notebooks/example_sedml.ipynb

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   "source": [
    "Create repressilator using SED-ML\n",
    "\n",
    "SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments.\n",
    "\n",
    "\n",
    "https://sed-ml.org/"
   ]
  },
  {
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   "outputs": [],
   "source": [
    "import os\n",
    "from pathlib import Path\n",
    "\n",
    "import libsedml"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "a38e30fd",
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    "execution": {
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   "source": [
    "\n",
    "\n",
    "def create_repressilator(sedml_path: Path) -> libsedml.SedDocument:\n",
    "    \"\"\"Create repressilator using SED-ML.\"\"\"\n",
    "    # create the document\n",
    "    doc = libsedml.SedDocument(1, 4)\n",
    "\n",
    "    # create a first model referencing an sbml file\n",
    "\n",
    "    \"\"\"\n",
    "    <listOfSimulations>\n",
    "        <uniformTimeCourse id=\"sim1\" initialTime=\"0\" outputStartTime=\"0\" outputEndTime=\"1000\" numberOfPoints=\"1000\">\n",
    "          <algorithm kisaoID=\"KISAO:0000019\"/>\n",
    "        </uniformTimeCourse>\n",
    "      </listOfSimulations>\n",
    "    \"\"\"\n",
    "    # create simulation\n",
    "    tc = doc.createUniformTimeCourse()\n",
    "    tc.setId(\"sim1\")\n",
    "    tc.setInitialTime(0.0)\n",
    "    tc.setOutputStartTime(0.0)\n",
    "    tc.setOutputEndTime(1000.0)\n",
    "    tc.setNumberOfPoints(1000)\n",
    "    # need to set the correct KISAO Term\n",
    "    alg = tc.createAlgorithm()\n",
    "    alg.setKisaoID(\"KISAO:0000019\")\n",
    "\n",
    "    \"\"\"\n",
    "    <listOfModels>\n",
    "    <model id=\"model1\" language=\"urn:sedml:language:sbml.level-3.version-1\" source=\"https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012_url.xml\"/>\n",
    "    <model id=\"model2\" language=\"urn:sedml:language:sbml.level-3.version-1\" source=\"#model1\">\n",
    "      <listOfChanges>\n",
    "        <changeAttribute target=\"/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='ps_0']/@value\" newValue=\"1.3e-05\"/>\n",
    "        <changeAttribute target=\"/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='ps_a']/@value\" newValue=\"0.013\"/>\n",
    "      </listOfChanges>\n",
    "    </model>\n",
    "    </listOfModels>\n",
    "    \"\"\"\n",
    "    # create a first model referencing an sbml file\n",
    "    model = doc.createModel()\n",
    "    model.setId(\"model1\")\n",
    "    model.setSource(\n",
    "        \"https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012_url.xml\"\n",
    "    )\n",
    "    model.setLanguage(\"urn:sedml:language:sbml.level-3.version-1\")\n",
    "\n",
    "    # create a second model modifying a variable of that other sbml file\n",
    "    model = doc.createModel()\n",
    "    model.setId(\"model2\")\n",
    "    model.setSource(\"#model1\")\n",
    "    model.setLanguage(\"urn:sedml:language:sbml.level-3.version-1\")\n",
    "\n",
    "    change = model.createChangeAttribute()\n",
    "    change.setTarget(\n",
    "        \"/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='ps_0']/@value\"\n",
    "    )\n",
    "    change.setNewValue(\"1.3e-05\")\n",
    "\n",
    "    change = model.createChangeAttribute()\n",
    "    change.setTarget(\n",
    "        \"/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='ps_a']/@value\"\n",
