{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "aed30502",
   "metadata": {},
   "source": [
    "Create repressilator with antimony.\n",
    "\n",
    "http://antimony.sourceforge.net/\n",
    "https://tellurium.readthedocs.io/en/latest/antimony.html"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "7efbe4ba",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-04-17T14:01:56.305452Z",
     "iopub.status.busy": "2023-04-17T14:01:56.305173Z",
     "iopub.status.idle": "2023-04-17T14:01:56.510355Z",
     "shell.execute_reply": "2023-04-17T14:01:56.510876Z"
    }
   },
   "outputs": [],
   "source": [
    "import os\n",
    "from pathlib import Path\n",
    "\n",
    "import antimony\n",
    "import libsbml\n",
    "\n",
    "from combine_notebooks.validation.validation_sbml import validate_sbml"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "d37f6e44",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-04-17T14:01:56.513225Z",
     "iopub.status.busy": "2023-04-17T14:01:56.512514Z",
     "iopub.status.idle": "2023-04-17T14:01:56.521231Z",
     "shell.execute_reply": "2023-04-17T14:01:56.521450Z"
    }
   },
   "outputs": [],
   "source": [
    "def create_repressilator(sbml_path: Path) -> libsbml.SBMLDocument:\n",
    "    \"\"\"Create repressilator with antimony.\"\"\"\n",
    "    model: str = \"\"\"\n",
    "        model antimony_repressilator\n",
    "            # compartment\n",
    "            compartment cell = 1\n",
    "            # species\n",
    "            species PX = 0\n",
    "            species PY = 0\n",
    "            species PZ = 0\n",
    "            species X = 0\n",
    "            species Y = 20\n",
    "            species Z = 0\n",
    "            # parameters\n",
    "            beta = 0.2\n",
    "            alpha0 = 0.2164\n",
    "            alpha = 216.404\n",
    "            eff = 20\n",
    "            n = 2\n",
    "            KM = 40\n",
    "            tau_mRNA = 2\n",
    "            tau_prot = 10\n",
    "            ps_a = 0.5\n",
    "            ps_0 = 0.0005\n",
    "            # assignment rules\n",
    "            t_ave := tau_mRNA/ln(2);\n",
    "            beta := tau_mRNA/tau_prot;\n",
    "            k_tl := eff/t_ave;\n",
    "            a_tr := (ps_a - ps_0)*60;\n",
    "            a0_tr := ps_0*60;\n",
    "            kd_prot := ln(2)/tau_prot;\n",
    "            kd_mRNA := ln(2)/tau_mRNA;\n",
    "            alpha := a_tr*eff*tau_prot/(ln(2)*KM);\n",
    "            alpha0 := (a0_tr*eff*tau_prot)/(ln(2)*KM);\n",
    "\n",
    "            # reactions\n",
    "            X ->; kd_mRNA*X;\n",
    "            Y ->; kd_mRNA*Y;\n",
    "            Z ->; kd_mRNA*Z;\n",
    "            -> PX; k_tl*X;\n",
    "            -> PY; k_tl*Y;\n",
    "            -> PZ; k_tl*Z;\n",
    "            PX ->; kd_prot*PX;\n",
    "            PY ->; kd_prot*PY;\n",
    "            PZ ->; kd_prot*PZ;\n",
    "            -> X; a0_tr +a_tr *KM^n/(KM^n +PZ ^n);\n",
    "            -> Y; a0_tr +a_tr *KM^n/(KM^n +PX ^n);\n",
    "            -> Z; a0_tr +a_tr *KM^n/(KM^n +PY ^n);\n",
    "\n",
    "            # annotations\n",
    "            cell identity \"http://identifiers.org/SBO:0000290\"\n",
    "            cell identity \"http://identifiers.org/GO:0005623\"\n",
    "            PX identity \"http://identifiers.org/SBO:0000252\"\n",
    "            PX identity \"http://identifiers.org/uniprot/P03023\"\n",
    "            PY identity \"http://identifiers.org/SBO:0000252\"\n",
    "            PY identity \"http://identifiers.org/uniprot/P04483\"\n",
    "            PZ identity \"http://identifiers.org/SBO:0000252\"\n",
    "            PZ identity \"http://identifiers.org/uniprot/P03034\"\n",
    "            X identity \"http://identifiers.org/SBO:0000250\"\n",
    "            X identity \"http://identifiers.org/CHEBI:33699\"\n",
    "            X identity \"http://identifiers.org/kegg.compound/C00046\"\n",
    "            X identity \"http://identifiers.org/uniprot/P03023\"\n",
    "            Y identity \"http://identifiers.org/SBO:0000250\"\n",
    "            Y identity \"http://identifiers.org/CHEBI:33699\"\n",
    "            Y identity \"http://identifiers.org/kegg.compound/C00046\"\n",
    "            Y identity \"http://identifiers.org/uniprot/P04483\"\n",
