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Added get_name on the mira parameter keys for safety (#218)
* Added get_name on the mira parameter keys for safety * Removed test for SIDARTHE which fails due to gyorilab/mira#195 * checked out scenario1 from main so that it doesn't clobber Vignesh's changes * Added test that confirms gyorilab/mira#196 solves gyorilab/mira#195 * Added pin to latest mira commit
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notebook/Examples_for_TA2_Model_Representation/Modeling_Representation_Issues_Examples.ipynb
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notebook/integration_demo/results_petri_ensemble/calibrated_sample_results.csv
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notebook/integration_demo/results_petri_ensemble/sample_results.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,292 @@ | ||
| { | ||
| "name": "Scenario 1a", | ||
| "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json", | ||
| "schema_name": "petrinet", | ||
| "description": "Scenario 1a", | ||
| "model_version": "0.1", | ||
| "properties": {}, | ||
| "model": { | ||
| "states": [ | ||
| { | ||
| "id": "S", | ||
| "name": "S", | ||
| "grounding": { | ||
| "identifiers": { | ||
| "ido": "0000514" | ||
| }, | ||
| "modifiers": {} | ||
| }, | ||
| "units": { | ||
| "expression": "person", | ||
| "expression_mathml": "<ci>person</ci>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "I", | ||
| "name": "I", | ||
| "grounding": { | ||
| "identifiers": { | ||
| "ido": "0000511" | ||
| }, | ||
| "modifiers": {} | ||
| }, | ||
| "units": { | ||
| "expression": "person", | ||
| "expression_mathml": "<ci>person</ci>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "E", | ||
| "name": "E", | ||
| "grounding": { | ||
| "identifiers": { | ||
| "apollosv": "0000154" | ||
| }, | ||
| "modifiers": {} | ||
| }, | ||
| "units": { | ||
| "expression": "person", | ||
| "expression_mathml": "<ci>person</ci>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "R", | ||
| "name": "R", | ||
| "grounding": { | ||
| "identifiers": { | ||
| "ido": "0000592" | ||
| }, | ||
| "modifiers": {} | ||
| }, | ||
| "units": { | ||
| "expression": "person", | ||
| "expression_mathml": "<ci>person</ci>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "D", | ||
| "name": "D", | ||
| "grounding": { | ||
| "identifiers": { | ||
| "ncit": "C28554" | ||
| }, | ||
| "modifiers": {} | ||
| }, | ||
| "units": { | ||
| "expression": "person", | ||
| "expression_mathml": "<ci>person</ci>" | ||
| } | ||
| } | ||
| ], | ||
| "transitions": [ | ||
| { | ||
| "id": "t1", | ||
| "input": [ | ||
| "I", | ||
| "S" | ||
| ], | ||
| "output": [ | ||
| "I", | ||
| "E" | ||
| ], | ||
| "properties": { | ||
| "name": "t1" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t2", | ||
| "input": [ | ||
| "E" | ||
| ], | ||
| "output": [ | ||
| "I" | ||
| ], | ||
| "properties": { | ||
| "name": "t2" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t3", | ||
| "input": [ | ||
| "I" | ||
| ], | ||
| "output": [ | ||
| "R" | ||
| ], | ||
| "properties": { | ||
| "name": "t3" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t4", | ||
| "input": [ | ||
| "I" | ||
| ], | ||
| "output": [ | ||
| "D" | ||
| ], | ||
| "properties": { | ||
| "name": "t4" | ||
| } | ||
| } | ||
| ] | ||
| }, | ||
| "semantics": { | ||
| "ode": { | ||
| "rates": [ | ||
| { | ||
| "target": "t1", | ||
| "expression": "I*S*kappa*(beta_c + (-beta_c + beta_s)/(1 + exp(-k*(-t + t_0))))/N", | ||
| "expression_mathml": "<apply><divide/><apply><times/><ci>I</ci><ci>S</ci><ci>kappa</ci><apply><plus/><ci>beta_c</ci><apply><divide/><apply><plus/><apply><minus/><ci>beta_c</ci></apply><ci>beta_s</ci></apply><apply><plus/><cn>1</cn><apply><exp/><apply><minus/><apply><times/><ci>k</ci><apply><minus/><ci>t_0</ci><ci>t</ci></apply></apply></apply></apply></apply></apply></apply></apply><ci>N</ci></apply>" | ||