    "    )\n",
    "    change.setNewValue(\"0.013\")\n",
    "\n",
    "    \"\"\"\n",
    "    <listOfTasks>\n",
    "    <task id=\"task1\" modelReference=\"model1\" simulationReference=\"sim1\"/>\n",
    "    <task id=\"task2\" modelReference=\"model2\" simulationReference=\"sim1\"/>\n",
    "    </listOfTasks>\n",
    "    \"\"\"\n",
    "    # create a task that uses the simulation and the model above\n",
    "    task = doc.createTask()\n",
    "    task.setId(\"task1\")\n",
    "    task.setModelReference(\"model1\")\n",
    "    task.setSimulationReference(\"sim1\")\n",
    "\n",
    "    # create a task that uses the simulation and the model above\n",
    "    task = doc.createTask()\n",
    "    task.setId(\"task2\")\n",
    "    task.setModelReference(\"model2\")\n",
    "    task.setSimulationReference(\"sim1\")\n",
    "\n",
    "    \"\"\"\n",
    "    <dataGenerator id=\"dg_0_0_0\" name=\"task1.time\">\n",
    "      <listOfVariables>\n",
    "        <variable id=\"task1_____time\" symbol=\"urn:sedml:symbol:time\" taskReference=\"task1\"/>\n",
    "      </listOfVariables>\n",
    "      <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n",
    "        <ci> task1_____time </ci>\n",
    "      </math>\n",
    "    </dataGenerator>\n",
    "    \"\"\"\n",
    "    # add a DataGenerator to hold the output for time\n",
    "    dg = doc.createDataGenerator()\n",
    "    dg.setId(\"dg_0_0_0\")\n",
    "    dg.setName(\"task1.time\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task1_____time\")\n",
    "    var.setTaskReference(\"task1\")\n",
    "    var.setSymbol(\"urn:sedml:symbol:time\")\n",
    "    dg.setMath(libsedml.parseFormula(\"task1_____time\"))\n",
    "\n",
    "    dg = doc.createDataGenerator()\n",
    "    dg.setId(\"dg_0_0_1\")\n",
    "    dg.setName(\"PX (lacI)\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task1_____PX\")\n",
    "    var.setTarget(\"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PX']\")\n",
    "    var.setTaskReference(\"task1\")\n",
    "    var.setModelReference(\"model1\")\n",
    "    dg.setMath(libsedml.parseFormula(\"task1_____PX\"))\n",
    "\n",
    "    dg = doc.createDataGenerator()\n",
    "    dg.setId(\"dg_0_1_1\")\n",
    "    dg.setName(\"PZ (cI)\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task1_____PZ\")\n",
    "    var.setTarget(\"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PZ']\")\n",
    "    var.setTaskReference(\"task1\")\n",
    "    var.setModelReference(\"model1\")\n",
    "    dg.setMath(libsedml.parseFormula(\"task1_____PZ\"))\n",
    "\n",
    "    dg = doc.createDataGenerator()\n",
    "    dg.setId(\"dg_0_2_1\")\n",
    "    dg.setName(\"PY (tetR)\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task1_____PY\")\n",
    "    var.setTarget(\"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PY']\")\n",
    "    var.setTaskReference(\"task1\")\n",
    "    var.setModelReference(\"model1\")\n",
    "    dg.setMath(libsedml.parseFormula(\"task1_____PY\"))\n",
    "\n",
    "    dg = doc.createDataGenerator()\n",
    "    dg.setId(\"dg_1_0_0\")\n",
    "    dg.setName(\"time\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task2_____time\")\n",
    "    var.setSymbol(\"urn:sedml:symbol:time\")\n",
    "    var.setTaskReference(\"task2\")\n",
    "    dg.setMath(libsedml.parseFormula(\"task2_____time\"))\n",
    "\n",
    "    dg = doc.createDataGenerator()\n",
    "    dg.setId(\"dg_1_0_1\")\n",
