{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "2fdd8a1a", "metadata": { "lines_to_next_cell": 0 }, "outputs": [], "source": [ "# \n", "# Example script for creating SBML repressilator with sbmlutils.\n", "\n", "\n", "# https://github.com/matthiaskoenig/libsbgn-python" ] }, { "cell_type": "code", "execution_count": 2, "id": "b3bdc3a6", "metadata": { "execution": { "iopub.execute_input": "2023-04-17T14:02:02.692509Z", "iopub.status.busy": "2023-04-17T14:02:02.692213Z", "iopub.status.idle": "2023-04-17T14:02:04.916146Z", "shell.execute_reply": "2023-04-17T14:02:04.916637Z" }, "lines_to_next_cell": 2 }, "outputs": [], "source": [ "import os\n", "from pathlib import Path\n", "\n", "from sbmlutils.factory import (\n", " AssignmentRule,\n", " Compartment,\n", " FactoryResult,\n", " Model,\n", " ModelUnits,\n", " Parameter,\n", " Reaction,\n", " Species,\n", " Units,\n", " create_model,\n", ")\n", "from sbmlutils.metadata import *\n", "from sbmlutils.metadata import BQB\n", "\n", "from combine_notebooks import RESULTS_DIR" ] }, { "cell_type": "code", "execution_count": 3, "id": "b48e09fa", "metadata": { "execution": { "iopub.execute_input": "2023-04-17T14:02:04.919375Z", "iopub.status.busy": "2023-04-17T14:02:04.918492Z", "iopub.status.idle": "2023-04-17T14:02:04.931709Z", "shell.execute_reply": "2023-04-17T14:02:04.932180Z" } }, "outputs": [], "source": [ "model = Model(\n", " \"repressilator_sbmlutils\",\n", " units=Units,\n", " model_units=ModelUnits(\n", " time=Units.second,\n", " substance=Units.mole,\n", " extent=Units.mole,\n", " volume=Units.litre,\n", " ),\n", " compartments=[\n", " Compartment(\n", " sid=\"cell\",\n", " value=1.0,\n", " sboTerm=\"SBO:0000290\",\n", " annotations=[(BQB.IS, \"obo.go/GO:0005623\")],\n", " )\n", " ],\n", " # obo.go/GO:3A0005623\n", " species=[\n", " Species(\n", " sid=\"PX\",\n", " compartment=\"cell\",\n", " name=\"LacI protein\",\n", " sboTerm=\"SBO:0000252\",\n", " initialAmount=0,\n", " hasOnlySubstanceUnits=True,\n", " annotations=[(BQB.IS, \"uniprot/P03023\")],\n", " ),\n", " Species(\n", " sid=\"PY\",\n", " compartment=\"cell\",\n", " name=\"TetR protein\",\n", " sboTerm=\"SBO:0000252\",\n", " initialAmount=0,\n", " hasOnlySubstanceUnits=True,\n", " annotations=[(BQB.IS, \"uniprot/P04483\")],\n", " ),\n", " Species(\n", " sid=\"PZ\",\n", " compartment=\"cell\",\n", " name=\"cI protein\",\n", " sboTerm=\"SBO:0000252\",\n", " initialAmount=0,\n", " hasOnlySubstanceUnits=True,\n", " annotations=[(BQB.IS, \"uniprot/P03034\")],\n", " ),\n", " Species(\n", " sid=\"X\",\n", " compartment=\"cell\",\n", " name=\"Lacl mRNA\",\n", " sboTerm=\"SBO:0000250\",\n", " initialAmount=20,\n", " hasOnlySubstanceUnits=True,\n", " annotations=[\n", " (BQB.IS_VERSION_OF, \"chebi/CHEBI:33699\"),\n", " (BQB.IS_VERSION_OF, \"kegg.compound/C00046\"),\n", " (BQB.ENCODES, \"uniprot/P03023\"),\n", " ],\n", " ),\n", " Species(\n", " sid=\"Y\",\n", " compartment=\"cell\",\n", " name=\"TetR mRNA\",\n", " sboTerm=\"SBO:0000250\",\n", " initialAmount=20,\n", " hasOnlySubstanceUnits=True,\n", " annotations=[\n", " (BQB.IS_VERSION_OF, \"chebi/CHEBI:33699\"),\n", " (BQB.IS_VERSION_OF, \"kegg.compound/C00046\"),\n", " (BQB.ENCODES, \"uniprot/P04483\"),\n", " ],\n", " ),\n", " Species(\n", " sid=\"Z\",\n", " compartment=\"cell\",\n", " name=\"cl mRNA\",\n", " sboTerm=\"SBO:0000250\",\n", " initialAmount=0,\n", " hasOnlySubstanceUnits=True,\n", " annotations=[\n", " (BQB.IS_VERSION_OF, \"chebi/CHEBI:33699\"),\n", " (BQB.IS_VERSION_OF, \"kegg.compound/C00046\"),\n", " (BQB.ENCODES, \"uniprot/P03034\"),\n", " ],\n", " ),\n", " ],\n", " parameters=[\n", " Parameter(sid=\"tau_mRNA\", name=\"mRNA half life\", constant=True, value=2.0),\n", " Parameter(sid=\"kd_mRNA\", name=\"kd_mRNA\", constant=False, sboTerm=\"SBO:0000356\"),\n", " Parameter(sid=\"k_tl\", name=\"k_tl\", constant=False, sboTerm=\"SBO:0000016\"),\n", " Parameter(\n", " sid=\"t_ave\",\n", " name=\"average mRNA life time\",\n", " constant=False,\n", " sboTerm=\"SBO:0000348\",\n", " ),\n", " Parameter(sid=\"eff\", name=\"translation efficiency\", constant=True, value=20),\n", " Parameter(sid=\"kd_prot\", name=\"kd_prot\", constant=False, sboTerm=\"SBO:0000356\"),\n", " Parameter(sid=\"tau_prot\", name=\"protien half life\", constant=True, value=10),\n", " Parameter(sid=\"a0_tr\", name=\"a0_tr\", constant=False, sboTerm=\"SBO:0000485\"),\n", " Parameter(sid=\"ps_0\", name=\"tps_repr\", constant=True, value=0.0005),\n", " Parameter(sid=\"ps_a\", name=\"tps_active\", constant=True, value=0.5),\n", " Parameter(sid=\"KM\", name=\"KM\", constant=True, value=40),\n", " Parameter(sid=\"n\", name=\"n\", constant=True, value=2.0),\n", " Parameter(sid=\"a_tr\", name=\"a_tr\", constant=False, sboTerm=\"SBO:0000186\"),\n", " ],\n", " rules=[\n", " AssignmentRule(\n", " variable=\"kd_mRNA\",\n", " sid=\"kd_mRNA\",\n", " value=\"ln(2) / tau_mRNA\",\n", " name=\"kd_MRNA\",\n", " sboTerm=None,\n", " ),\n", " AssignmentRule(\n", " variable=\"t_ave\",\n", " sid=\"t_ave\",\n", " value=\"tau_mRNA / ln(2)\",\n", " name=\"t_ave\",\n", " sboTerm=None,\n", " ),\n", " AssignmentRule(\n", " variable=\"k_tl\", sid=\"k_tl\", value=\"eff / t_ave\", name=\"k_tl\", sboTerm=None\n", " ),\n", " AssignmentRule(\n", " variable=\"kd_prot\",\n", " sid=\"kd_prot\",\n", " value=\"ln(2) / tau_prot\",\n", " name=\"kd_prot\",\n", " sboTerm=None,\n", " ),\n", " AssignmentRule(\n", " variable=\"a0_tr\", sid=\"a0_tr\", value=\"ps_0 * 60\", name=\"a0_tr\", sboTerm=None\n", " ),\n", " AssignmentRule(\n", " variable=\"a_tr\",\n", " sid=\"a_tr\",\n", " value=\"(ps_a - ps_0) * 60\",\n", " name=\"a_tr\",\n", " sboTerm=None,\n", " ),\n", " ],\n", " reactions=[\n", " Reaction(\n", " sid=\"Reaction1\",\n", " sboTerm=\"SBO:0000179\",\n", " name=\"degradation of LacI transcripts\",\n", " reversible=False,\n", " equation=\"X -> \",\n", " formula=(\"kd_mRNA * X\", None),\n", " annotations=[(BQB.IS_VERSION_OF, \"obo.go/GO:0006402\")],\n", " ),\n", " Reaction(\n", " sid=\"Reaction2\",\n", " sboTerm=\"SBO:0000179\",\n", " name=\"degradation of TetR transcripts\",\n", " reversible=False,\n", " equation=\"Y -> \",\n", " formula=(\"kd_mRNA * Y\", None),\n", " annotations=[(BQB.IS_VERSION_OF, \"obo.go/GO:0006402\")],\n", " ),\n", " Reaction(\n", " sid=\"Reaction3\",\n", " sboTerm=\"SBO:0000179\",\n", " name=\"degradation of CI transcripts\",\n", " reversible=False,\n", " equation=\"Z -> \",\n", " formula=(\"kd_mRNA * Z\", None),\n", " annotations=[(BQB.IS_VERSION_OF, \"obo.go/GO:0006402\")],\n", " ),\n", " Reaction(\n", " sid=\"Reaction4\",\n", " sboTerm=\"SBO:0000184\",\n", " name=\"translation of LacI\",\n", " reversible=False,\n", " equation=\" -> PX [X]\",\n", " formula=(\"k_tl * X\", None),\n", " annotations=[(BQB.IS_VERSION_OF, \"obo.go/GO:0006412\")],\n", " ),\n", " Reaction(\n", " sid=\"Reaction5\",\n", " sboTerm=\"SBO:0000184\",\n", " name=\"translation of TetR\",\n", " reversible=False,\n", " equation=\" -> PY [Y]\",\n", " formula=(\"k_tl * Y\", None),\n", " annotations=[(BQB.IS_VERSION_OF, \"obo.go/GO:0006412\")],\n", " ),\n", " Reaction(\n", " sid=\"Reaction6\",\n", " sboTerm=\"SBO:0000184\",\n", " name=\"translation of CI\",\n", " reversible=False,\n", " equation=\" -> PZ [Z]\",\n", " formula=(\"k_tl *Z\", None),\n", " annotations=[(BQB.IS_VERSION_OF, \"obo.go/GO:0006412\")],\n", " ),\n", " Reaction(\n", " sid=\"Reaction7\",\n", " sboTerm=\"SBO:0000179\",\n", " name=\"degradation of LacI\",\n", " reversible=False,\n", " equation=\"PX -> \",\n", " formula=(\"kd_prot * PX\", None),\n", " annotations=[(BQB.IS_VERSION_OF, \"obo.go/GO:0030163\")],\n", " ),\n", " Reaction(\n", " sid=\"Reaction8\",\n", " sboTerm=\"SBO:0000179\",\n", " name=\"degradation of TetR\",\n", " reversible=False,\n", " equation=\"PY -> \",\n", " formula=(\"kd_prot * PY\", None),\n", " annotations=[(BQB.IS_VERSION_OF, \"obo.go/GO:0030163\")],\n", " ),\n", " Reaction(\n", " sid=\"Reaction9\",\n", " sboTerm=\"SBO:0000179\",\n", " name=\"degradation of CI\",\n", " reversible=False,\n", " equation=\"PZ -> \",\n", " formula=(\"kd_prot * PZ\", None),\n", " annotations=[(BQB.IS_VERSION_OF, \"obo.go/GO:0030163\")],\n", " ),\n", " Reaction(\n", " sid=\"Reaction10\",\n", " sboTerm=\"SBO:0000183\",\n", " name=\"transcription of LacI\",\n", " reversible=False,\n", " equation=\" -> X [PZ]\",\n", " formula=(\n", " \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PZ, n))\",\n", " None,\n", " ),\n", " annotations=[(BQB.IS_VERSION_OF, \"obo.go/GO:0006351\")],\n", " ),\n", " Reaction(\n", " sid=\"Reaction11\",\n", " sboTerm=\"SBO:0000183\",\n", " name=\"transcription of TetR\",\n", " reversible=False,\n", " equation=\" -> Y [PX]\",\n", " formula=(\n", " \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PX, n))\",\n", " None,\n", " ),\n", " annotations=[(BQB.IS_VERSION_OF, \"obo.go/GO:0006351\")],\n", " ),\n", " Reaction(\n", " sid=\"Reaction12\",\n", " sboTerm=\"SBO:0000184\",\n", " name=\"transcription of CI\",\n", " reversible=False,\n", " equation=\" -> Z [PY]\",\n", " formula=(\n", " \"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PY, n))\",\n", " None,\n", " ),\n", " annotations=[(BQB.IS_VERSION_OF, \"obo.go/GO:0006351\")],\n", " ),\n", " ],\n", ")" ] }, { "cell_type": "code", "execution_count": 4, "id": "bdbd7604", "metadata": { "execution": { "iopub.execute_input": "2023-04-17T14:02:04.935619Z", "iopub.status.busy": "2023-04-17T14:02:04.934430Z", "iopub.status.idle": "2023-04-17T14:02:04.938575Z", "shell.execute_reply": "2023-04-17T14:02:04.938961Z" } }, "outputs": [], "source": [ "\n", "\n", "def create_repressilator(sbml_path: Path) -> FactoryResult:\n", " \"\"\"Create the repressilator model in the results_dir.