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",