">\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_Reaction5\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006412\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfProducts>\n",
      "          <speciesReference species=\"PY\"/>\n",
      "        </listOfProducts>\n",
      "        <listOfModifiers>\n",
      "          <modifierSpeciesReference sboTerm=\"SBO:0000461\" species=\"Y\"/>\n",
      "        </listOfModifiers>\n",
      "        <kineticLaw sboTerm=\"SBO:0000049\">\n",
      "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <ci> k_tl </ci>\n",
      "              <ci> Y </ci>\n",
      "            </apply>\n",
      "          </math>\n",
      "        </kineticLaw>\n",
      "      </reaction>\n",
      "      <reaction metaid=\"meta_Reaction6\" sboTerm=\"SBO:0000184\" id=\"Reaction6\" name=\"translation of CI\" reversible=\"false\">\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_Reaction6\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006412\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfProducts>\n",
      "          <speciesReference species=\"PZ\"/>\n",
      "        </listOfProducts>\n",
      "        <listOfModifiers>\n",
      "          <modifierSpeciesReference sboTerm=\"SBO:0000461\" species=\"Z\"/>\n",
      "        </listOfModifiers>\n",
      "        <kineticLaw sboTerm=\"SBO:0000049\">\n",
      "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <ci> k_tl </ci>\n",
      "              <ci> Z </ci>\n",
      "            </apply>\n",
      "          </math>\n",
      "        </kineticLaw>\n",
      "      </reaction>\n",
      "      <reaction metaid=\"meta_Reaction7\" sboTerm=\"SBO:0000179\" id=\"Reaction7\" name=\"degradation of LacI\" reversible=\"false\">\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_Reaction7\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0030163\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfReactants>\n",
      "          <speciesReference species=\"PX\"/>\n",
      "        </listOfReactants>\n",
      "        <kineticLaw sboTerm=\"SBO:0000049\">\n",
      "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <ci> kd_prot </ci>\n",
      "              <ci> PX </ci>\n",
      "            </apply>\n",
      "          </math>\n",
      "        </kineticLaw>\n",
      "      </reaction>\n",
      "      <reaction metaid=\"meta_Reaction8\" sboTerm=\"SBO:0000179\" id=\"Reaction8\" name=\"degradation of TetR\" reversible=\"false\">\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_Reaction8\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0030163\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfReactants>\n",
      "          <speciesReference species=\"PY\"/>\n",
      "        </listOfReactants>\n",
      "        <kineticLaw sboTerm=\"SBO:0000049\">\n",
      "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <ci> kd_prot </ci>\n",
      "              <ci> PY </ci>\n",
      "            </apply>\n",
      "          </math>\n",
      "        </kineticLaw>\n",
      "      </reaction>\n",
      "      <reaction metaid=\"meta_Reaction9\" sboTerm=\"SBO:0000179\" id=\"Reaction9\" name=\"degradation of CI\" reversible=\"false\">\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_Reaction9\">\n",
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      "                <rdf:Bag>\n",
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      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfReactants>\n",
      "          <speciesReference species=\"PZ\"/>\n",
      "        </listOfReactants>\n",
      "        <kineticLaw sboTerm=\"SBO:0000049\">\n",
      "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <ci> kd_prot </ci>\n",
      "              <ci> PZ </ci>\n",
      "            </apply>\n",
      "          </math>\n",
      "        </kineticLaw>\n",
      "      </reaction>\n",
      "      <reaction metaid=\"meta_Reaction10\" sboTerm=\"SBO:0000183\" id=\"Reaction10\" name=\"transcription of LacI\" reversible=\"false\">\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_Reaction10\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006351\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfProducts>\n",
      "          <speciesReference species=\"X\"/>\n",
      "        </listOfProducts>\n",
      "        <listOfModifiers>\n",
      "          <modifierSpeciesReference sboTerm=\"SBO:0000536\" species=\"PZ\"/>\n",
      "        </listOfModifiers>\n",
      "        <kineticLaw>\n",
      "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "            <apply>\n",
      "              <plus/>\n",
      "              <ci> a0_tr </ci>\n",
      "              <apply>\n",
      "                <divide/>\n",
      "                <apply>\n",
      "                  <times/>\n",
      "                  <ci> a_tr </ci>\n",
      "                  <apply>\n",
      "                    <power/>\n",
