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updated MapsTo
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‎examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb‎

Lines changed: 115 additions & 60 deletions
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@@ -63,6 +63,24 @@
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "ae833529",
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"metadata": {},
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"outputs": [],
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"source": [
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"B0032_rbs = sbol2.ComponentDefinition('B0032', sbol2.BIOPAX_DNA)\n",
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"B0032_rbs.name = 'B0032_rbs'\n",
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"B0032_rbs.addRole(sbol2.SO_RBS)\n",
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"doc.addComponentDefinition(B0032_rbs)\n",
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"\n",
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"B0015_terminator = sbol2.ComponentDefinition('B0015', sbol2.BIOPAX_DNA)\n",
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"B0015_terminator.name = 'B0015_terminator'\n",
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"B0015_terminator.addRole(sbol2.SO_TERMINATOR)\n",
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"doc.addComponentDefinition(B0015_terminator)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "cell-005",
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"metadata": {},
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"outputs": [],
@@ -90,92 +108,129 @@
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"doc.addComponentDefinition(pR)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"id": "cedd52b6",
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"metadata": {},
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"outputs": [],
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"source": [
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"# The toggle switch's behavior is defined by two protein pools\n",
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"LacI_protein = sbol2.ComponentDefinition('LacI_protein', sbol2.BIOPAX_PROTEIN)\n",
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"LacI_protein.name = 'LacI Protein'\n",
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"LacI_protein.addRole('http://identifiers.org/ncit/NCIT:C17207') # 'Transcriptional factor'\n",
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"doc.addComponentDefinition(LacI_protein)\n",
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"\n",
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"cI_protein = sbol2.ComponentDefinition('cI_protein', sbol2.BIOPAX_PROTEIN)\n",
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"cI_protein.name = 'Lambda cI Protein'\n",
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"cI_protein.addRole('http://identifiers.org/ncit/NCIT:C17208') # 'Transcriptional factor'\n",
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"doc.addComponentDefinition(cI_protein) "
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]
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},
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{
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"cell_type": "markdown",
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"id": "cell-006",
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"id": "cell-008",
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"metadata": {},
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"source": [
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"## Define the Inverter Modules (Lower-Level Subsystems)\n",
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"\n",
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"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",
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"## Define the Toggle Switch Module (Higher-Level Circuit)\n",
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"\n",
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"- **LacI Inverter**: Takes LacI as input to repress the pLac promoter, which produces the cI protein.\n",
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"- **cI Inverter**: Takes cI as input to repress the pR promoter, which produces the LacI protein."
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"This `ModuleDefinition` represents the complete genetic toggle switch. From this high-level perspective, we only care about the two key players: the LacI protein and the cI protein."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "cell-007",
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"execution_count": 10,
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"id": "cell-009",
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"metadata": {},
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"outputs": [],
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"source": [
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"# 1. LacI Inverter Module (LacI represses production of cI)\n",
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"lacI_inverter_md = sbol2.ModuleDefinition('LacI_Inverter')\n",
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"\n",
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"# Functional Components of the LacI inverter\n",
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"lacI_tf_fc = lacI_inverter_md.functionalComponents.create('laci_transcription_factor')\n",
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"lacI_tf_fc.definition = lacI_cds\n",
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"lacI_tf_fc.access = sbol2.SBOL_ACCESS_PUBLIC\n",
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"lacI_tf_fc.direction = sbol2.SBOL_DIRECTION_IN\n",
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"\n",
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"pLac_fc = lacI_inverter_md.functionalComponents.create('pLac_promoter')\n",
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"pLac_fc.definition = pLac\n",
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"pLac.access = sbol2.SBOL_ACCESS_PRIVATE\n",
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"\n",
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"cI_gene_product_fc = lacI_inverter_md.functionalComponents.create('cI_gene_product')\n",
