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Author: GeneCodeSavvy

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

@@ -129,6 +129,8 @@
     "gene_out.direction = sbol2.SBOL_DIRECTION_OUT\n",
     "\n",
     "\n",
+    "\n",
+    "\n",
     "# 2. cI Inverter Module (cI represses production of LacI)\n",
     "ci_inverter_md = sbol2.ModuleDefinition('cI_Inverter')\n",
     "\n",
@@ -234,16 +236,19 @@
     "\n",
     "# Map 2: cI protein is the output of the LacI inverter\n",
     "map2 = laci_inverter_instance.mapsTos.create('map_ci_out')\n",
+    "map2.refinement = sbol2.SBOL_REFINEMENT_USE_REMOTE\n",
     "map2.local = ci_fc.identity\n",
     "map2.remote = gene_out.identity\n",
     "\n",
     "# Map 3: cI protein is the input to the cI inverter\n",
     "map3 = ci_inverter_instance.mapsTos.create('map_ci_in')\n",
+    "map3.refinement = sbol2.SBOL_REFINEMENT_USE_LOCAL\n",
     "map3.local = ci_fc.identity\n",
     "map3.remote = tf_in_2.identity\n",
     "\n",
     "# Map 4: LacI protein is the output of the cI inverter\n",
     "map4 = ci_inverter_instance.mapsTos.create('map_laci_out')\n",
+    "map3.refinement = sbol2.SBOL_REFINEMENT_USE_LOCAL\n",
     "map4.local = laci_fc.identity\n",
     "map4.remote = gene_out_2.identity"
    ]
@@ -277,6 +282,78 @@
     "else:\n",
     "    print(report)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "08dadc57-f545-4814-bda2-f0603de35a91",
+   "metadata": {},
+   "source": [
+    "## Define the Inverter Modules (Lower-Level Subsystems)\n",
+    "\n",
+    "A toggle switch is composed of two inverters. We define each as a `ModuleDefinition`. Each inverter has an input (the repressor protein), a regulated promoter, and an output (the protein it produces). We also add `Interaction` objects to specify the biological function: repression.\n",
+    "\n",
+    "- **LacI Inverter**: Takes LacI as input to repress the pLac promoter, which produces the cI protein.\n",
+    "- **cI Inverter**: Takes cI as input to repress the pR promoter, which produces the LacI protein."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "5f444c97-d461-4db7-9d05-572457b994a3",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<sbol2.property.OwnedObject at 0x10642a1d0>"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# Create the repression interactions for the toggle switch\n",
+    "# Interaction: LacI represses LacI production\n",
+    "LacI_represses_pLac_interaction = sbol2.Interaction('LacI_represses_pLac_interaction')\n",
+    "LacI_represses_pLac_interaction.interaction_type = sbol2.SBO_INHIBITION\n",
+    "toggle_switch_md.interactions.add(LacI_represses_pLac_interaction)\n",
+    "\n",
+    "# Participation: TetR as inhibitor\n",
+    "tetR_inhibitor_part = LacI_represses_pLac_interaction.participations.create('TetR_inhibitor_part')\n",
+    "tetR_inhibitor_part.roles = [sbol2.SBO_INHIBITOR]\n",
+    "tetR_inhibitor_part.participant = tetR_protein_fc_parent.identity # Correct: participant is in toggle_switch_md\n",
+    "\n",
+    "# Participation: pLac_promoter as inhibited target\n",
+    "lacI_target_part = LacI_represses_pLac_interaction.participations.create('LacI_target_part')\n",
+    "lacI_target_part.roles = [sbol2.SBO_INHIBITED]\n",
+    "lacI_target_part.participant = pLac_promoter_fc_parent.identity # Correct: participant is in toggle_switch_md\n",
+    "\n",
+    "\n",
+    "# Interaction: LacI represses TetR production\n",
+    "lacI_represses_tetR_interaction = sbol2.Interaction('LacI_represses_TetR_interaction')\n",
+    "lacI_represses_tetR_interaction.interaction_type = sbol2.SBO_INHIBITION\n",
+    "toggle_switch_md.interactions.add(lacI_represses_tetR_interaction)\n",
+    "\n",
+    "# Participation: LacI as inhibitor\n",
+    "lacI_inhibitor_part = lacI_represses_tetR_interaction.participations.create('LacI_inhibitor_part')\n",
+    "lacI_inhibitor_part.roles = [sbol2.SBO_INHIBITOR]\n",
+    "lacI_inhibitor_part.participant = lacI_protein_fc_parent.identity # Correct: participant is in toggle_switch_md\n",
+    "\n",
+    "# Participation: pTet_promoter as inhibited target\n",
+    "tetR_target_part = lacI_represses_tetR_interaction.participations.create('TetR_target_part')\n",
+    "tetR_target_part.roles = [sbol2.SBO_INHIBITED]\n",
+    "tetR_target_part.participant = pTet_promoter_fc_parent.identity # Correct: participant is in toggle_switch_md"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c621aca1-57ef-4752-a47a-0dea6f0bebb6",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {