notebooks/example_cellml.ipynb

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   "cell_type": "markdown",
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   },
   "source": [
    "Example script for creating SBML repressilator with cellml."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "323c5084",
   "metadata": {
    "lines_to_next_cell": 0
   },
   "source": [
    "https://www.cellml.org/getting-started/tutorials/COR-tutorial\n",
    "https://models.physiomeproject.org/exposure/bee9fb9df261ba69b51897f2e49b1691/elowitz_leibler_2000.cellml/view?searchterm=repressilator\n",
    "\n",
    "https://libcellml.org/documentation/v0.2.0/user/tutorials/tutorial3/index"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "50acd56d",
   "metadata": {
    "lines_to_next_cell": 2
   },
   "source": [
    "opencor: https://opencor.ws/downloads/index.html\n",
    "\n",
    "Issues: https://github.com/cellml/libcellml/issues/1017"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "64dfe7f0",
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   "outputs": [],
   "source": [
    "import os\n",
    "from pathlib import Path\n",
    "\n",
    "import libcellml\n",
    "import libsbml\n",
    "\n",
    "from combine_notebooks.cellml_utilities import print_model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "3351b567",
   "metadata": {
    "execution": {
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   "outputs": [],
   "source": [
    "def create_repressilator(cellml_path: Path) -> libcellml.Model:\n",
    "    \"\"\"Create CellML repressilator and save to Path.\"\"\"\n",
    "    model = libcellml.Model()\n",
    "    model.setName(\"repressilator\")\n",
    "\n",
    "    \"\"\"\n",
    "    <units name=\"minute\">\n",
    "      <unit units=\"second\" multiplier=\"60\"/>\n",
    "    </units>\n",
    "    <units name=\"first_order_rate_constant\">\n",
    "        <unit units=\"minute\" exponent=\"-1\"/>\n",
    "    </units>\n",
    "    \"\"\"\n",
    "    minute = libcellml.Units(\"minute\")\n",
    "    minute.addUnit(\"second\", 1, 60)\n",
    "    model.addUnits(minute)\n",
    "\n",
    "    # first_order_rate_constant = libcellml.Units(\"minute\")\n",
    "    # first_order_rate_constant.addUnit(\"minute\")\n",
    "    # model.addUnits(first_order_rate_constant)\n",
    "    ##############################################################################################\n",
    "    \"\"\"\n",
    "    <component name=\"environment\">\n",
    "      <variable units=\"minute\" public_interface=\"out\" name=\"time\" cmeta:id=\"environment_time\"/>\n",
    "    </component>\n",
    "    \"\"\"\n",
    "    comp_env = libcellml.Component()\n",
    "    comp_env.setName(\"environment\")\n",
    "    model.addComponent(comp_env)\n",
    "\n",
    "    var_n = libcellml.Variable()\n",
    "    var_n.setName(\"time\")\n",
    "    var_n.setInterfaceType(\"out\")\n",
    "    var_n.setUnits(\"minute\")\n",
    "    var_n.setId(\"environment_time\")\n",
    "    comp_env.addVariable(var_n)\n",
    "\n",
    "    comp_parameters = libcellml.Component()\n",
    "    comp_parameters.setName(\"parameters\")\n",
    "    model.addComponent(comp_parameters)\n",
    "\n",
    "    # var n: dimensionless {init: 2, pub: out};\n",
    "    var_n = libcellml.Variable()\n",
    "    var_n.setName(\"n\")\n",
    "    var_n.setInitialValue(2.0)\n",
    "    var_n.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_n)\n",
    "\n",
    "    var_alpha_0 = libcellml.Variable()\n",
    "    var_alpha_0.setName(\"alpha_0\")\n",
    "    var_alpha_0.setInitialValue(0.216)\n",
    "    var_alpha_0.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_alpha_0)\n",
    "\n",
    "    var_alpha = libcellml.Variable()\n",
    "    var_alpha.setName(\"alpha\")\n",
    "    var_alpha.setInitialValue(216)\n",
    "    var_alpha.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_alpha)\n",
    "\n",
    "    var_beta = libcellml.Variable()\n",
    "    var_beta.setName(\"beta\")\n",
    "    var_beta.setInitialValue(0.2)\n",
    "    var_beta.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_beta)\n",
    "\n",
    "    var_K_m = libcellml.Variable()\n",
    "    var_K_m.setName(\"K_m\")\n",
    "    var_K_m.setInitialValue(40)\n",
    "    var_K_m.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_K_m)\n",
    "\n",
    "    var_efficiency = libcellml.Variable()\n",
    "    var_efficiency.setName(\"efficiency\")\n",
    "    var_efficiency.setInitialValue(20)\n",
    "    var_efficiency.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_efficiency)\n",
    "\n",
    "    var_mRNA_halflife = libcellml.Variable()\n",
    "    var_mRNA_halflife.setName(\"mRNA_halflife\")\n",
    "    var_mRNA_halflife.setInitialValue(2)\n",
    "    var_mRNA_halflife.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_mRNA_halflife)\n",
    "\n",
    "    var_t_ave = libcellml.Variable()\n",
    "    var_t_ave.setName(\"t_ave\")\n",
    "    var_t_ave.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_t_ave)\n",
    "\n",
    "    # var_eff = libcellml.Variable()\n",
    "    # var_eff.setName(\"eff\")\n",
    "    # var_eff.setInitialValue(20)\n",
    "    # var_eff.setUnits(\"minute\")\n",
    "    # comp_parameters.addVariable(var_eff)\n",
    "\n",
    "    # start with math\n",
    "    math_ast1: libsbml.ASTNode = libsbml.parseL3Formula(\"mRNA_halflife/ln(2)\")\n",
    "    math_str = libsbml.writeMathMLToString(math_ast1)\n",
    "    print(math_str)\n",
    "    math_header = '<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">'\n",
    "    #    Include the MathML strings in the component.\n",
    "    math_str = \"\\n\".join([math_header] + math_str.split(\"\\n\")[2:])\n",
    "    print(math_str)\n",
    "    comp_parameters.setMath(math_str)\n",
    "\n",
    "    ##############################################################################################\n",
    "\n",
    "    comp_parameters = libcellml.Component()\n",
    "    comp_parameters.setName(\"M_lacl\")\n",