\"\"\"\n", " results = create_model(\n", " model=model,\n", " filepath=sbml_path,\n", " sbml_level=2,\n", " sbml_version=3,\n", " )\n", " return results" ] }, { "cell_type": "code", "execution_count": 5, "id": "4a87ee59", "metadata": { "execution": { "iopub.execute_input": "2023-04-17T14:02:04.940924Z", "iopub.status.busy": "2023-04-17T14:02:04.940312Z", "iopub.status.idle": "2023-04-17T14:02:05.106579Z", "shell.execute_reply": "2023-04-17T14:02:05.106992Z" } }, "outputs": [ { "data": { "text/html": [ "
─────────────────────────────────────────────────── Create SBML ───────────────────────────────────────────────────\n",
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INFO     Create SBML for model 'repressilator_sbmlutils'                                            factory.py:3526\n",
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WARNING  'name' should be set on 'Model(sid='repressilator_sbmlutils', packages=[<Package.COMP_V1:   factory.py:441\n",
       "         'comp-v1'>], model_units=<sbmlutils.factory.ModelUnits object at 0x7f0b8800b8b0>,                         \n",
       "         units=<class 'sbmlutils.factory.Units'>, compartments=[cell = 1.0 [None]],                                \n",
       "         species=[<sbmlutils.factory.Species object at 0x7f0b8800b850>, <sbmlutils.factory.Species                 \n",
       "         object at 0x7f0b8800b820>, <sbmlutils.factory.Species object at 0x7f0b8800b7f0>,                          \n",
       "         <sbmlutils.factory.Species object at 0x7f0b8800b7c0>, <sbmlutils.factory.Species object at                \n",
       "         0x7f0b8800b790>, <sbmlutils.factory.Species object at 0x7f0b8800b760>],                                   \n",
       "         parameters=[tau_mRNA = 2.0 [None], kd_mRNA = None [None], k_tl = None [None], t_ave = None                \n",
       "         [None], eff = 20 [None], kd_prot = None [None], tau_prot = 10 [None], a0_tr = None [None],                \n",
       "         ps_0 = 0.0005 [None], ps_a = 0.5 [None], KM = 40 [None], n = 2.0 [None], a_tr = None                      \n",
       "         [None]], rules=[kd_mRNA = ln(2) / tau_mRNA [UnitDefinition(dimensionless, dimensionless)],                \n",
       "         t_ave = tau_mRNA / ln(2) [UnitDefinition(dimensionless, dimensionless)], k_tl = eff / t_ave               \n",
       "         [UnitDefinition(dimensionless, dimensionless)], kd_prot = ln(2) / tau_prot                                \n",
       "         [UnitDefinition(dimensionless, dimensionless)], a0_tr = ps_0 * 60                                         \n",
       "         [UnitDefinition(dimensionless, dimensionless)], a_tr = (ps_a - ps_0) * 60                                 \n",
       "         [UnitDefinition(dimensionless, dimensionless)]], reactions=[<sbmlutils.factory.Reaction                   \n",
       "         object at 0x7f0b8800b340>, <sbmlutils.factory.Reaction object at 0x7f0b8800b1f0>,                         \n",
       "         <sbmlutils.factory.Reaction object at 0x7f0b8800b220>, <sbmlutils.factory.Reaction object                 \n",
       "         at 0x7f0b8800b130>, <sbmlutils.factory.Reaction object at 0x7f0b8800afe0>,                                \n",
       "         <sbmlutils.factory.Reaction object at 0x7f0b8800b040>, <sbmlutils.factory.Reaction object                 \n",
       "         at 0x7f0b8800aef0>, <sbmlutils.factory.Reaction object at 0x7f0b8800ae30>,                                \n",
       "         <sbmlutils.factory.Reaction object at 0x7f0b8800ad70>, <sbmlutils.factory.Reaction object                 \n",
       "         at 0x7f0b8800acb0>, <sbmlutils.factory.Reaction object at 0x7f0b8800abf0>,                                \n",
       "         <sbmlutils.factory.Reaction object at 0x7f0b8800ab30>], _FrozenClass__isfrozen=True)'                     \n",
       "