    "    dg.setName(\"PX (lacI)\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task2_____PX\")\n",
    "    var.setTarget(\"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PX']\")\n",
    "    var.setTaskReference(\"task2\")\n",
    "    var.setModelReference(\"model2\")\n",
    "    dg.setMath(libsedml.parseFormula(\"task2_____PX\"))\n",
    "\n",
    "    dg = doc.createDataGenerator()\n",
    "    dg.setId(\"dg_1_1_1\")\n",
    "    dg.setName(\"PZ (cI)\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task2_____PZ\")\n",
    "    var.setTarget(\"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PZ']\")\n",
    "    var.setTaskReference(\"task2\")\n",
    "    var.setModelReference(\"model2\")\n",
    "    dg.setMath(libsedml.parseFormula(\"task2_____PZ\"))\n",
    "\n",
    "    dg = doc.createDataGenerator()\n",
    "    dg.setId(\"dg_1_2_1\")\n",
    "    dg.setName(\"PY (tetR)\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task2_____PY\")\n",
    "    var.setTarget(\"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PY']\")\n",
    "    var.setTaskReference(\"task2\")\n",
    "    var.setModelReference(\"model2\")\n",
    "    dg.setMath(libsedml.parseFormula(\"task2_____PY\"))\n",
    "\n",
    "    dg = doc.createDataGenerator()\n",
    "    dg.setId(\"dg_2_0_0\")\n",
    "    dg.setName(\"PX/max(PX) (lacI normalized)\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task1_____PX\")\n",
    "    var.setTarget(\"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PX']\")\n",
    "    var.setTaskReference(\"task1\")\n",
    "    var.setModelReference(\"model1\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task1_____PX_max\")\n",
    "    var.setTarget(\"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PX']\")\n",
    "    var.setTaskReference(\"task1\")\n",
    "    var.setModelReference(\"model1\")\n",
    "    var.setDimensionTerm(\"KISAO:0000828\")\n",
    "    dg.setMath(libsedml.parseFormula(\"task1_____PX / task1_____PX_max\"))\n",
    "\n",
    "    dg = doc.createDataGenerator()\n",
    "    dg.setId(\"dg_2_0_1\")\n",
    "    dg.setName(\"PZ/max(PZ) (cI normalized)\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task1_____PZ\")\n",
    "    var.setTarget(\"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PZ']\")\n",
    "    var.setTaskReference(\"task1\")\n",
    "    var.setModelReference(\"model1\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task1_____PZ_max\")\n",
    "    var.setTarget(\"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PX']\")\n",
    "    var.setTaskReference(\"task1\")\n",
    "    var.setModelReference(\"model1\")\n",
    "    var.setDimensionTerm(\"KISAO:0000828\")\n",
    "    dg.setMath(libsedml.parseFormula(\"task1_____PZ / task1_____PZ_max\"))\n",
    "\n",
    "    dg = doc.createDataGenerator()\n",
    "    dg.setId(\"dg_2_1_0\")\n",
    "    dg.setName(\"PY/max(PY) (tetR normalized)\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task1_____PY\")\n",
    "    var.setTarget(\"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PY']\")\n",
    "    var.setTaskReference(\"task1\")\n",
    "    var.setModelReference(\"model1\")\n",
    "    var = dg.createVariable()\n",
    "    var.setId(\"task1_____PY_max\")\n",
    "    var.setTarget(\"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PY']\")\n",
    "    var.setTaskReference(\"task1\")\n",
    "    var.setModelReference(\"model1\")\n",
    "    var.setDimensionTerm(\"KISAO:0000828\")\n",
    "    dg.setMath(libsedml.parseFormula(\"task1_____PY / task1_____PY_max\"))\n",