    "    model.addComponent(comp_parameters)\n",
    "\n",
    "    # var n: dimensionless {init: 2, pub: out};\n",
    "    var_n = libcellml.Variable()\n",
    "    var_n.setName(\"M_lacl\")\n",
    "    var_n.setInitialValue(5.0)\n",
    "    var_n.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_n)\n",
    "\n",
    "    var_alpha = libcellml.Variable()\n",
    "    var_alpha.setName(\"alpha\")\n",
    "    var_alpha.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_alpha)\n",
    "\n",
    "    var_beta = libcellml.Variable()\n",
    "    var_beta.setName(\"P_cl\")\n",
    "    # var_beta.setInitialValue(0.2)\n",
    "    var_beta.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_beta)\n",
    "\n",
    "    var_beta = libcellml.Variable()\n",
    "    var_beta.setName(\"n\")\n",
    "    # var_beta.setInitialValue(0.2)\n",
    "    var_beta.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_beta)\n",
    "\n",
    "    var_alpha_0 = libcellml.Variable()\n",
    "    var_alpha_0.setName(\"alpha_0\")\n",
    "    var_alpha_0.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_alpha_0)\n",
    "\n",
    "    var_K_m = libcellml.Variable()\n",
    "    var_K_m.setName(\"K_m\")\n",
    "    # var_K_m.setInitialValue(40)\n",
    "    var_K_m.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_K_m)\n",
    "\n",
    "    var_efficiency = libcellml.Variable()\n",
    "    var_efficiency.setName(\"efficiency\")\n",
    "    # var_efficiency.setInitialValue(20)\n",
    "    var_efficiency.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_efficiency)\n",
    "\n",
    "    var_t_ave = libcellml.Variable()\n",
    "    var_t_ave.setName(\"t_ave\")\n",
    "    var_t_ave.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_t_ave)\n",
    "\n",
    "    var_mRNA_halflife = libcellml.Variable()\n",
    "    var_mRNA_halflife.setName(\"time\")\n",
    "    # var_mRNA_halflife.setInitialValue(2)\n",
    "    var_mRNA_halflife.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_mRNA_halflife)\n",
    "\n",
    "    # var_eff = libcellml.Variable()\n",
    "    # var_eff.setName(\"eff\")\n",
    "    # var_eff.setInitialValue(20)\n",
    "    # var_eff.setUnits(\"minute\")\n",
    "    # comp_parameters.addVariable(var_eff)\n",
    "\n",
    "    # start with math\n",
    "    math_ast1 = libsbml.parseL3Formula(\n",
    "        \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PZ, n))\"\n",
    "    )\n",
    "    math_str = libsbml.writeMathMLToString(math_ast1)\n",
    "    print(math_str)\n",
    "    math_header = '<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">'\n",
    "    #    Include the MathML strings in the component.\n",
    "    math_str = \"\\n\".join([math_header] + math_str.split(\"\\n\")[2:])\n",
    "    print(math_str)\n",
    "    comp_parameters.setMath(math_str)\n",
    "\n",
    "    ##############################################################################################\n",
    "\n",
    "    comp_parameters = libcellml.Component()\n",
    "    comp_parameters.setName(\"M_tetR\")\n",
    "    model.addComponent(comp_parameters)\n",
    "\n",
    "    # var n: dimensionless {init: 2, pub: out};\n",
    "    var_n = libcellml.Variable()\n",
    "    var_n.setName(\"M_tetR\")\n",
    "    var_n.setInitialValue(0.0)\n",
    "    var_n.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_n)\n",
    "\n",
    "    var_alpha = libcellml.Variable()\n",
    "    var_alpha.setName(\"alpha\")\n",
    "    var_alpha.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_alpha)\n",
    "\n",
    "    var_beta = libcellml.Variable()\n",
    "    var_beta.setName(\"P_lacl\")\n",
    "    # var_beta.setInitialValue(0.2)\n",
    "    var_beta.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_beta)\n",
    "\n",
    "    var_beta = libcellml.Variable()\n",
    "    var_beta.setName(\"n\")\n",
    "    # var_beta.setInitialValue(0.2)\n",
    "    var_beta.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_beta)\n",
    "\n",
    "    var_alpha_0 = libcellml.Variable()\n",
    "    var_alpha_0.setName(\"alpha_0\")\n",
    "    var_alpha_0.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_alpha_0)\n",
    "\n",
    "    var_K_m = libcellml.Variable()\n",
    "    var_K_m.setName(\"K_m\")\n",
    "    # var_K_m.setInitialValue(40)\n",
    "    var_K_m.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_K_m)\n",
    "\n",
    "    var_efficiency = libcellml.Variable()\n",
    "    var_efficiency.setName(\"efficiency\")\n",
    "    # var_efficiency.setInitialValue(20)\n",
    "    var_efficiency.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_efficiency)\n",
    "\n",
    "    var_t_ave = libcellml.Variable()\n",
    "    var_t_ave.setName(\"t_ave\")\n",
    "    var_t_ave.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_t_ave)\n",
    "\n",
    "    var_mRNA_halflife = libcellml.Variable()\n",
    "    var_mRNA_halflife.setName(\"time\")\n",
    "    # var_mRNA_halflife.setInitialValue(2)\n",
    "    var_mRNA_halflife.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_mRNA_halflife)\n",
    "\n",
    "    # var_eff = libcellml.Variable()\n",
    "    # var_eff.setName(\"eff\")\n",
    "    # var_eff.setInitialValue(20)\n",
    "    # var_eff.setUnits(\"minute\")\n",
    "    # comp_parameters.addVariable(var_eff)\n",
    "\n",
    "    # start with math\n",
    "    math_ast1 = libsbml.parseL3Formula(\n",
    "        \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PZ, n))\"\n",
    "    )\n",
    "    math_str = libsbml.writeMathMLToString(math_ast1)\n",
    "    print(math_str)\n",
    "    math_header = '<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">'\n",
    "    #    Include the MathML strings in the component.\n",
    "    math_str = \"\\n\".join([math_header] + math_str.split(\"\\n\")[2:])\n",
    "    print(math_str)\n",
    "    comp_parameters.setMath(math_str)\n",
    "\n",
    "    ##############################################################################################\n",
    "\n",