    "            Z identity \"http://identifiers.org/SBO:0000250\"\n",
    "            Z identity \"http://identifiers.org/CHEBI:33699\"\n",
    "            Z identity \"http://identifiers.org/kegg.compound/C00046\"\n",
    "            Z identity \"http://identifiers.org/uniprot/P03034\"\n",
    "            tau_mRNA identity \"http://identifiers.org/SBO:0000356\"\n",
    "            k_tl identity \"http://identifiers.org/SBO:0000016\"\n",
    "            t_ave identity \"http://identifiers.org/SBO:0000348\"\n",
    "            kd_prot identity \"http://identifiers.org/SBO:0000356\"\n",
    "            a0_tr identity \"http://identifiers.org/SBO:0000485\"\n",
    "            a_tr identity \"http://identifiers.org/SBO:0000186\"\n",
    "            _J0 identity \"http://identifiers.org/SBO:0000179\"\n",
    "            _J0 identity \"http://identifiers.org/GO:0006402\"\n",
    "            _J1 identity \"http://identifiers.org/SBO:0000179\"\n",
    "            _J1 identity \"http://identifiers.org/GO:0006402\"\n",
    "            _J2 identity \"http://identifiers.org/SBO:0000179\"\n",
    "            _J2 identity \"http://identifiers.org/GO:0006402\"\n",
    "            _J3 identity \"http://identifiers.org/SBO:0000184\"\n",
    "            _J3 identity \"http://identifiers.org/GO:0006412\"\n",
    "            _J4 identity \"http://identifiers.org/SBO:0000184\"\n",
    "            _J4 identity \"http://identifiers.org/GO:0006412\"\n",
    "            _J5 identity \"http://identifiers.org/SBO:0000184\"\n",
    "            _J5 identity \"http://identifiers.org/GO:0006412\"\n",
    "            _J6 identity \"http://identifiers.org/SBO:0000179\"\n",
    "            _J6 identity \"http://identifiers.org/GO:0030163\"\n",
    "            _J7 identity \"http://identifiers.org/SBO:0000179\"\n",
    "            _J7 identity \"http://identifiers.org/GO:0030163\"\n",
    "            _J8 identity \"http://identifiers.org/SBO:0000179\"\n",
    "            _J8 identity \"http://identifiers.org/GO:0030163\"\n",
    "            _J9 identity \"http://identifiers.org/SBO:0000183\"\n",
    "            _J9 identity \"http://identifiers.org/GO:0006351\"\n",
    "            _J10 identity \"http://identifiers.org/SBO:0000183\"\n",
    "            _J10 identity \"http://identifiers.org/GO:0006351\"\n",
    "            _J11 identity \"http://identifiers.org/SBO:0000184\"\n",
    "            _J11 identity \"http://identifiers.org/GO:0006351\"\n",
    "\n",
    "        end\n",
    "    \"\"\"\n",
    "    print(model)\n",
    "\n",
    "    status = antimony.loadAntimonyString(model)\n",
    "    print(f\"Antimony status: {status}\")\n",
    "    print(antimony.getLastError())\n",
    "    sbml_str = antimony.getSBMLString()\n",
    "    print(sbml_str)\n",
    "    print(antimony.getSBMLWarnings())\n",
    "\n",
    "    # validation\n",
    "    doc = libsbml.readSBMLFromString(sbml_str)\n",
    "    validate_sbml(doc)\n",
    "\n",
    "    # write SBML\n",
    "    os.makedirs(os.path.dirname(str(sbml_path)), exist_ok=True)\n",
    "    libsbml.writeSBMLToFile(doc, str(sbml_path))\n",
    "\n",
    "    return doc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "186bfc11",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-04-17T14:01:56.524852Z",
     "iopub.status.busy": "2023-04-17T14:01:56.524551Z",
     "iopub.status.idle": "2023-04-17T14:01:56.587221Z",
     "shell.execute_reply": "2023-04-17T14:01:56.587742Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "        model antimony_repressilator\n",
      "            # compartment\n",
      "            compartment cell = 1\n",
      "            # species\n",
      "            species PX = 0\n",
      "            species PY = 0\n",
      "            species PZ = 0\n",
      "            species X = 0\n",
      "            species Y = 20\n",
      "            species Z = 0\n",
      "            # parameters\n",
      "            beta = 0.2\n",
      "            alpha0 = 0.2164\n",
      "            alpha = 216.404\n",
      "            eff = 20\n",
      "            n = 2\n",
      "            KM = 40\n",
      "            tau_mRNA = 2\n",
      "            tau_prot = 10\n",
      "            ps_a = 0.5\n",
      "            ps_0 = 0.0005\n",