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KM = \u001b[0m\u001b[1;36m40\u001b[0m\u001b[39m \u001b[0m\u001b[1;39m[\u001b[0m\u001b[3;35mNone\u001b[0m\u001b[1;39m]\u001b[0m\u001b[39m, n = \u001b[0m\u001b[1;36m2.0\u001b[0m\u001b[39m \u001b[0m\u001b[1;39m[\u001b[0m\u001b[3;35mNone\u001b[0m\u001b[1;39m]\u001b[0m\u001b[39m, a_tr = \u001b[0m\u001b[3;35mNone\u001b[0m\u001b[39m \u001b[0m \u001b[2m \u001b[0m\n", " \u001b[1;39m[\u001b[0m\u001b[3;35mNone\u001b[0m\u001b[1;39m]\u001b[0m\u001b[1;39m]\u001b[0m\u001b[39m, \u001b[0m\u001b[33mrules\u001b[0m\u001b[39m=\u001b[0m\u001b[1;39m[\u001b[0m\u001b[39mkd_mRNA = \u001b[0m\u001b[1;35mln\u001b[0m\u001b[1;39m(\u001b[0m\u001b[1;36m2\u001b[0m\u001b[1;39m)\u001b[0m\u001b[39m \u001b[0m\u001b[35m/\u001b[0m\u001b[39m tau_mRNA \u001b[0m\u001b[1;39m[\u001b[0m\u001b[1;35mUnitDefinition\u001b[0m\u001b[1;39m(\u001b[0m\u001b[39mdimensionless, dimensionless\u001b[0m\u001b[1;39m)\u001b[0m\u001b[1;39m]\u001b[0m\u001b[39m, \u001b[0m \u001b[2m \u001b[0m\n", " \u001b[39mt_ave = tau_mRNA \u001b[0m\u001b[35m/\u001b[0m\u001b[39m \u001b[0m\u001b[1;35mln\u001b[0m\u001b[1;39m(\u001b[0m\u001b[1;36m2\u001b[0m\u001b[1;39m)\u001b[0m\u001b[39m \u001b[0m\u001b[1;39m[\u001b[0m\u001b[1;35mUnitDefinition\u001b[0m\u001b[1;39m(\u001b[0m\u001b[39mdimensionless, dimensionless\u001b[0m\u001b[1;39m)\u001b[0m\u001b[1;39m]\u001b[0m\u001b[39m, k_tl = eff \u001b[0m\u001b[35m/\u001b[0m\u001b[39m t_ave\u001b[0m \u001b[2m \u001b[0m\n", " \u001b[1;39m[\u001b[0m\u001b[1;35mUnitDefinition\u001b[0m\u001b[1;39m(\u001b[0m\u001b[39mdimensionless, dimensionless\u001b[0m\u001b[1;39m)\u001b[0m\u001b[1;39m]\u001b[0m\u001b[39m, kd_prot = \u001b[0m\u001b[1;35mln\u001b[0m\u001b[1;39m(\u001b[0m\u001b[1;36m2\u001b[0m\u001b[1;39m)\u001b[0m\u001b[39m \u001b[0m\u001b[35m/\u001b[0m\u001b[39m tau_prot \u001b[0m \u001b[2m \u001b[0m\n", " \u001b[1;39m[\u001b[0m\u001b[1;35mUnitDefinition\u001b[0m\u001b[1;39m(\u001b[0m\u001b[39mdimensionless, dimensionless\u001b[0m\u001b[1;39m)\u001b[0m\u001b[1;39m]\u001b[0m\u001b[39m, a0_tr = ps_0 * \u001b[0m\u001b[1;36m60\u001b[0m\u001b[39m \u001b[0m \u001b[2m \u001b[0m\n", " \u001b[1;39m[\u001b[0m\u001b[1;35mUnitDefinition\u001b[0m\u001b[1;39m(\u001b[0m\u001b[39mdimensionless, dimensionless\u001b[0m\u001b[1;39m)\u001b[0m\u001b[1;39m]\u001b[0m\u001b[39m, a_tr = \u001b[0m\u001b[1;39m(\u001b[0m\u001b[39mps_a - ps_0\u001b[0m\u001b[1;39m)\u001b[0m\u001b[39m * \u001b[0m\u001b[1;36m60\u001b[0m\u001b[39m \u001b[0m \u001b[2m \u001b[0m\n", " \u001b[1;39m[\u001b[0m\u001b[1;35mUnitDefinition\u001b[0m\u001b[1;39m(\u001b[0m\u001b[39mdimensionless, dimensionless\u001b[0m\u001b[1;39m)\u001b[0m\u001b[1;39m]\u001b[0m\u001b[1;39m]\u001b[0m\u001b[39m, \u001b[0m\u001b[33mreactions\u001b[0m\u001b[39m=\u001b[0m\u001b[1;39m[\u001b[0m\u001b[39m, , \u001b[0m \u001b[2m \u001b[0m\n", " \u001b[39m, , , \u001b[0m \u001b[2m \u001b[0m\n", " \u001b[39m, , , \u001b[0m \u001b[2m \u001b[0m\n", " \u001b[39m, , , \u001b[0m \u001b[2m \u001b[0m\n", " \u001b[39m\u001b[0m\u001b[1m]\u001b[0m, 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WARNING  'sboTerm' should be set on 'Parameter(tau_mRNA, mRNA half life)'                            factory.py:466\n",
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WARNING  'sboTerm' should be set on 'Parameter(ps_0, tps_repr)'                                      factory.py:466\n",
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WARNING  'sboTerm' should be set on 'Parameter(ps_a, tps_active)'                                    factory.py:466\n",
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WARNING  'name' should be set on 'Compartment(cell, SBO:0000290, [(<BQB.IS: 'BQB_IS'>,               factory.py:441\n",
       "         'obo.go/GO:0005623')])'                                                                                   \n",
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────────────────────────────────────────────────── Validate SBML ──────────────────────────────────────────────────\n",
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       "valid                    : TRUE\n",
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WARNING  E0: SBML unit consistency (core, L231, code)                                             validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <assignmentRule> <math> expression 'log(2) / tau_mRNA' cannot be fully                  \n",
       "         checked. Unit consistency reported as either no errors or further unit errors related to                  \n",
       "         this object may not be accurate.                                                                          \n",
       "                                                                                                                   \n",
       "
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WARNING  E1: SBML unit consistency (core, L243, code)                                             validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <assignmentRule> <math> expression 'tau_mRNA / log(2)' cannot be fully                  \n",
       "         checked. Unit consistency reported as either no errors or further unit errors related to                  \n",
       "         this object may not be accurate.                                                                          \n",
       "                                                                                                                   \n",
       "
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WARNING  E2: SBML unit consistency (core, L255, code)                                             validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <assignmentRule> <math> expression 'eff / t_ave' cannot be fully                        \n",
       "         checked. Unit consistency reported as either no errors or further unit errors related to                  \n",
       "         this object may not be accurate.                                                                          \n",
       "                                                                                                                   \n",
       "
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WARNING  E3: SBML unit consistency (core, L264, code)                                             validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <assignmentRule> <math> expression 'log(2) / tau_prot' cannot be fully                  \n",
       "         checked. Unit consistency reported as either no errors or further unit errors related to                  \n",
       "         this object may not be accurate.                                                                          \n",
       "                                                                                                                   \n",
       "
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WARNING  E4: SBML unit consistency (core, L276, code)                                             validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <assignmentRule> <math> expression 'ps_0 * 60' cannot be fully                          \n",
       "         checked. Unit consistency reported as either no errors or further unit errors related to                  \n",
       "         this object may not be accurate.                                                                          \n",
       "                                                                                                                   \n",
       "
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WARNING  E5: SBML unit consistency (core, L285, code)                                             validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <assignmentRule> <math> expression '(ps_a - ps_0) * 60' cannot be                       \n",
       "         fully checked. Unit consistency reported as either no errors or further unit errors                       \n",
       "         related to this object may not be accurate.                                                               \n",
       "                                                                                                                   \n",
       "
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WARNING  E6: SBML unit consistency (core, L320, code)                                             validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <kineticLaw> <math> expression 'kd_mRNA * X' cannot be fully checked.                   \n",
       "         Unit consistency reported as either no errors or further unit errors related to this                      \n",
       "         object may not be accurate.                                                                               \n",
       "                                                                                                                   \n",
       "
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WARNING  E7: SBML unit consistency (core, L350, code)                                             validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <kineticLaw> <math> expression 'kd_mRNA * Y' cannot be fully checked.                   \n",
       "         Unit consistency reported as either no errors or further unit errors related to this                      \n",
       "         object may not be accurate.                                                                               \n",
       "                                                                                                                   \n",
       "
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WARNING  E8: SBML unit consistency (core, L380, code)                                             validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <kineticLaw> <math> expression 'kd_mRNA * Z' cannot be fully checked.                   \n",
       "         Unit consistency reported as either no errors or further unit errors related to this                      \n",
       "         object may not be accurate.                                                                               \n",
       "                                                                                                                   \n",
       "
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WARNING  E9: SBML unit consistency (core, L413, code)                                             validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <kineticLaw> <math> expression 'k_tl * X' cannot be fully checked.                      \n",
       "         Unit consistency reported as either no errors or further unit errors related to this                      \n",
       "         object may not be accurate.                                                                               \n",
       "                                                                                                                   \n",
       "
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WARNING  E10: SBML unit consistency (core, L446, code)                                            validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <kineticLaw> <math> expression 'k_tl * Y' cannot be fully checked.                      \n",
       "         Unit consistency reported as either no errors or further unit errors related to this                      \n",
       "         object may not be accurate.                                                                               \n",
       "                                                                                                                   \n",
       "
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WARNING  E11: SBML unit consistency (core, L479, code)                                            validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <kineticLaw> <math> expression 'k_tl * Z' cannot be fully checked.                      \n",
       "         Unit consistency reported as either no errors or further unit errors related to this                      \n",
       "         object may not be accurate.                                                                               \n",
       "                                                                                                                   \n",
       "
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WARNING  E12: SBML unit consistency (core, L509, code)                                            validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <kineticLaw> <math> expression 'kd_prot * PX' cannot be fully checked.                  \n",
       "         Unit consistency reported as either no errors or further unit errors related to this                      \n",
       "         object may not be accurate.                                                                               \n",
       "                                                                                                                   \n",
       "
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WARNING  E13: SBML unit consistency (core, L539, code)                                            validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <kineticLaw> <math> expression 'kd_prot * PY' cannot be fully checked.                  \n",
       "         Unit consistency reported as either no errors or further unit errors related to this                      \n",
       "         object may not be accurate.                                                                               \n",
       "                                                                                                                   \n",
       "
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WARNING  E14: SBML unit consistency (core, L569, code)                                            validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <kineticLaw> <math> expression 'kd_prot * PZ' cannot be fully checked.                  \n",
       "         Unit consistency reported as either no errors or further unit errors related to this                      \n",
       "         object may not be accurate.                                                                               \n",
       "                                                                                                                   \n",
       "
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WARNING  E15: SBML unit consistency (core, L602, code)                                            validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <kineticLaw> <math> expression 'a0_tr + a_tr * pow(KM, n) / (pow(KM,                    \n",
       "         n) + pow(PZ, n))' cannot be fully checked. Unit consistency reported as either no errors                  \n",
       "         or further unit errors related to this object may not be accurate.                                        \n",
       "                                                                                                                   \n",
       "
\n" ], "text/plain": [ "\u001b[31mWARNING \u001b[0m \u001b[30;47mE15: SBML unit consistency \u001b[0m\u001b[1;30;47m(\u001b[0m\u001b[30;47mcore, L602, code\u001b[0m\u001b[1;30;47m)\u001b[0m \u001b]8;id=182298;file:///home/vboxuser/.local/lib/python3.10/site-packages/sbmlutils/validation.py\u001b\\\u001b[2mvalidation.py\u001b[0m\u001b]8;;\u001b\\\u001b[2m:\u001b[0m\u001b]8;id=456180;file:///home/vboxuser/.local/lib/python3.10/site-packages/sbmlutils/validation.py#186\u001b\\\u001b[2m186\u001b[0m\u001b]8;;\u001b\\\n", " \u001b[1;38;5;172;40m[\u001b[0m\u001b[38;5;172;40mWarning\u001b[0m\u001b[1;38;5;172;40m]\u001b[0m\u001b[38;5;172;40m Missing unit declarations on parameters or literal numbers in expression\u001b[0m \u001b[2m \u001b[0m\n", " In situations where a mathematical expression contains literal numbers or parameters \u001b[2m \u001b[0m\n", " whose units have not been declared, it is not possible to verify accurately the \u001b[2m \u001b[0m\n", " consistency of the units in the expression. \u001b[2m \u001b[0m\n", " The units of the \u001b[1m<\u001b[0m\u001b[1;95mkineticLaw\u001b[0m\u001b[39m> \u001b[0m expression \u001b[32m'a0_tr + a_tr * pow\u001b[0m\u001b[32m(\u001b[0m\u001b[32mKM, n\u001b[0m\u001b[32m)\u001b[0m\u001b[32m / \u001b[0m\u001b[32m(\u001b[0m\u001b[32mpow\u001b[0m\u001b[32m(\u001b[0m\u001b[32mKM, \u001b[0m \u001b[2m \u001b[0m\n", " \u001b[32mn\u001b[0m\u001b[32m)\u001b[0m\u001b[32m + pow\u001b[0m\u001b[32m(\u001b[0m\u001b[32mPZ, n\u001b[0m\u001b[32m)\u001b[0m\u001b[32m)\u001b[0m\u001b[32m'\u001b[0m cannot be fully checked. Unit consistency reported as either no errors \u001b[2m \u001b[0m\n", " or further unit errors related to this object may not be accurate. \u001b[2m \u001b[0m\n", " \u001b[2m \u001b[0m\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
WARNING  E16: SBML unit consistency (core, L659, code)                                            validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <kineticLaw> <math> expression 'a0_tr + a_tr * pow(KM, n) / (pow(KM,                    \n",
       "         n) + pow(PX, n))' cannot be fully checked. Unit consistency reported as either no errors                  \n",
       "         or further unit errors related to this object may not be accurate.                                        \n",
       "                                                                                                                   \n",
       "
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WARNING  E17: SBML unit consistency (core, L716, code)                                            validation.py:186\n",
       "         [Warning] Missing unit declarations on parameters or literal numbers in expression                        \n",
       "         In situations where a mathematical expression contains literal numbers or parameters                      \n",
       "         whose units have not been declared, it is not possible to verify accurately the                           \n",
       "         consistency of the units in the expression.                                                               \n",
       "          The units of the <kineticLaw> <math> expression 'a0_tr + a_tr * pow(KM, n) / (pow(KM,                    \n",
       "         n) + pow(PY, n))' cannot be fully checked. Unit consistency reported as either no errors                  \n",
       "         or further unit errors related to this object may not be accurate.                                        \n",
       "                                                                                                                   \n",
       "
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WARNING  E18: Modeling practice (core, L144, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
       "         consistency of units and helps make it easier to detect potential errors in models.                       \n",
       "          The <parameter> with the id 'tau_mRNA' does not have a 'units' attribute.                                \n",