    "    comp_parameters = libcellml.Component()\n",
    "    comp_parameters.setName(\"M_cl\")\n",
    "    model.addComponent(comp_parameters)\n",
    "\n",
    "    # var n: dimensionless {init: 2, pub: out};\n",
    "    var_n = libcellml.Variable()\n",
    "    var_n.setName(\"M_cl\")\n",
    "    var_n.setInitialValue(15.0)\n",
    "    var_n.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_n)\n",
    "\n",
    "    var_alpha = libcellml.Variable()\n",
    "    var_alpha.setName(\"alpha\")\n",
    "    var_alpha.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_alpha)\n",
    "\n",
    "    var_beta = libcellml.Variable()\n",
    "    var_beta.setName(\"P_tetR\")\n",
    "    # var_beta.setInitialValue(0.2)\n",
    "    var_beta.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_beta)\n",
    "\n",
    "    var_beta = libcellml.Variable()\n",
    "    var_beta.setName(\"n\")\n",
    "    # var_beta.setInitialValue(0.2)\n",
    "    var_beta.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_beta)\n",
    "\n",
    "    var_alpha_0 = libcellml.Variable()\n",
    "    var_alpha_0.setName(\"alpha_0\")\n",
    "    var_alpha_0.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_alpha_0)\n",
    "\n",
    "    var_K_m = libcellml.Variable()\n",
    "    var_K_m.setName(\"K_m\")\n",
    "    # var_K_m.setInitialValue(40)\n",
    "    var_K_m.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_K_m)\n",
    "\n",
    "    var_efficiency = libcellml.Variable()\n",
    "    var_efficiency.setName(\"efficiency\")\n",
    "    # var_efficiency.setInitialValue(20)\n",
    "    var_efficiency.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_efficiency)\n",
    "\n",
    "    var_t_ave = libcellml.Variable()\n",
    "    var_t_ave.setName(\"t_ave\")\n",
    "    var_t_ave.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_t_ave)\n",
    "\n",
    "    var_mRNA_halflife = libcellml.Variable()\n",
    "    var_mRNA_halflife.setName(\"time\")\n",
    "    # var_mRNA_halflife.setInitialValue(2)\n",
    "    var_mRNA_halflife.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_mRNA_halflife)\n",
    "\n",
    "    # var_eff = libcellml.Variable()\n",
    "    # var_eff.setName(\"eff\")\n",
    "    # var_eff.setInitialValue(20)\n",
    "    # var_eff.setUnits(\"minute\")\n",
    "    # comp_parameters.addVariable(var_eff)\n",
    "\n",
    "    # start with math\n",
    "    math_ast1 = libsbml.parseL3Formula(\n",
    "        \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PZ, n))\"\n",
    "    )\n",
    "    math_str = libsbml.writeMathMLToString(math_ast1)\n",
    "    print(math_str)\n",
    "    math_header = '<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">'\n",
    "    #    Include the MathML strings in the component.\n",
    "    math_str = \"\\n\".join([math_header] + math_str.split(\"\\n\")[2:])\n",
    "    print(math_str)\n",
    "    comp_parameters.setMath(math_str)\n",
    "\n",
    "    ##############################################################################################\n",
    "\n",
    "    comp_parameters = libcellml.Component()\n",
    "    comp_parameters.setName(\"P_lacl\")\n",
    "    model.addComponent(comp_parameters)\n",
    "\n",
    "    # var n: dimensionless {init: 2, pub: out};\n",
    "    var_n = libcellml.Variable()\n",
    "    var_n.setName(\"P_lacl\")\n",
    "    var_n.setInitialValue(0.0)\n",
    "    var_n.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_n)\n",
    "\n",
    "    var_alpha = libcellml.Variable()\n",
    "    var_alpha.setName(\"beta\")\n",
    "    var_alpha.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_alpha)\n",
    "\n",
    "    var_beta = libcellml.Variable()\n",
    "    var_beta.setName(\"M_lacl\")\n",
    "    # var_beta.setInitialValue(0.2)\n",
    "    var_beta.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_beta)\n",
    "\n",
    "    var_t_ave = libcellml.Variable()\n",
    "    var_t_ave.setName(\"t_ave\")\n",
    "    var_t_ave.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_t_ave)\n",
    "\n",
    "    var_K_m = libcellml.Variable()\n",
    "    var_K_m.setName(\"K_m\")\n",
    "    # var_K_m.setInitialValue(40)\n",
    "    var_K_m.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_K_m)\n",
    "\n",
    "    var_efficiency = libcellml.Variable()\n",
    "    var_efficiency.setName(\"efficiency\")\n",
    "    # var_efficiency.setInitialValue(20)\n",
    "    var_efficiency.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_efficiency)\n",
    "\n",
    "    var_mRNA_halflife = libcellml.Variable()\n",
    "    var_mRNA_halflife.setName(\"time\")\n",
    "    # var_mRNA_halflife.setInitialValue(2)\n",
    "    var_mRNA_halflife.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_mRNA_halflife)\n",
    "\n",
    "    # var_eff = libcellml.Variable()\n",
    "    # var_eff.setName(\"eff\")\n",
    "    # var_eff.setInitialValue(20)\n",
    "    # var_eff.setUnits(\"minute\")\n",
    "    # comp_parameters.addVariable(var_eff)\n",
    "\n",
    "    # start with math\n",
    "    math_ast1 = libsbml.parseL3Formula(\n",
    "        \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PZ, n))\"\n",
    "    )\n",
    "    math_str = libsbml.writeMathMLToString(math_ast1)\n",
    "    print(math_str)\n",
    "    math_header = '<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">'\n",
    "    #    Include the MathML strings in the component.\n",
    "    math_str = \"\\n\".join([math_header] + math_str.split(\"\\n\")[2:])\n",
    "    print(math_str)\n",
    "    comp_parameters.setMath(math_str)\n",
    "\n",
    "    ##############################################################################################\n",
    "\n",
    "    comp_parameters = libcellml.Component()\n",
    "    comp_parameters.setName(\"P_tetR\")\n",
    "    model.addComponent(comp_parameters)\n",
    "\n",
    "    # var n: dimensionless {init: 2, pub: out};\n",
    "    var_n = libcellml.Variable()\n",
    "    var_n.setName(\"P_tetR\")\n",
    "    var_n.setInitialValue(0.0)\n",