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"cI_gene_product_fc.definition = cI_cds\n",
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"cI_gene_product_fc.access = sbol2.SBOL_ACCESS_PUBLIC\n",
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"cI_gene_product_fc.direction = sbol2.SBOL_DIRECTION_OUT\n",
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"\n",
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"\n",
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"\n",
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"# 2. cI Inverter Module (cI represses production of LacI)\n",
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"cI_inverter_md = sbol2.ModuleDefinition('cI_Inverter')\n",
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"toggle_md = sbol2.ModuleDefinition('toggle_switch')\n",
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"\n",
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"# Functional Components of the cI inverter\n",
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"cI_tf_fc = cI_inverter_md.functionalComponents.create('cI_transcription_factor')\n",
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"cI_tf_fc.definition = cI_cds\n",
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"cI_tf_fc.access = sbol2.SBOL_ACCESS_PUBLIC\n",
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"cI_tf_fc.direction = sbol2.SBOL_DIRECTION_IN\n",
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"# create functional components by calling.using protein ComponentDefinitions\n",
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"\n",
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"pR_fc = cI_inverter_md.functionalComponents.create('pR_promoter')\n",
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"pR_fc.definition = pR\n",
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"pR_fc.access = sbol2.SBOL_ACCESS_PRIVATE\n",
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"lacI_prot_fc = toggle_md.functionalComponents.create('LacI_protein_toggle')\n",
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"lacI_prot_fc.definition = LacI_protein\n",
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"lacI_prot_fc.direction = sbol2.SBOL_DIRECTION_IN_OUT\n",
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"\n",
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"lacI_gene_product_fc = cI_inverter_md.functionalComponents.create('LacI_gene_product')\n",
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"lacI_gene_product_fc.definition = lacI_cds\n",
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"lacI_gene_product_fc.access = sbol2.SBOL_ACCESS_PUBLIC\n",
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"lacI_gene_product_fc.direction = sbol2.SBOL_DIRECTION_OUT"
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"cI_prot_fc = toggle_md.functionalComponents.create('cI_protein_toggle')\n",
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"cI_prot_fc.definition = cI_protein\n",
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"cI_prot_fc.direction = sbol2.SBOL_DIRECTION_IN_OUT"
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]
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},
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{
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"cell_type": "markdown",
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"id": "cell-008",
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"id": "cell-006",
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"metadata": {},
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"source": [
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"## Define the Toggle Switch Module (Higher-Level Circuit)\n",
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"## Define the Inverter Modules (Lower-Level Subsystems)\n",
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"\n",
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"This `ModuleDefinition` represents the complete genetic toggle switch. From this high-level perspective, we only care about the two key players: the LacI protein and the cI protein."
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"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",
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"\n",
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"- **LacI Inverter**: Takes LacI as input to repress the pLac promoter, which produces the cI protein.\n",
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"- **cI Inverter**: Takes cI as input to repress the pR promoter, which produces the LacI protein."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"id": "cell-009",
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"execution_count": 24,
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"id": "cell-007",
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"metadata": {},
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"outputs": [],
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"source": [
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"toggle_md = sbol2.ModuleDefinition('toggle_switch')\n",
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"# 1. LacI Inverter Module (LacI represses production of cI)\n",
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"lacI_inverter_md = sbol2.ModuleDefinition('LacI_Inverter')\n",
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"\n",
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"# The toggle switch's behavior is defined by two protein pools\n",
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"lacI_prot_fc = toggle_md.functionalComponents.create('LacI_protein')\n",
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"lacI_prot_fc.definition = lacI_cds\n",
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"lacI_inverter_plac_comp = sbol2.component.Component('pLac_promoter', pLac.identity)\n",
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"lacI_inverter_b0032_rbs = sbol2.component.Component('B0032_rbs', B0032_rbs.identity)\n",
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"lacI_inverter_cI_cds = sbol2.component.Component('cI_cds', cI_cds.identity)\n",
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"lacI_inverter_b0015_terminator = sbol2.component.Component('B0015_terminator', B0015_terminator.identity)\n",
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"\n",
