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notebooks/hackathon_2023.07/sir_flux_span_ode_semantics.json
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| { | ||
| "name": "SIR-Two-City-Flux Stratified Model", | ||
| "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json", | ||
| "schema_name": "petrinet", | ||
| "description": "SIR disease model stratified spatially between two cities model created by Patrick", | ||
| "model_version": "0.1", | ||
| "properties": {}, | ||
| "model": { | ||
| "states": [ | ||
| { | ||
| "id": "S1", | ||
| "name": "S_Rgn1", | ||
| "grounding": { | ||
| "identifiers": { | ||
| "ido": "a" | ||
| }, | ||
| "modifiers": {} | ||
| } | ||
| }, | ||
| { | ||
| "id": "I1", | ||
| "name": "I_Rgn1", | ||
| "grounding": { | ||
| "identifiers": { | ||
| "ido": "b" | ||
| }, | ||
| "modifiers": {} | ||
| } | ||
| }, | ||
| { | ||
| "id": "R1", | ||
| "name": "R_Rgn1", | ||
| "grounding": { | ||
| "identifiers": { | ||
| "ido": "c" | ||
| }, | ||
| "modifiers": {} | ||
| } | ||
| }, | ||
| { | ||
| "id": "S2", | ||
| "name": "S_Rgn2", | ||
| "grounding": { | ||
| "identifiers": { | ||
| "ido": "d" | ||
| }, | ||
| "modifiers": {} | ||
| } | ||
| }, | ||
| { | ||
| "id": "I2", | ||
| "name": "I_Rgn2", | ||
| "grounding": { | ||
| "identifiers": { | ||
| "ido": "e" | ||
| }, | ||
| "modifiers": {} | ||
| } | ||
| }, | ||
| { | ||
| "id": "R2", | ||
| "name": "R_Rgn2", | ||
| "grounding": { | ||
| "identifiers": { | ||
| "ido": "f" | ||
| }, | ||
| "modifiers": {} | ||
| } | ||
| } | ||
| ], | ||
| "transitions": [ | ||
| { | ||
| "id": "t1", | ||
| "input": [ | ||
| "I1", | ||
| "S1" | ||
| ], | ||
| "output": [ | ||
| "I1", | ||
| "I1" | ||
| ], | ||
| "properties": { | ||
| "name": "t1" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t2", | ||
| "input": [ | ||
| "I1" | ||
| ], | ||
| "output": [ | ||
| "R1" | ||
| ], | ||
| "properties": { | ||
| "name": "t2" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t3", | ||
| "input": [ | ||
| "I2", | ||
| "S2" | ||
| ], | ||
| "output": [ | ||
| "I2", | ||
| "I2" | ||
| ], | ||
| "properties": { | ||
| "name": "t3" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t4", | ||
| "input": [ | ||
| "I2" | ||
| ], | ||
| "output": [ | ||
| "R2" | ||
| ], | ||
| "properties": { | ||
| "name": "t4" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t5", | ||
| "input": [ | ||
| "S1" | ||
| ], | ||
| "output": [ | ||
| "S2" | ||
| ], | ||
| "properties": { | ||
| "name": "t5" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t6", | ||
| "input": [ | ||
| "S2" | ||
| ], | ||
| "output": [ | ||
| "S1" | ||
| ], | ||
| "properties": { | ||
| "name": "t6" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t7", | ||
| "input": [ | ||
| "I1" | ||
| ], | ||
| "output": [ | ||
| "I2" | ||
| ], | ||
| "properties": { | ||
| "name": "t7" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t8", | ||
| "input": [ | ||
| "I2" | ||
| ], | ||
| "output": [ | ||
| "I1" | ||
| ], | ||
| "properties": { | ||
| "name": "t8" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t9", | ||
| "input": [ | ||
| "R1" | ||
| ], | ||
| "output": [ | ||
| "R2" | ||
| ], | ||
| "properties": { | ||
| "name": "t9" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t10", | ||
| "input": [ | ||
| "R2" | ||
| ], | ||
| "output": [ | ||
| "R1" | ||
| ], | ||
| "properties": { | ||
| "name": "t10" | ||
| } | ||