    "    var_n.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_n)\n",
    "\n",
    "    var_alpha = libcellml.Variable()\n",
    "    var_alpha.setName(\"beta\")\n",
    "    var_alpha.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_alpha)\n",
    "\n",
    "    var_beta = libcellml.Variable()\n",
    "    var_beta.setName(\"M_tetR\")\n",
    "    # var_beta.setInitialValue(0.2)\n",
    "    var_beta.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_beta)\n",
    "\n",
    "    var_t_ave = libcellml.Variable()\n",
    "    var_t_ave.setName(\"t_ave\")\n",
    "    var_t_ave.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_t_ave)\n",
    "\n",
    "    var_K_m = libcellml.Variable()\n",
    "    var_K_m.setName(\"K_m\")\n",
    "    # var_K_m.setInitialValue(40)\n",
    "    var_K_m.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_K_m)\n",
    "\n",
    "    var_efficiency = libcellml.Variable()\n",
    "    var_efficiency.setName(\"efficiency\")\n",
    "    # var_efficiency.setInitialValue(20)\n",
    "    var_efficiency.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_efficiency)\n",
    "\n",
    "    var_mRNA_halflife = libcellml.Variable()\n",
    "    var_mRNA_halflife.setName(\"time\")\n",
    "    # var_mRNA_halflife.setInitialValue(2)\n",
    "    var_mRNA_halflife.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_mRNA_halflife)\n",
    "\n",
    "    # var_eff = libcellml.Variable()\n",
    "    # var_eff.setName(\"eff\")\n",
    "    # var_eff.setInitialValue(20)\n",
    "    # var_eff.setUnits(\"minute\")\n",
    "    # comp_parameters.addVariable(var_eff)\n",
    "\n",
    "    # start with math\n",
    "    math_ast1 = libsbml.parseL3Formula(\n",
    "        \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PZ, n))\"\n",
    "    )\n",
    "    math_str = libsbml.writeMathMLToString(math_ast1)\n",
    "    print(math_str)\n",
    "    math_header = '<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">'\n",
    "    #    Include the MathML strings in the component.\n",
    "    math_str = \"\\n\".join([math_header] + math_str.split(\"\\n\")[2:])\n",
    "    print(math_str)\n",
    "    comp_parameters.setMath(math_str)\n",
    "\n",
    "    ##############################################################################################\n",
    "\n",
    "    comp_parameters = libcellml.Component()\n",
    "    comp_parameters.setName(\"P_cl\")\n",
    "    model.addComponent(comp_parameters)\n",
    "\n",
    "    # var n: dimensionless {init: 2, pub: out};\n",
    "    var_n = libcellml.Variable()\n",
    "    var_n.setName(\"P_cl\")\n",
    "    var_n.setInitialValue(0.0)\n",
    "    var_n.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_n)\n",
    "\n",
    "    var_alpha = libcellml.Variable()\n",
    "    var_alpha.setName(\"beta\")\n",
    "    var_alpha.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_alpha)\n",
    "\n",
    "    var_beta = libcellml.Variable()\n",
    "    var_beta.setName(\"M_cl\")\n",
    "    # var_beta.setInitialValue(0.2)\n",
    "    var_beta.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_beta)\n",
    "\n",
    "    var_t_ave = libcellml.Variable()\n",
    "    var_t_ave.setName(\"t_ave\")\n",
    "    var_t_ave.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_t_ave)\n",
    "\n",
    "    var_K_m = libcellml.Variable()\n",
    "    var_K_m.setName(\"K_m\")\n",
    "    # var_K_m.setInitialValue(40)\n",
    "    var_K_m.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_K_m)\n",
    "\n",
    "    var_efficiency = libcellml.Variable()\n",
    "    var_efficiency.setName(\"efficiency\")\n",
    "    # var_efficiency.setInitialValue(20)\n",
    "    var_efficiency.setUnits(\"dimensionless\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_efficiency)\n",
    "\n",
    "    var_mRNA_halflife = libcellml.Variable()\n",
    "    var_mRNA_halflife.setName(\"time\")\n",
    "    # var_mRNA_halflife.setInitialValue(2)\n",
    "    var_mRNA_halflife.setUnits(\"minute\")\n",
    "    # var_n.setInterfaceType()\n",
    "    comp_parameters.addVariable(var_mRNA_halflife)\n",
    "\n",
    "    # var_eff = libcellml.Variable()\n",
    "    # var_eff.setName(\"eff\")\n",
    "    # var_eff.setInitialValue(20)\n",
    "    # var_eff.setUnits(\"minute\")\n",
    "    # comp_parameters.addVariable(var_eff)\n",
    "\n",
    "    # start with math\n",
    "    math_ast1 = libsbml.parseL3Formula(\n",
    "        \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PZ, n))\"\n",
    "    )\n",
    "    math_str = libsbml.writeMathMLToString(math_ast1)\n",
    "    print(math_str)\n",
    "    math_header = '<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">'\n",
    "    #    Include the MathML strings in the component.\n",
    "    math_str = \"\\n\".join([math_header] + math_str.split(\"\\n\")[2:])\n",
    "    print(math_str)\n",
    "    comp_parameters.setMath(math_str)\n",
    "    ############################################################\n",
    "\n",
    "    comp_env = libcellml.Component()\n",
    "\n",
    "    model.addComponent(comp_env)\n",
    "\n",
    "    #  Checking that it worked\n",
    "    print(\"-\" * 80)\n",
    "    print_model(model)\n",
    "    print(\"-\" * 80)\n",
    "\n",
    "    # Save model\n",
    "    printer = libcellml.Printer()\n",
    "    serialised_model: str = printer.printModel(model)\n",
    "    print(\"-\" * 80)\n",
    "    print(serialised_model)\n",
    "    print(\"-\" * 80)\n",
    "\n",
    "    os.makedirs(os.path.dirname(cellml_path), exist_ok=True)\n",
    "    with open(cellml_path, \"w\") as f_cellml:\n",
    "        f_cellml.write(serialised_model)\n",
    "\n",
    "    return model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "8e20ee50",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-04-17T14:01:48.808524Z",
     "iopub.status.busy": "2023-04-17T14:01:48.807875Z",
     "iopub.status.idle": "2023-04-17T14:01:48.811810Z",
     "shell.execute_reply": "2023-04-17T14:01:48.812175Z"
    }
   },