    "\n",
    "    # add a 2d plot\n",
    "    plot = doc.createPlot2D()\n",
    "    plot.setId(\"timecourse\")\n",
    "    plot.setName(\"Timecourse of repressilator\")\n",
    "    curve = plot.createCurve()\n",
    "    curve.setId(\"plot_0__plot_0_0_0__plot_0_0_1\")\n",
    "    curve.setLogX(False)\n",
    "    curve.setLogY(False)\n",
    "    curve.setXDataReference(\"dg_0_0_0\")\n",
    "    curve.setYDataReference(\"dg_0_0_1\")\n",
    "    curve = plot.createCurve()\n",
    "    curve.setId(\"plot_0__plot_0_0_0__plot_0_1_1\")\n",
    "    curve.setLogX(False)\n",
    "    curve.setLogY(False)\n",
    "    curve.setXDataReference(\"dg_0_0_0\")\n",
    "    curve.setYDataReference(\"dg_0_1_1\")\n",
    "    curve = plot.createCurve()\n",
    "    curve.setId(\"plot_0__plot_0_0_0__plot_0_2_1\")\n",
    "    curve.setLogX(False)\n",
    "    curve.setLogY(False)\n",
    "    curve.setXDataReference(\"dg_0_0_0\")\n",
    "    curve.setYDataReference(\"dg_0_2_1\")\n",
    "\n",
    "    # add a 2d plot\n",
    "    plot = doc.createPlot2D()\n",
    "    plot.setId(\"preprocessing\")\n",
    "    plot.setName(\"Timecourse after pre-processing\")\n",
    "    curve = plot.createCurve()\n",
    "    curve.setId(\"plot_1__plot_1_0_0__plot_1_0_1\")\n",
    "    curve.setLogX(False)\n",
    "    curve.setLogY(False)\n",
    "    curve.setXDataReference(\"dg_1_0_0\")\n",
    "    curve.setYDataReference(\"dg_1_0_1\")\n",
    "    curve = plot.createCurve()\n",
    "    curve.setId(\"plot_1__plot_1_0_0__plot_1_1_1\")\n",
    "    curve.setLogX(False)\n",
    "    curve.setLogY(False)\n",
    "    curve.setXDataReference(\"dg_1_0_0\")\n",
    "    curve.setYDataReference(\"dg_1_1_1\")\n",
    "    curve = plot.createCurve()\n",
    "    curve.setId(\"plot_1__plot_1_0_0__plot_1_2_1\")\n",
    "    curve.setLogX(False)\n",
    "    curve.setLogY(False)\n",
    "    curve.setXDataReference(\"dg_1_0_0\")\n",
    "    curve.setYDataReference(\"dg_1_2_1\")\n",
    "\n",
    "    # add a 2d plot\n",
    "    plot = doc.createPlot2D()\n",
    "    plot.setId(\"postprocessing\")\n",
    "    plot.setName(\"Timecourse after post-processing\")\n",
    "    curve = plot.createCurve()\n",
    "    curve.setId(\"plot_2__plot_2_0_0__plot_2_0_1\")\n",
    "    curve.setLogX(False)\n",
    "    curve.setLogY(False)\n",
    "    curve.setXDataReference(\"dg_2_0_0\")\n",
    "    curve.setYDataReference(\"dg_2_0_1\")\n",
    "    curve = plot.createCurve()\n",
    "    curve.setId(\"plot_2__plot_2_1_0__plot_2_0_0\")\n",
    "    curve.setLogX(False)\n",
    "    curve.setLogY(False)\n",
    "    curve.setXDataReference(\"dg_2_1_0\")\n",
    "    curve.setYDataReference(\"dg_2_0_0\")\n",
    "    curve = plot.createCurve()\n",
    "    curve.setId(\"plot_2__plot_2_0_1__plot_2_1_0\")\n",
    "    curve.setLogX(False)\n",
    "    curve.setLogY(False)\n",
    "    curve.setXDataReference(\"dg_2_0_1\")\n",
    "    curve.setYDataReference(\"dg_2_1_0\")\n",
    "\n",
    "    # write doc\n",
    "    os.makedirs(os.path.dirname(str(sedml_path)), exist_ok=True)\n",
    "    libsedml.writeSedML(doc, str(sedml_path))\n",
    "    return doc"
   ]
  },
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   "outputs": [],
   "source": [
    "if __name__ == \"__main__\":\n",
    "    from combine_notebooks import RESULTS_DIR\n",
    "\n",
    "    create_repressilator(sedml_path=RESULTS_DIR / \"repressilator_sedml.xml\")"
   ]
  }
 ],
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