diff --git a/notebooks/hackathon_2023.07/scenario1.ipynb b/notebooks/hackathon_2023.07/scenario1.ipynb index f09d93b67..47b34d7f9 100644 --- a/notebooks/hackathon_2023.07/scenario1.ipynb +++ b/notebooks/hackathon_2023.07/scenario1.ipynb @@ -1,6 +1,7 @@ { "cells": [ { + "attachments": {}, "cell_type": "markdown", "id": "c947d97c", "metadata": {}, @@ -38,13 +39,14 @@ "day_units = Unit(expression=sympy.Symbol('day'))\n", "per_day_units = Unit(expression=1/sympy.Symbol('day'))\n", "dimensionless_units = Unit(expression=sympy.Integer('1'))\n", + "per_day_per_person_units = Unit(expression=1/(sympy.Symbol('day')*sympy.Symbol('person')))\n", "\n", "c = {\n", - " 'S': Concept(name='S', units=person_units),\n", - " 'E': Concept(name='E', units=person_units),\n", - " 'I': Concept(name='I', units=person_units),\n", - " 'R': Concept(name='R', units=person_units),\n", - " 'D': Concept(name='D', units=person_units)\n", + " 'S': Concept(name='S', units=person_units, identifiers={'ido': '0000514'}),\n", + " 'E': Concept(name='E', units=person_units, identifiers={'apollosv': '0000154'}),\n", + " 'I': Concept(name='I', units=person_units, identifiers={'ido': '0000511'}),\n", + " 'R': Concept(name='R', units=person_units, identifiers={'ido': '0000592'}),\n", + " 'D': Concept(name='D', units=person_units, identifiers={'ncit': 'C28554'}),\n", "}\n", "\n", "\n", @@ -54,13 +56,13 @@ " 'alpha': Parameter(name='alpha', value=0.000064, units=dimensionless_units),\n", " 'rho': Parameter(name='rho', value=1/9, units=per_day_units),\n", " 'N': Parameter(name='N', value=5_600_000, units=person_units),\n", - " 'beta_s': Parameter(name='beta_s', value=1),\n", - " 'beta_c': Parameter(name='beta_c', value=0.4),\n", - " 't_0': Parameter(name='t_0', value=89, unts=day_units),\n", + " 'beta_s': Parameter(name='beta_s', value=1, units=per_day_per_person_units),\n", + " 'beta_c': Parameter(name='beta_c', value=0.4, units=per_day_per_person_units),\n", + " 't_0': Parameter(name='t_0', value=89, unts=day_units, units=day_units),\n", " # D=11, gamma = 1/D, R_0 = 5 and\n", " # beta = R_0 * gamma * mask(t) so kappa = 5/11\n", - " 'kappa': Parameter(name='kappa', value=5/11),\n", - " 'k': Parameter(name='k', value=5.0)\n", + " 'kappa': Parameter(name='kappa', value=5/11, units=per_day_units),\n", + " 'k': Parameter(name='k', value=5.0, units=dimensionless_units),\n", "}\n", "\n", "initials = {\n", @@ -118,6 +120,7 @@ ] }, { + "attachments": {}, "cell_type": "markdown", "id": "48e4ed6a", "metadata": {}, @@ -137,8 +140,8 @@ "outputs": [], "source": [ "k_1, k_2, t_1, beta_nc = sympy.symbols('k_1 k_2 t_1 beta_nc')\n", - "parameters['k_1'] = Parameter(name='k_1', value=5.0)\n", - "parameters['k_2'] = Parameter(name='k_2', value=1.0)\n", + "parameters['k_1'] = Parameter(name='k_1', value=5.0, units=dimensionless_units)\n", + "parameters['k_2'] = Parameter(name='k_2', value=1.0, units=dimensionless_units)\n", "parameters['t_1'] = Parameter(name='t_1', value=154, units=day_units)\n", "parameters['beta_nc'] = Parameter(name='beta_nc', value=0.5)\n", "tm.parameters = parameters\n", @@ -191,6 +194,7 @@ ] }, { + "attachments": {}, "cell_type": "markdown", "id": "6e3374f9", "metadata": {}, @@ -207,7 +211,7 @@ "outputs": [], "source": [ "epsilon = sympy.Symbol('epsilon')\n", - "parameters['epsilon'] = Parameter(name='epsilon', value=1/90)\n", + "parameters['epsilon'] = Parameter(name='epsilon', value=1/90, units=per_day_units)\n", "tm.parameters = parameters\n", "tm.annotations = Annotations(name='Scenario 1d')\n", "t5 = NaturalConversion(subject=c['R'],\n", diff --git a/notebooks/hackathon_2023.07/scenario1_a.json b/notebooks/hackathon_2023.07/scenario1_a.json index ba8340bcc..5b544c230 100644 --- a/notebooks/hackathon_2023.07/scenario1_a.json +++ b/notebooks/hackathon_2023.07/scenario1_a.json @@ -11,7 +11,9 @@ "id": "S", "name": "S", "grounding": { - "identifiers": {}, + "identifiers": { + "ido": "0000514" + }, "modifiers": {} }, "units": { @@ -23,7 +25,9 @@ "id": "I", "name": "I", "grounding": { - "identifiers": {}, + "identifiers": { + "ido": "0000511" + }, "modifiers": {} }, "units": { @@ -35,7 +39,9 @@ "id": "E", "name": "E", "grounding": { - "identifiers": {}, + "identifiers": { + "apollosv": "0000154" + }, "modifiers": {} }, "units": { @@ -47,7 +53,9 @@ "id": "R", "name": "R", "grounding": { - "identifiers": {}, + "identifiers": { + "ido": "0000592" + }, "modifiers": {} }, "units": { @@ -59,7 +67,9 @@ "id": "D", "name": "D", "grounding": { - "identifiers": {}, + "identifiers": { + "ncit": "C28554" + }, "modifiers": {} }, "units": { @@ -183,23 +193,43 @@ }, { "id": "beta_c", - "value": 0.4 + "value": 0.4, + "units": { + "expression": "1/(day*person)", + "expression_mathml": "1dayperson" + } }, { "id": "beta_s", - "value": 1.0 + "value": 1.0, + "units": { + "expression": "1/(day*person)", + "expression_mathml": "1dayperson" + } }, { "id": "k", - "value": 5.0 + "value": 5.0, + "units": { + "expression": "1", + "expression_mathml": "1" + } }, { "id": "kappa", - "value": 0.45454545454545453 + "value": 0.45454545454545453, + "units": { + "expression": "1/day", + "expression_mathml": "day-1" + } }, { "id": "t_0", - "value": 89.0 + "value": 89.0, + "units": { + "expression": "day", + "expression_mathml": "day" + } }, { "id": "delta", diff --git a/notebooks/hackathon_2023.07/scenario1_c.json b/notebooks/hackathon_2023.07/scenario1_c.json index 8ba689ceb..08c79f5cb 100644 --- a/notebooks/hackathon_2023.07/scenario1_c.json +++ b/notebooks/hackathon_2023.07/scenario1_c.json @@ -11,7 +11,9 @@ "id": "S", "name": "S", "grounding": { - "identifiers": {}, + "identifiers": { + "ido": "0000514" + }, "modifiers": {} }, "units": { @@ -23,7 +25,9 @@ "id": "I", "name": "I", "grounding": { - "identifiers": {}, + "identifiers": { + "ido": "0000511" + }, "modifiers": {} }, "units": { @@ -35,7 +39,9 @@ "id": "E", "name": "E", "grounding": { - "identifiers": {}, + "identifiers": { + "apollosv": "0000154" + }, "modifiers": {} }, "units": { @@ -47,7 +53,9 @@ "id": "R", "name": "R", "grounding": { - "identifiers": {}, + "identifiers": { + "ido": "0000592" + }, "modifiers": {} }, "units": { @@ -59,7 +67,9 @@ "id": "D", "name": "D", "grounding": { - "identifiers": {}, + "identifiers": { + "ncit": "C28554" + }, "modifiers": {} }, "units": { @@ -175,7 +185,11 @@ "parameters": [ { "id": "beta_c", - "value": 0.4 + "value": 0.4, + "units": { + "expression": "1/(day*person)", + "expression_mathml": "1dayperson" + } }, { "id": "beta_nc", @@ -183,23 +197,43 @@ }, { "id": "beta_s", - "value": 1.0 + "value": 1.0, + "units": { + "expression": "1/(day*person)", + "expression_mathml": "1dayperson" + } }, { "id": "k_1", - "value": 5.0 + "value": 5.0, + "units": { + "expression": "1", + "expression_mathml": "1" + } }, { "id": "k_2", - "value": 1.0 + "value": 1.0, + "units": { + "expression": "1", + "expression_mathml": "1" + } }, { "id": "kappa", - "value": 0.45454545454545453 + "value": 0.45454545454545453, + "units": { + "expression": "1/day", + "expression_mathml": "day-1" + } }, { "id": "t_0", - "value": 89.0 + "value": 89.0, + "units": { + "expression": "day", + "expression_mathml": "day" + } }, { "id": "t_1", diff --git a/notebooks/hackathon_2023.07/scenario1_d.json b/notebooks/hackathon_2023.07/scenario1_d.json index f96862efe..05dc7aa91 100644 --- a/notebooks/hackathon_2023.07/scenario1_d.json +++ b/notebooks/hackathon_2023.07/scenario1_d.json @@ -11,7 +11,9 @@ "id": "S", "name": "S", "grounding": { - "identifiers": {}, + "identifiers": { + "ido": "0000514" + }, "modifiers": {} }, "units": { @@ -23,7 +25,9 @@ "id": "I", "name": "I", "grounding": { - "identifiers": {}, + "identifiers": { + "ido": "0000511" + }, "modifiers": {} }, "units": { @@ -35,7 +39,9 @@ "id": "E", "name": "E", "grounding": { - "identifiers": {}, + "identifiers": { + "apollosv": "0000154" + }, "modifiers": {} }, "units": { @@ -47,7 +53,9 @@ "id": "R", "name": "R", "grounding": { - "identifiers": {}, + "identifiers": { + "ido": "0000592" + }, "modifiers": {} }, "units": { @@ -59,7 +67,9 @@ "id": "D", "name": "D", "grounding": { - "identifiers": {}, + "identifiers": { + "ncit": "C28554" + }, "modifiers": {} }, "units": { @@ -175,7 +185,11 @@ "parameters": [ { "id": "beta_c", - "value": 0.4 + "value": 0.4, + "units": { + "expression": "1/(day*person)", + "expression_mathml": "1dayperson" + } }, { "id": "beta_nc", @@ -183,23 +197,43 @@ }, { "id": "beta_s", - "value": 1.0 + "value": 1.0, + "units": { + "expression": "1/(day*person)", + "expression_mathml": "1dayperson" + } }, { "id": "k_1", - "value": 5.0 + "value": 5.0, + "units": { + "expression": "1", + "expression_mathml": "1" + } }, { "id": "k_2", - "value": 1.0 + "value": 1.0, + "units": { + "expression": "1", + "expression_mathml": "1" + } }, { "id": "kappa", - "value": 0.45454545454545453 + "value": 0.45454545454545453, + "units": { + "expression": "1/day", + "expression_mathml": "day-1" + } }, { "id": "t_0", - "value": 89.0 + "value": 89.0, + "units": { + "expression": "day", + "expression_mathml": "day" + } }, { "id": "t_1",