   "outputs": [],
   "source": [
    "def validate_model(model: libcellml.Model) -> None:\n",
    "    \"\"\"Validate existing model.\"\"\"\n",
    "    # Validation\n",
    "    validator = libcellml.Validator()\n",
    "    validator.validateModel(model)\n",
    "    num_validation_issues = validator.issueCount()\n",
    "    print(f\"The validator has found {num_validation_issues} issues!\")\n",
    "    #      Retrieve the issues, and print their description, url, reference, and\n",
    "    #      type of item stored to the terminal.  The type of stored item is\n",
    "    #      available as an enum, which can be turned into a string for output using\n",
    "    #      the utility function, getItemTypeFromEnum(type).\n",
    "\n",
    "    for e in range(0, num_validation_issues):\n",
    "        issue = validator.issue(e)\n",
    "        reference = issue.referenceHeading()\n",
    "        print(\"  Validator issue[{}]:\".format(e))\n",
    "        print(\"     Description: {}\".format(issue.description()))\n",
    "        # print('     Type of item stored: {}'.format(cellmlElementTypeAsString(issue.item().type())))\n",
    "        print(\"     URL: {}\".format(issue.url()))\n",
    "        if reference != \"\":\n",
    "            print(\"    See section {} in the CellML specification.\".format(reference))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "830a788b",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-04-17T14:01:48.814043Z",
     "iopub.status.busy": "2023-04-17T14:01:48.813414Z",
     "iopub.status.idle": "2023-04-17T14:01:48.942214Z",
     "shell.execute_reply": "2023-04-17T14:01:48.942604Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
      "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
      "  <apply>\n",
      "    <divide/>\n",
      "    <ci> mRNA_halflife </ci>\n",
      "    <apply>\n",
      "      <ln/>\n",
      "      <cn type=\"integer\"> 2 </cn>\n",
      "    </apply>\n",
      "  </apply>\n",
      "</math>\n",
      "<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">\n",
      "  <apply>\n",
      "    <divide/>\n",
      "    <ci> mRNA_halflife </ci>\n",
      "    <apply>\n",
      "      <ln/>\n",
      "      <cn type=\"integer\"> 2 </cn>\n",
      "    </apply>\n",
      "  </apply>\n",
      "</math>\n",
      "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\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",
      "<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">\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",
      "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\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",
      "<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">\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",
      "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\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",
      "<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">\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",
      "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\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",
      "<math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">\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",
      "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\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",
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      "        </apply>\n",
      "      </apply>\n",
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      "          <ci> n </ci>\n",
      "        </apply>\n",
      "        <apply>\n",
      "          <power/>\n",
      "          <ci> PZ </ci>\n",
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      "        </apply>\n",
      "      </apply>\n",
      "    </apply>\n",
      "  </apply>\n",
      "</math>\n",
      "--------------------------------------------------------------------------------\n",
      "MODEL: 'repressilator'\n",
      "    UNITS: 1 custom units\n",
      "        [0]: minute\n",
      "    COMPONENTS: 9 components\n",
      "        [0]: 'environment'\n",
      "            VARIABLES: 1 variables\n",
      "                [0]: time [minute]\n",
      "        [1]: 'parameters'\n",
      "            VARIABLES: 8 variables\n",
      "                [0]: n [dimensionless], initial = 2\n",
      "                [1]: alpha_0 [dimensionless], initial = 0.216\n",
      "                [2]: alpha [dimensionless], initial = 216\n",
      "                [3]: beta [dimensionless], initial = 0.2\n",
      "                [4]: K_m [dimensionless], initial = 40\n",
      "                [5]: efficiency [dimensionless], initial = 20\n",
      "                [6]: mRNA_halflife [minute], initial = 2\n",
      "                [7]: t_ave [minute]\n",
      "        [2]: 'M_lacl'\n",
      "            VARIABLES: 9 variables\n",
      "                [0]: M_lacl [dimensionless], initial = 5\n",
      "                [1]: alpha [dimensionless]\n",
      "                [2]: P_cl [dimensionless]\n",
      "                [3]: n [dimensionless]\n",
      "                [4]: alpha_0 [dimensionless]\n",
      "                [5]: K_m [dimensionless]\n",
      "                [6]: efficiency [dimensionless]\n",
      "                [7]: t_ave [minute]\n",
      "                [8]: time [minute]\n",
      "        [3]: 'M_tetR'\n",
      "            VARIABLES: 9 variables\n",
      "                [0]: M_tetR [dimensionless], initial = 0\n",
      "                [1]: alpha [dimensionless]\n",
      "                [2]: P_lacl [dimensionless]\n",
      "                [3]: n [dimensionless]\n",
      "                [4]: alpha_0 [dimensionless]\n",
      "                [5]: K_m [dimensionless]\n",
      "                [6]: efficiency [dimensionless]\n",
      "                [7]: t_ave [minute]\n",
      "                [8]: time [minute]\n",
      "        [4]: 'M_cl'\n",
      "            VARIABLES: 9 variables\n",
      "                [0]: M_cl [dimensionless], initial = 15\n",