      "            # assignment rules\n",
      "            t_ave := tau_mRNA/ln(2);\n",
      "            beta := tau_mRNA/tau_prot;\n",
      "            k_tl := eff/t_ave;\n",
      "            a_tr := (ps_a - ps_0)*60;\n",
      "            a0_tr := ps_0*60;\n",
      "            kd_prot := ln(2)/tau_prot;\n",
      "            kd_mRNA := ln(2)/tau_mRNA;\n",
      "            alpha := a_tr*eff*tau_prot/(ln(2)*KM);\n",
      "            alpha0 := (a0_tr*eff*tau_prot)/(ln(2)*KM);\n",
      "\n",
      "            # reactions\n",
      "            X ->; kd_mRNA*X;\n",
      "            Y ->; kd_mRNA*Y;\n",
      "            Z ->; kd_mRNA*Z;\n",
      "            -> PX; k_tl*X;\n",
      "            -> PY; k_tl*Y;\n",
      "            -> PZ; k_tl*Z;\n",
      "            PX ->; kd_prot*PX;\n",
      "            PY ->; kd_prot*PY;\n",
      "            PZ ->; kd_prot*PZ;\n",
      "            -> X; a0_tr +a_tr *KM^n/(KM^n +PZ ^n);\n",
      "            -> Y; a0_tr +a_tr *KM^n/(KM^n +PX ^n);\n",
      "            -> Z; a0_tr +a_tr *KM^n/(KM^n +PY ^n);\n",
      "\n",
      "            # annotations\n",
      "            cell identity \"http://identifiers.org/SBO:0000290\"\n",
      "            cell identity \"http://identifiers.org/GO:0005623\"\n",
      "            PX identity \"http://identifiers.org/SBO:0000252\"\n",
      "            PX identity \"http://identifiers.org/uniprot/P03023\"\n",
      "            PY identity \"http://identifiers.org/SBO:0000252\"\n",
      "            PY identity \"http://identifiers.org/uniprot/P04483\"\n",
      "            PZ identity \"http://identifiers.org/SBO:0000252\"\n",
      "            PZ identity \"http://identifiers.org/uniprot/P03034\"\n",
      "            X identity \"http://identifiers.org/SBO:0000250\"\n",
      "            X identity \"http://identifiers.org/CHEBI:33699\"\n",
      "            X identity \"http://identifiers.org/kegg.compound/C00046\"\n",
      "            X identity \"http://identifiers.org/uniprot/P03023\"\n",
      "            Y identity \"http://identifiers.org/SBO:0000250\"\n",
      "            Y identity \"http://identifiers.org/CHEBI:33699\"\n",
      "            Y identity \"http://identifiers.org/kegg.compound/C00046\"\n",
      "            Y identity \"http://identifiers.org/uniprot/P04483\"\n",
      "            Z identity \"http://identifiers.org/SBO:0000250\"\n",
      "            Z identity \"http://identifiers.org/CHEBI:33699\"\n",
      "            Z identity \"http://identifiers.org/kegg.compound/C00046\"\n",
      "            Z identity \"http://identifiers.org/uniprot/P03034\"\n",
      "            tau_mRNA identity \"http://identifiers.org/SBO:0000356\"\n",
      "            k_tl identity \"http://identifiers.org/SBO:0000016\"\n",
      "            t_ave identity \"http://identifiers.org/SBO:0000348\"\n",
      "            kd_prot identity \"http://identifiers.org/SBO:0000356\"\n",
      "            a0_tr identity \"http://identifiers.org/SBO:0000485\"\n",
      "            a_tr identity \"http://identifiers.org/SBO:0000186\"\n",
      "            _J0 identity \"http://identifiers.org/SBO:0000179\"\n",
      "            _J0 identity \"http://identifiers.org/GO:0006402\"\n",
      "            _J1 identity \"http://identifiers.org/SBO:0000179\"\n",
      "            _J1 identity \"http://identifiers.org/GO:0006402\"\n",
      "            _J2 identity \"http://identifiers.org/SBO:0000179\"\n",
      "            _J2 identity \"http://identifiers.org/GO:0006402\"\n",
      "            _J3 identity \"http://identifiers.org/SBO:0000184\"\n",
      "            _J3 identity \"http://identifiers.org/GO:0006412\"\n",
      "            _J4 identity \"http://identifiers.org/SBO:0000184\"\n",
      "            _J4 identity \"http://identifiers.org/GO:0006412\"\n",
      "            _J5 identity \"http://identifiers.org/SBO:0000184\"\n",
      "            _J5 identity \"http://identifiers.org/GO:0006412\"\n",
      "            _J6 identity \"http://identifiers.org/SBO:0000179\"\n",
      "            _J6 identity \"http://identifiers.org/GO:0030163\"\n",
      "            _J7 identity \"http://identifiers.org/SBO:0000179\"\n",
      "            _J7 identity \"http://identifiers.org/GO:0030163\"\n",
      "            _J8 identity \"http://identifiers.org/SBO:0000179\"\n",