      "                    <ci> KM </ci>\n",
      "                    <ci> n </ci>\n",
      "                  </apply>\n",
      "                </apply>\n",
      "                <apply>\n",
      "                  <plus/>\n",
      "                  <apply>\n",
      "                    <power/>\n",
      "                    <ci> KM </ci>\n",
      "                    <ci> n </ci>\n",
      "                  </apply>\n",
      "                  <apply>\n",
      "                    <power/>\n",
      "                    <ci> PZ </ci>\n",
      "                    <ci> n </ci>\n",
      "                  </apply>\n",
      "                </apply>\n",
      "              </apply>\n",
      "            </apply>\n",
      "          </math>\n",
      "        </kineticLaw>\n",
      "      </reaction>\n",
      "      <reaction metaid=\"meta_Reaction11\" sboTerm=\"SBO:0000183\" id=\"Reaction11\" name=\"transcription of TetR\" reversible=\"false\">\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",
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      "              </bqbiol:isVersionOf>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfProducts>\n",
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      "              <apply>\n",
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      "                <apply>\n",
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      "                    <ci> n </ci>\n",
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      "                <apply>\n",
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      "                  <apply>\n",
      "                    <power/>\n",
      "                    <ci> KM </ci>\n",
      "                    <ci> n </ci>\n",
      "                  </apply>\n",
      "                  <apply>\n",
      "                    <power/>\n",
      "                    <ci> PX </ci>\n",
      "                    <ci> n </ci>\n",
      "                  </apply>\n",
      "                </apply>\n",
      "              </apply>\n",
      "            </apply>\n",
      "          </math>\n",
      "        </kineticLaw>\n",
      "      </reaction>\n",
      "      <reaction metaid=\"meta_Reaction12\" sboTerm=\"SBO:0000183\" id=\"Reaction12\" name=\"transcription of CI\" reversible=\"false\">\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_Reaction12\">\n",
      "              <bqbiol:isVersionOf>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006351\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:isVersionOf>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfProducts>\n",
      "          <speciesReference species=\"Z\"/>\n",
      "        </listOfProducts>\n",
      "        <listOfModifiers>\n",
      "          <modifierSpeciesReference sboTerm=\"SBO:0000536\" species=\"PY\"/>\n",
      "        </listOfModifiers>\n",
      "        <kineticLaw>\n",
      "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "            <apply>\n",
      "              <plus/>\n",
      "              <ci> a0_tr </ci>\n",
      "              <apply>\n",
      "                <divide/>\n",
      "                <apply>\n",
      "                  <times/>\n",
      "                  <ci> a_tr </ci>\n",
      "                  <apply>\n",
      "                    <power/>\n",
      "                    <ci> KM </ci>\n",
      "                    <ci> n </ci>\n",
      "                  </apply>\n",
      "                </apply>\n",
      "                <apply>\n",
      "                  <plus/>\n",
      "                  <apply>\n",
      "                    <power/>\n",
      "                    <ci> KM </ci>\n",
      "                    <ci> n </ci>\n",
      "                  </apply>\n",
      "                  <apply>\n",
      "                    <power/>\n",
      "                    <ci> PY </ci>\n",
      "                    <ci> n </ci>\n",
      "                  </apply>\n",
      "                </apply>\n",
      "              </apply>\n",
      "            </apply>\n",
      "          </math>\n",
      "        </kineticLaw>\n",
      "      </reaction>\n",
      "    </listOfReactions>\n",
      "  </model>\n",
      "</sbml>\n",
      "\n",
      "--------------------------------------------------------------------------------\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_sbml_libsbml.xml\"\n",
    "    )"
   ]
  }
 ],
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   "notebook_metadata_filter": "-all"
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  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
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  "language_info": {
   "codemirror_mode": {
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    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
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