      "                [1]: alpha [dimensionless]\n",
      "                [2]: P_tetR [dimensionless]\n",
      "                [3]: n [dimensionless]\n",
      "                [4]: alpha_0 [dimensionless]\n",
      "                [5]: K_m [dimensionless]\n",
      "                [6]: efficiency [dimensionless]\n",
      "                [7]: t_ave [minute]\n",
      "                [8]: time [minute]\n",
      "        [5]: 'P_lacl'\n",
      "            VARIABLES: 7 variables\n",
      "                [0]: P_lacl [dimensionless], initial = 0\n",
      "                [1]: beta [dimensionless]\n",
      "                [2]: M_lacl [dimensionless]\n",
      "                [3]: t_ave [minute]\n",
      "                [4]: K_m [dimensionless]\n",
      "                [5]: efficiency [dimensionless]\n",
      "                [6]: time [minute]\n",
      "        [6]: 'P_tetR'\n",
      "            VARIABLES: 7 variables\n",
      "                [0]: P_tetR [dimensionless], initial = 0\n",
      "                [1]: beta [dimensionless]\n",
      "                [2]: M_tetR [dimensionless]\n",
      "                [3]: t_ave [minute]\n",
      "                [4]: K_m [dimensionless]\n",
      "                [5]: efficiency [dimensionless]\n",
      "                [6]: time [minute]\n",
      "        [7]: 'P_cl'\n",
      "            VARIABLES: 7 variables\n",
      "                [0]: P_cl [dimensionless], initial = 0\n",
      "                [1]: beta [dimensionless]\n",
      "                [2]: M_cl [dimensionless]\n",
      "                [3]: t_ave [minute]\n",
      "                [4]: K_m [dimensionless]\n",
      "                [5]: efficiency [dimensionless]\n",
      "                [6]: time [minute]\n",
      "        [8]: ''\n",
      "            VARIABLES: 0 variables\n",
      "--------------------------------------------------------------------------------\n",
      "--------------------------------------------------------------------------------\n",
      "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
      "<model xmlns=\"http://www.cellml.org/cellml/2.0#\" name=\"repressilator\">\n",
      "  <units name=\"minute\">\n",
      "    <unit exponent=\"60\" prefix=\"1\" units=\"second\"/>\n",
      "  </units>\n",
      "  <component name=\"environment\">\n",
      "    <variable name=\"time\" units=\"minute\" interface=\"out\" id=\"environment_time\"/>\n",
      "  </component>\n",
      "  <component name=\"parameters\">\n",
      "    <variable name=\"n\" units=\"dimensionless\" initial_value=\"2\"/>\n",
      "    <variable name=\"alpha_0\" units=\"dimensionless\" initial_value=\"0.216\"/>\n",
      "    <variable name=\"alpha\" units=\"dimensionless\" initial_value=\"216\"/>\n",
      "    <variable name=\"beta\" units=\"dimensionless\" initial_value=\"0.2\"/>\n",
      "    <variable name=\"K_m\" units=\"dimensionless\" initial_value=\"40\"/>\n",
      "    <variable name=\"efficiency\" units=\"dimensionless\" initial_value=\"20\"/>\n",
      "    <variable name=\"mRNA_halflife\" units=\"minute\" initial_value=\"2\"/>\n",
      "    <variable name=\"t_ave\" units=\"minute\"/>\n",
      "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">\n",
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      "        <ci>mRNA_halflife</ci>\n",
      "        <apply>\n",
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      "          <cn type=\"integer\">2</cn>\n",
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      "      </apply>\n",
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      "    <variable name=\"M_lacl\" units=\"dimensionless\" initial_value=\"5\"/>\n",
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      "    <variable name=\"P_cl\" units=\"dimensionless\"/>\n",
      "    <variable name=\"n\" units=\"dimensionless\"/>\n",
      "    <variable name=\"alpha_0\" units=\"dimensionless\"/>\n",
      "    <variable name=\"K_m\" units=\"dimensionless\"/>\n",
      "    <variable name=\"efficiency\" units=\"dimensionless\"/>\n",
      "    <variable name=\"t_ave\" units=\"minute\"/>\n",
      "    <variable name=\"time\" units=\"minute\"/>\n",
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      "              <ci>n</ci>\n",
      "            </apply>\n",
      "          </apply>\n",
      "        </apply>\n",
      "      </apply>\n",
      "    </math>\n",
      "  </component>\n",
      "  <component name=\"M_tetR\">\n",
      "    <variable name=\"M_tetR\" units=\"dimensionless\" initial_value=\"0\"/>\n",
      "    <variable name=\"alpha\" units=\"dimensionless\"/>\n",
      "    <variable name=\"P_lacl\" units=\"dimensionless\"/>\n",
      "    <variable name=\"n\" units=\"dimensionless\"/>\n",
      "    <variable name=\"alpha_0\" units=\"dimensionless\"/>\n",
      "    <variable name=\"K_m\" units=\"dimensionless\"/>\n",
      "    <variable name=\"efficiency\" units=\"dimensionless\"/>\n",
      "    <variable name=\"t_ave\" units=\"minute\"/>\n",
      "    <variable name=\"time\" units=\"minute\"/>\n",
      "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">\n",
      "      <apply>\n",
      "        <plus/>\n",
      "        <ci>a0_tr</ci>\n",
      "        <apply>\n",
      "          <divide/>\n",
      "          <apply>\n",
      "            <times/>\n",
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      "            <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",
      "  </component>\n",
      "  <component name=\"M_cl\">\n",
      "    <variable name=\"M_cl\" units=\"dimensionless\" initial_value=\"15\"/>\n",
      "    <variable name=\"alpha\" units=\"dimensionless\"/>\n",
      "    <variable name=\"P_tetR\" units=\"dimensionless\"/>\n",
      "    <variable name=\"n\" units=\"dimensionless\"/>\n",
      "    <variable name=\"alpha_0\" units=\"dimensionless\"/>\n",
      "    <variable name=\"K_m\" units=\"dimensionless\"/>\n",
      "    <variable name=\"efficiency\" units=\"dimensionless\"/>\n",