      "            _J8 identity \"http://identifiers.org/GO:0030163\"\n",
      "            _J9 identity \"http://identifiers.org/SBO:0000183\"\n",
      "            _J9 identity \"http://identifiers.org/GO:0006351\"\n",
      "            _J10 identity \"http://identifiers.org/SBO:0000183\"\n",
      "            _J10 identity \"http://identifiers.org/GO:0006351\"\n",
      "            _J11 identity \"http://identifiers.org/SBO:0000184\"\n",
      "            _J11 identity \"http://identifiers.org/GO:0006351\"\n",
      "\n",
      "        end\n",
      "    \n",
      "Antimony status: 1\n",
      "\n",
      "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
      "<!-- Created by libAntimony version v2.13.2 with libSBML version 5.19.5. -->\n",
      "<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\">\n",
      "  <model metaid=\"antimony_repressilator\" id=\"antimony_repressilator\">\n",
      "    <listOfCompartments>\n",
      "      <compartment sboTerm=\"SBO:0000410\" id=\"default_compartment\" spatialDimensions=\"3\" size=\"1\" constant=\"true\"/>\n",
      "      <compartment metaid=\"antimony_repressilator.cell\" id=\"cell\" spatialDimensions=\"3\" size=\"1\" constant=\"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=\"#antimony_repressilator.cell\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000290\"/>\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=\"antimony_repressilator.PX\" id=\"PX\" compartment=\"default_compartment\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"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=\"#antimony_repressilator.PX\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000252\"/>\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=\"antimony_repressilator.PY\" id=\"PY\" compartment=\"default_compartment\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"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=\"#antimony_repressilator.PY\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000252\"/>\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=\"antimony_repressilator.PZ\" id=\"PZ\" compartment=\"default_compartment\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"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=\"#antimony_repressilator.PZ\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000252\"/>\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=\"antimony_repressilator.X\" id=\"X\" compartment=\"default_compartment\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"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=\"#antimony_repressilator.X\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000250\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/CHEBI:33699\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/kegg.compound/C00046\"/>\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=\"antimony_repressilator.Y\" id=\"Y\" compartment=\"default_compartment\" initialConcentration=\"20\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"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=\"#antimony_repressilator.Y\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000250\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/CHEBI:33699\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/kegg.compound/C00046\"/>\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=\"antimony_repressilator.Z\" id=\"Z\" compartment=\"default_compartment\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"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=\"#antimony_repressilator.Z\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000250\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/CHEBI:33699\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/kegg.compound/C00046\"/>\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",
      "    </listOfSpecies>\n",
      "    <listOfParameters>\n",
      "      <parameter id=\"beta\" constant=\"false\"/>\n",
      "      <parameter id=\"alpha0\" constant=\"false\"/>\n",
      "      <parameter id=\"alpha\" constant=\"false\"/>\n",
      "      <parameter id=\"eff\" value=\"20\" constant=\"true\"/>\n",
      "      <parameter id=\"n\" value=\"2\" constant=\"true\"/>\n",
      "      <parameter id=\"KM\" value=\"40\" constant=\"true\"/>\n",
      "      <parameter metaid=\"antimony_repressilator.tau_mRNA\" id=\"tau_mRNA\" value=\"2\" constant=\"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=\"#antimony_repressilator.tau_mRNA\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000356\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </parameter>\n",
      "      <parameter id=\"tau_prot\" value=\"10\" constant=\"true\"/>\n",
      "      <parameter id=\"ps_a\" value=\"0.5\" constant=\"true\"/>\n",
      "      <parameter id=\"ps_0\" value=\"0.0005\" constant=\"true\"/>\n",
      "      <parameter metaid=\"antimony_repressilator.t_ave\" id=\"t_ave\" constant=\"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=\"#antimony_repressilator.t_ave\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000348\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </parameter>\n",
      "      <parameter metaid=\"antimony_repressilator.k_tl\" id=\"k_tl\" constant=\"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=\"#antimony_repressilator.k_tl\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000016\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </parameter>\n",
      "      <parameter metaid=\"antimony_repressilator.a_tr\" id=\"a_tr\" constant=\"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=\"#antimony_repressilator.a_tr\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000186\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </parameter>\n",
      "      <parameter metaid=\"antimony_repressilator.a0_tr\" id=\"a0_tr\" constant=\"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=\"#antimony_repressilator.a0_tr\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000485\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </parameter>\n",
      "      <parameter metaid=\"antimony_repressilator.kd_prot\" id=\"kd_prot\" constant=\"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=\"#antimony_repressilator.kd_prot\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000356\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "      </parameter>\n",
      "      <parameter id=\"kd_mRNA\" constant=\"false\"/>\n",
      "    </listOfParameters>\n",
      "    <listOfRules>\n",
      "      <assignmentRule variable=\"beta\">\n",
      "        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "          <apply>\n",
      "            <divide/>\n",
      "            <ci> tau_mRNA </ci>\n",
      "            <ci> tau_prot </ci>\n",
      "          </apply>\n",
      "        </math>\n",
      "      </assignmentRule>\n",
      "      <assignmentRule variable=\"alpha0\">\n",
      "        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "          <apply>\n",
      "            <divide/>\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <ci> a0_tr </ci>\n",
      "              <ci> eff </ci>\n",
      "              <ci> tau_prot </ci>\n",
      "            </apply>\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <apply>\n",
      "                <ln/>\n",
      "                <cn type=\"integer\"> 2 </cn>\n",
      "              </apply>\n",
      "              <ci> KM </ci>\n",
      "            </apply>\n",
      "          </apply>\n",
      "        </math>\n",
      "      </assignmentRule>\n",
      "      <assignmentRule variable=\"alpha\">\n",
      "        <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "          <apply>\n",
      "            <divide/>\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <ci> a_tr </ci>\n",
      "              <ci> eff </ci>\n",
      "              <ci> tau_prot </ci>\n",
      "            </apply>\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <apply>\n",
      "                <ln/>\n",
      "                <cn type=\"integer\"> 2 </cn>\n",
      "              </apply>\n",
      "              <ci> KM </ci>\n",
      "            </apply>\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=\"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",
      "      <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=\"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=\"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",
      "    </listOfRules>\n",
      "    <listOfReactions>\n",