| } | ||
| ] | ||
| }, | ||
| "semantics": { | ||
| "ode": { | ||
| "rates": [ | ||
| { | ||
| "target": "t1", | ||
| "expression": "I1*S1*beta", | ||
| "expression_mathml": "<apply><times/><ci>I1</ci><ci>S1</ci><ci>beta</ci></apply>" | ||
| }, | ||
| { | ||
| "target": "t2", | ||
| "expression": "I1*gamma", | ||
| "expression_mathml": "<apply><times/><ci>I1</ci><ci>gamma</ci></apply>" | ||
| }, | ||
| { | ||
| "target": "t3", | ||
| "expression": "I2*S2*beta", | ||
| "expression_mathml": "<apply><times/><ci>I2</ci><ci>S2</ci><ci>beta</ci></apply>" | ||
| }, | ||
| { | ||
| "target": "t4", | ||
| "expression": "I2*gamma", | ||
| "expression_mathml": "<apply><times/><ci>I2</ci><ci>gamma</ci></apply>" | ||
| }, | ||
| { | ||
| "target": "t5", | ||
| "expression": "S1*p_2_0", | ||
| "expression_mathml": "<apply><times/><ci>S1</ci><ci>p_2_0</ci></apply>" | ||
| }, | ||
| { | ||
| "target": "t6", | ||
| "expression": "S2*p_2_1", | ||
| "expression_mathml": "<apply><times/><ci>S2</ci><ci>p_2_1</ci></apply>" | ||
| }, | ||
| { | ||
| "target": "t7", | ||
| "expression": "I1*p_2_0", | ||
| "expression_mathml": "<apply><times/><ci>I1</ci><ci>p_2_0</ci></apply>" | ||
| }, | ||
| { | ||
| "target": "t8", | ||
| "expression": "I2*p_2_1", | ||
| "expression_mathml": "<apply><times/><ci>I2</ci><ci>p_2_1</ci></apply>" | ||
| }, | ||
| { | ||
| "target": "t9", | ||
| "expression": "R1*p_2_0", | ||
| "expression_mathml": "<apply><times/><ci>R1</ci><ci>p_2_0</ci></apply>" | ||
| }, | ||
| { | ||
| "target": "t10", | ||
| "expression": "R2*p_2_1", | ||
| "expression_mathml": "<apply><times/><ci>R2</ci><ci>p_2_1</ci></apply>" | ||
| } | ||
| ], | ||
| "initials": [ | ||
| { | ||
| "target": "S1", | ||
| "expression": "500.000000000000", | ||
| "expression_mathml": "<cn>500.0</cn>" | ||
| }, | ||
| { | ||
| "target": "I1", | ||
| "expression": "0.500000000000000", | ||
| "expression_mathml": "<cn>0.5</cn>" | ||
| }, | ||
| { | ||
| "target": "R1", | ||
| "expression": "0.0", | ||
| "expression_mathml": "<cn>0.0</cn>" | ||
| }, | ||
| { | ||
| "target": "S2", | ||
| "expression": "500.000000000000", | ||
| "expression_mathml": "<cn>500.0</cn>" | ||
| }, | ||
| { | ||
| "target": "I2", | ||
| "expression": "0.500000000000000", | ||
| "expression_mathml": "<cn>0.5</cn>" | ||
| }, | ||
| { | ||
| "target": "R2", | ||
| "expression": "0.0", | ||
| "expression_mathml": "<cn>0.0</cn>" | ||
| } | ||
| ], | ||
| "parameters": [ | ||
| { | ||
| "id": "beta", | ||
| "value": 0.027, | ||
| "distribution": { | ||
| "type": "StandardUniform1", | ||
| "parameters": { | ||
| "minimum": 0.026, | ||
| "maximum": 0.028 | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "id": "gamma", | ||
| "value": 0.14, | ||
| "distribution": { | ||
| "type": "StandardUniform1", | ||
| "parameters": { | ||
| "minimum": 0.1, | ||
| "maximum": 0.18 | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "id": "p_2_0", | ||
| "value": 1.0 | ||
| }, | ||
| { | ||
| "id": "p_2_1", | ||
| "value": 1.0 | ||
| } | ||
| ], | ||
| "observables": [], | ||
| "time": null | ||
| } | ||
| }, | ||
| "metadata": { | ||
| "annotations": { | ||
| "license": null, | ||
| "authors": [], | ||
| "references": [], | ||
| "time_scale": null, | ||
| "time_start": null, | ||
| "time_end": null, | ||
| "locations": [], | ||
| "pathogens": [], | ||
| "diseases": [], | ||
| "hosts": [], | ||
| "model_types": [] | ||
| } | ||
| } | ||
| } |