      "    <variable name=\"t_ave\" units=\"minute\"/>\n",
      "    <variable name=\"time\" units=\"minute\"/>\n",
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      "            <apply>\n",
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      "              <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",
      "  </component>\n",
      "  <component name=\"P_lacl\">\n",
      "    <variable name=\"P_lacl\" units=\"dimensionless\" initial_value=\"0\"/>\n",
      "    <variable name=\"beta\" units=\"dimensionless\"/>\n",
      "    <variable name=\"M_lacl\" units=\"dimensionless\"/>\n",
      "    <variable name=\"t_ave\" units=\"minute\"/>\n",
      "    <variable name=\"K_m\" units=\"dimensionless\"/>\n",
      "    <variable name=\"efficiency\" units=\"dimensionless\"/>\n",
      "    <variable name=\"time\" units=\"minute\"/>\n",
      "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">\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",
      "  </component>\n",
      "  <component name=\"P_tetR\">\n",
      "    <variable name=\"P_tetR\" units=\"dimensionless\" initial_value=\"0\"/>\n",
      "    <variable name=\"beta\" units=\"dimensionless\"/>\n",
      "    <variable name=\"M_tetR\" units=\"dimensionless\"/>\n",
      "    <variable name=\"t_ave\" units=\"minute\"/>\n",
      "    <variable name=\"K_m\" units=\"dimensionless\"/>\n",
      "    <variable name=\"efficiency\" units=\"dimensionless\"/>\n",
      "    <variable name=\"time\" units=\"minute\"/>\n",
      "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">\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",
      "  </component>\n",
      "  <component name=\"P_cl\">\n",
      "    <variable name=\"P_cl\" units=\"dimensionless\" initial_value=\"0\"/>\n",
      "    <variable name=\"beta\" units=\"dimensionless\"/>\n",
      "    <variable name=\"M_cl\" units=\"dimensionless\"/>\n",
      "    <variable name=\"t_ave\" units=\"minute\"/>\n",
      "    <variable name=\"K_m\" units=\"dimensionless\"/>\n",
      "    <variable name=\"efficiency\" units=\"dimensionless\"/>\n",
      "    <variable name=\"time\" units=\"minute\"/>\n",
      "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:cellml=\"http://www.cellml.org/cellml/2.0#\">\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",
      "  </component>\n",
      "  <component/>\n",
      "</model>\n",
      "\n",
      "--------------------------------------------------------------------------------\n",
      "The validator has found 42 issues!\n",
      "  Validator issue[0]:\n",
      "     Description: Variable 'time' in component 'environment' has an invalid interface attribute value 'out'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB08.html?issue=VARIABLE_INTERFACE\n",
      "    See section 2.8.2.1 in the CellML specification.\n",
      "  Validator issue[1]:\n",
      "     Description: Math cn element with the value '2' does not have a valid cellml:units attribute. CellML identifiers must contain one or more basic Latin alphabetic characters.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB13.html?issue=MATH_CN_UNITS\n",
      "    See section 2.12.4 in the CellML specification.\n",
      "  Validator issue[2]:\n",
      "     Description: MathML ci element has the child text 'a0_tr' which does not correspond with any variable names present in component 'M_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[3]:\n",
      "     Description: MathML ci element has the child text 'a_tr' which does not correspond with any variable names present in component 'M_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[4]:\n",
      "     Description: MathML ci element has the child text 'KM' which does not correspond with any variable names present in component 'M_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[5]:\n",
      "     Description: MathML ci element has the child text 'KM' which does not correspond with any variable names present in component 'M_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[6]:\n",
      "     Description: MathML ci element has the child text 'PZ' which does not correspond with any variable names present in component 'M_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[7]:\n",
      "     Description: MathML ci element has the child text 'a0_tr' which does not correspond with any variable names present in component 'M_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[8]:\n",
      "     Description: MathML ci element has the child text 'a_tr' which does not correspond with any variable names present in component 'M_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[9]:\n",
      "     Description: MathML ci element has the child text 'KM' which does not correspond with any variable names present in component 'M_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[10]:\n",
      "     Description: MathML ci element has the child text 'KM' which does not correspond with any variable names present in component 'M_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[11]:\n",
      "     Description: MathML ci element has the child text 'PZ' which does not correspond with any variable names present in component 'M_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[12]:\n",
      "     Description: MathML ci element has the child text 'a0_tr' which does not correspond with any variable names present in component 'M_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[13]:\n",
      "     Description: MathML ci element has the child text 'a_tr' which does not correspond with any variable names present in component 'M_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[14]:\n",
      "     Description: MathML ci element has the child text 'KM' which does not correspond with any variable names present in component 'M_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[15]:\n",
      "     Description: MathML ci element has the child text 'KM' which does not correspond with any variable names present in component 'M_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[16]:\n",