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"# LacI Inverter Transcriptional Unit Component Definition\n",
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"lacI_engineered_region = sbol2.ComponentDefinition('LacI_Engineered_Region', sbol2.BIOPAX_DNA)\n",
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"lacI_engineered_region.name = 'LacI Engineered Region'\n",
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"lacI_engineered_region.addRole('http://identifiers.org/so/SO:0000804') \n",
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"lacI_engineered_region.components.add(lacI_inverter_plac_comp)\n",
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"lacI_engineered_region.components.add(lacI_inverter_b0032_rbs)\n",
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"lacI_engineered_region.components.add(lacI_inverter_cI_cds)\n",
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"lacI_engineered_region.components.add(lacI_inverter_b0015_terminator)\n",
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"doc.addComponentDefinition(lacI_engineered_region)\n",
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"\n",
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"# LacI Inverter Proteins\n",
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"lacI_prot_fc_lacI_inverter = lacI_inverter_md.functionalComponents.create('LacI_protein_LacI_inverter')\n",
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"lacI_prot_fc_lacI_inverter.definition = LacI_protein\n",
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"lacI_prot_fc_lacI_inverter.direction = sbol2.SBOL_DIRECTION_IN_OUT\n",
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"\n",
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"cI_prot_fc_lacI_inverter = lacI_inverter_md.functionalComponents.create('cI_protein_LacI_inverter')\n",
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"cI_prot_fc_lacI_inverter.definition = cI_protein\n",
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"cI_prot_fc_lacI_inverter.direction = sbol2.SBOL_DIRECTION_IN_OUT\n",
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"\n",
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"\n",
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"# 2. cI Inverter Module (cI represses production of LacI)\n",
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"cI_inverter_md = sbol2.ModuleDefinition('cI_Inverter')\n",
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"\n",
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"cI_inverter_pR_comp = sbol2.component.Component('pR_promoter', pR.identity)\n",
212+
"cI_inverter_b0032_rbs = sbol2.component.Component('B0032_rbs', B0032_rbs.identity)\n",
213+
"cI_inverter_lacI_cds = sbol2.component.Component('lacI_cds', lacI_cds.identity)\n",
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"cI_inverter_b0015_terminator = sbol2.component.Component('B0015_terminator', B0015_terminator.identity) \n",
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"\n",
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"# cI Inverter Transcriptional Unit Component Definition\n",
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"cI_engineered_region = sbol2.ComponentDefinition('cI_Engineered_Region', sbol2.BIOPAX_DNA)\n",
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"cI_engineered_region.name = 'cI Engineered Region'\n",
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"cI_engineered_region.addRole('http://identifiers.org/so/SO:0000804') \n",
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"cI_engineered_region.components.add(cI_inverter_pR_comp)\n",
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"cI_engineered_region.components.add(cI_inverter_b0032_rbs)\n",
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"cI_engineered_region.components.add(cI_inverter_lacI_cds)\n",
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"cI_engineered_region.components.add(cI_inverter_b0015_terminator)\n",
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"doc.addComponentDefinition(cI_engineered_region)\n",
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"\n",
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"# cI Inverter Proteins\n",
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"lacI_prot_fc = cI_inverter_md.functionalComponents.create('LacI_protein_cI_inverter')\n",
228+
"lacI_prot_fc.definition = LacI_protein\n",
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"lacI_prot_fc.direction = sbol2.SBOL_DIRECTION_IN_OUT\n",
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"\n",
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"cI_prot_fc = toggle_md.functionalComponents.create('cI_protein')\n",
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"cI_prot_fc.definition = cI_cds\n",
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"cI_prot_fc.direction = sbol2.SBOL_DIRECTION_IN_OUT"
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"cI_prot_fc = cI_inverter_md.functionalComponents.create('cI_protein_cI_inverter')\n",
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"cI_prot_fc.definition = cI_protein\n",
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"cI_prot_fc.direction = sbol2.SBOL_DIRECTION_IN_OUT "
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]
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},
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{
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": 25,
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"id": "cell-010b",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"execution_count": null,
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"id": "9cdcd7c0-e419-4106-b7f3-7c8aba06fd7e",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "cell-012",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"execution_count": null,
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"id": "cell-014",
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"metadata": {},
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"outputs": [
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"display_name": "GLLDB",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.13.5"
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"version": "3.9.19"
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}
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},
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"nbformat": 4,

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