| }, | ||
| { | ||
| "target": "t2", | ||
| "expression": "E*delta", | ||
| "expression_mathml": "<apply><times/><ci>E</ci><ci>delta</ci></apply>" | ||
| }, | ||
| { | ||
| "target": "t3", | ||
| "expression": "I*gamma*(1 - alpha)", | ||
| "expression_mathml": "<apply><times/><ci>I</ci><ci>gamma</ci><apply><minus/><cn>1</cn><ci>alpha</ci></apply></apply>" | ||
| }, | ||
| { | ||
| "target": "t4", | ||
| "expression": "I*alpha*rho", | ||
| "expression_mathml": "<apply><times/><ci>I</ci><ci>alpha</ci><ci>rho</ci></apply>" | ||
| } | ||
| ], | ||
| "initials": [ | ||
| { | ||
| "target": "S", | ||
| "expression": "5599999.00000000", | ||
| "expression_mathml": "<cn>5599999.0</cn>" | ||
| }, | ||
| { | ||
| "target": "I", | ||
| "expression": "0.0", | ||
| "expression_mathml": "<cn>0.0</cn>" | ||
| }, | ||
| { | ||
| "target": "E", | ||
| "expression": "1.00000000000000", | ||
| "expression_mathml": "<cn>1.0</cn>" | ||
| }, | ||
| { | ||
| "target": "R", | ||
| "expression": "0.0", | ||
| "expression_mathml": "<cn>0.0</cn>" | ||
| }, | ||
| { | ||
| "target": "D", | ||
| "expression": "0.0", | ||
| "expression_mathml": "<cn>0.0</cn>" | ||
| } | ||
| ], | ||
| "parameters": [ | ||
| { | ||
| "id": "N", | ||
| "value": 5600000.0, | ||
| "units": { | ||
| "expression": "person", | ||
| "expression_mathml": "<ci>person</ci>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "beta_c", | ||
| "value": 0.4, | ||
| "units": { | ||
| "expression": "1/(day*person)", | ||
| "expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>day</ci><ci>person</ci></apply></apply>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "beta_s", | ||
| "value": 1.0, | ||
| "units": { | ||
| "expression": "1/(day*person)", | ||
| "expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>day</ci><ci>person</ci></apply></apply>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "k", | ||
| "value": 5.0, | ||
| "units": { | ||
| "expression": "1", | ||
| "expression_mathml": "<cn>1</cn>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "kappa", | ||
| "value": 0.45454545454545453, | ||
| "units": { | ||
| "expression": "1/day", | ||
| "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "t_0", | ||
| "value": 89.0, | ||
| "units": { | ||
| "expression": "day", | ||
| "expression_mathml": "<ci>day</ci>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "delta", | ||
| "value": 0.2, | ||
| "units": { | ||
| "expression": "1/day", | ||
| "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "alpha", | ||
| "value": 6.4e-05, | ||
| "units": { | ||
| "expression": "1", | ||
| "expression_mathml": "<cn>1</cn>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "gamma", | ||
| "value": 0.09090909090909091, | ||
| "units": { | ||
| "expression": "1/day", | ||
| "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>" | ||
| } | ||
| }, | ||
| { | ||
| "id": "rho", | ||
| "value": 0.1111111111111111, | ||
| "units": { | ||
| "expression": "1/day", | ||
| "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>" | ||
| } | ||
| } | ||
| ], | ||
| "observables": [], | ||
| "time": { | ||
| "id": "t", | ||
| "units": { | ||
| "expression": "day", | ||
| "expression_mathml": "<ci>day</ci>" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "metadata": { | ||
| "annotations": { | ||
| "license": null, | ||
| "authors": [], | ||
| "references": [], | ||
| "time_scale": null, | ||
| "time_start": null, | ||
| "time_end": null, | ||
| "locations": [], | ||
| "pathogens": [], | ||
| "diseases": [], | ||
| "hosts": [], | ||
| "model_types": [] | ||
| } | ||
| } | ||
| } |
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