      "     Description: MathML ci element has the child text 'PZ' which does not correspond with any variable names present in component 'M_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[17]:\n",
      "     Description: MathML ci element has the child text 'a0_tr' which does not correspond with any variable names present in component 'P_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[18]:\n",
      "     Description: MathML ci element has the child text 'a_tr' which does not correspond with any variable names present in component 'P_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[19]:\n",
      "     Description: MathML ci element has the child text 'KM' which does not correspond with any variable names present in component 'P_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[20]:\n",
      "     Description: MathML ci element has the child text 'n' which does not correspond with any variable names present in component 'P_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[21]:\n",
      "     Description: MathML ci element has the child text 'KM' which does not correspond with any variable names present in component 'P_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[22]:\n",
      "     Description: MathML ci element has the child text 'n' which does not correspond with any variable names present in component 'P_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[23]:\n",
      "     Description: MathML ci element has the child text 'PZ' which does not correspond with any variable names present in component 'P_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[24]:\n",
      "     Description: MathML ci element has the child text 'n' which does not correspond with any variable names present in component 'P_lacl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[25]:\n",
      "     Description: MathML ci element has the child text 'a0_tr' which does not correspond with any variable names present in component 'P_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[26]:\n",
      "     Description: MathML ci element has the child text 'a_tr' which does not correspond with any variable names present in component 'P_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[27]:\n",
      "     Description: MathML ci element has the child text 'KM' which does not correspond with any variable names present in component 'P_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[28]:\n",
      "     Description: MathML ci element has the child text 'n' which does not correspond with any variable names present in component 'P_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[29]:\n",
      "     Description: MathML ci element has the child text 'KM' which does not correspond with any variable names present in component 'P_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[30]:\n",
      "     Description: MathML ci element has the child text 'n' which does not correspond with any variable names present in component 'P_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[31]:\n",
      "     Description: MathML ci element has the child text 'PZ' which does not correspond with any variable names present in component 'P_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[32]:\n",
      "     Description: MathML ci element has the child text 'n' which does not correspond with any variable names present in component 'P_tetR'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[33]:\n",
      "     Description: MathML ci element has the child text 'a0_tr' which does not correspond with any variable names present in component 'P_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[34]:\n",
      "     Description: MathML ci element has the child text 'a_tr' which does not correspond with any variable names present in component 'P_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[35]:\n",
      "     Description: MathML ci element has the child text 'KM' which does not correspond with any variable names present in component 'P_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[36]:\n",
      "     Description: MathML ci element has the child text 'n' which does not correspond with any variable names present in component 'P_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[37]:\n",
      "     Description: MathML ci element has the child text 'KM' which does not correspond with any variable names present in component 'P_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[38]:\n",
      "     Description: MathML ci element has the child text 'n' which does not correspond with any variable names present in component 'P_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[39]:\n",
      "     Description: MathML ci element has the child text 'PZ' which does not correspond with any variable names present in component 'P_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[40]:\n",
      "     Description: MathML ci element has the child text 'n' which does not correspond with any variable names present in component 'P_cl'.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB12.html?issue=MATH_CI_VARIABLE_REF\n",
      "    See section 2.12.3 in the CellML specification.\n",
      "  Validator issue[41]:\n",
      "     Description: Component '' does not have a valid name attribute. CellML identifiers must contain one or more basic Latin alphabetic characters.\n",
      "     URL: https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specB07.html?issue=COMPONENT_NAME\n",
      "    See section 2.7.1 in the CellML specification.\n"
     ]
    }
   ],
   "source": [
    "if __name__ == \"__main__\":\n",
    "    from combine_notebooks import RESULTS_DIR\n",
    "\n",
    "    cellml_path: Path = RESULTS_DIR / \"repressilator_cellml.cellml\"\n",
    "    model = create_repressilator(cellml_path)\n",
    "    validate_model(model)"
   ]
  }
 ],
 "metadata": {
  "jupytext": {
   "cell_metadata_filter": "-all",
   "main_language": "python",
   "notebook_metadata_filter": "-all"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}