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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 * bump mira (#227) * bump mira * bumped AMR file --------- Co-authored-by: Jeremy Zucker <djinnome@gmail.com> Co-authored-by: Sam Witty <samawitty@gmail.com>
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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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{ | ||
"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>" | ||
} | ||
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{ | ||
"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": {} | ||
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"units": { | ||
"expression": "person", | ||
"expression_mathml": "<ci>person</ci>" | ||
} | ||
} | ||
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"transitions": [ | ||
{ | ||
"id": "t1", | ||
"input": [ | ||
"I", | ||
"S" | ||
], | ||
"output": [ | ||
"I", | ||
"E" | ||
], | ||
"properties": { | ||
"name": "t1" | ||
} | ||
}, | ||
{ | ||
"id": "t2", | ||
"input": [ | ||
"E" | ||
], | ||
"output": [ | ||
"I" | ||
], | ||
"properties": { | ||
"name": "t2" | ||
} | ||
}, | ||
{ | ||
"id": "t3", | ||
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"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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