       "                                                                                                                   \n",
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WARNING  E19: Modeling practice (core, L145, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
       "         consistency of units and helps make it easier to detect potential errors in models.                       \n",
       "          The <parameter> with the id 'kd_mRNA' does not have a 'units' attribute.                                 \n",
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WARNING  E20: Modeling practice (core, L158, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
       "         consistency of units and helps make it easier to detect potential errors in models.                       \n",
       "          The <parameter> with the id 'k_tl' does not have a 'units' attribute.                                    \n",
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WARNING  E21: Modeling practice (core, L171, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
       "         consistency of units and helps make it easier to detect potential errors in models.                       \n",
       "          The <parameter> with the id 't_ave' does not have a 'units' attribute.                                   \n",
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WARNING  E22: Modeling practice (core, L184, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
       "         consistency of units and helps make it easier to detect potential errors in models.                       \n",
       "          The <parameter> with the id 'eff' does not have a 'units' attribute.                                     \n",
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WARNING  E23: Modeling practice (core, L185, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
       "         consistency of units and helps make it easier to detect potential errors in models.                       \n",
       "          The <parameter> with the id 'kd_prot' does not have a 'units' attribute.                                 \n",
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WARNING  E24: Modeling practice (core, L198, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
       "         consistency of units and helps make it easier to detect potential errors in models.                       \n",
       "          The <parameter> with the id 'tau_prot' does not have a 'units' attribute.                                \n",
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WARNING  E25: Modeling practice (core, L199, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
       "         consistency of units and helps make it easier to detect potential errors in models.                       \n",
       "          The <parameter> with the id 'a0_tr' does not have a 'units' attribute.                                   \n",
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WARNING  E26: Modeling practice (core, L212, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
       "         consistency of units and helps make it easier to detect potential errors in models.                       \n",
       "          The <parameter> with the id 'ps_0' does not have a 'units' attribute.                                    \n",
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WARNING  E27: Modeling practice (core, L213, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
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WARNING  E28: Modeling practice (core, L214, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
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WARNING  E29: Modeling practice (core, L215, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
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WARNING  E30: Modeling practice (core, L216, code)                                                validation.py:186\n",
       "         [Warning] It's best to declare units for every parameter in a model                                       \n",
       "         As a principle of best modeling practice, the units of a <parameter> should be declared                   \n",
       "         rather than be left undefined. Doing so improves the ability of software to check the                     \n",
       "         consistency of units and helps make it easier to detect potential errors in models.                       \n",
       "          The <parameter> with the id 'a_tr' does not have a 'units' attribute.                                    \n",
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