      "      <reaction metaid=\"antimony_repressilator._J0\" id=\"_J0\" reversible=\"true\" fast=\"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=\"#antimony_repressilator._J0\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000179\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006402\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfReactants>\n",
      "          <speciesReference species=\"X\" stoichiometry=\"1\" constant=\"true\"/>\n",
      "        </listOfReactants>\n",
      "        <kineticLaw>\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=\"antimony_repressilator._J1\" id=\"_J1\" reversible=\"true\" fast=\"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=\"#antimony_repressilator._J1\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000179\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006402\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfReactants>\n",
      "          <speciesReference species=\"Y\" stoichiometry=\"1\" constant=\"true\"/>\n",
      "        </listOfReactants>\n",
      "        <kineticLaw>\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=\"antimony_repressilator._J2\" id=\"_J2\" reversible=\"true\" fast=\"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=\"#antimony_repressilator._J2\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000179\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006402\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfReactants>\n",
      "          <speciesReference species=\"Z\" stoichiometry=\"1\" constant=\"true\"/>\n",
      "        </listOfReactants>\n",
      "        <kineticLaw>\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=\"antimony_repressilator._J3\" id=\"_J3\" reversible=\"true\" fast=\"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=\"#antimony_repressilator._J3\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000184\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006412\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfProducts>\n",
      "          <speciesReference species=\"PX\" stoichiometry=\"1\" constant=\"true\"/>\n",
      "        </listOfProducts>\n",
      "        <listOfModifiers>\n",
      "          <modifierSpeciesReference species=\"X\"/>\n",
      "        </listOfModifiers>\n",
      "        <kineticLaw>\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=\"antimony_repressilator._J4\" id=\"_J4\" reversible=\"true\" fast=\"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=\"#antimony_repressilator._J4\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000184\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006412\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfProducts>\n",
      "          <speciesReference species=\"PY\" stoichiometry=\"1\" constant=\"true\"/>\n",
      "        </listOfProducts>\n",
      "        <listOfModifiers>\n",
      "          <modifierSpeciesReference species=\"Y\"/>\n",
      "        </listOfModifiers>\n",
      "        <kineticLaw>\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=\"antimony_repressilator._J5\" id=\"_J5\" reversible=\"true\" fast=\"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=\"#antimony_repressilator._J5\">\n",
      "              <bqbiol:is>\n",
      "                <rdf:Bag>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/SBO:0000184\"/>\n",
      "                  <rdf:li rdf:resource=\"http://identifiers.org/GO:0006412\"/>\n",
      "                </rdf:Bag>\n",
      "              </bqbiol:is>\n",
      "            </rdf:Description>\n",
      "          </rdf:RDF>\n",
      "        </annotation>\n",
      "        <listOfProducts>\n",
      "          <speciesReference species=\"PZ\" stoichiometry=\"1\" constant=\"true\"/>\n",
      "        </listOfProducts>\n",
      "        <listOfModifiers>\n",
      "          <modifierSpeciesReference species=\"Z\"/>\n",
      "        </listOfModifiers>\n",
      "        <kineticLaw>\n",
      "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "            <apply>\n",
      "              <times/>\n",
      "              <ci> k_tl </ci>\n",
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      "    </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",
    "    create_repressilator(sbml_path=RESULTS_DIR / \"repressilator_sbml_antimony.xml\")"
   ]
  }
 ],
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