diff --git a/notebooks/evaluation_2024.03/epi_scenario3/SEIR_scenario3_petrinet.json b/notebooks/evaluation_2024.03/epi_scenario3/SEIR_scenario3_petrinet.json
new file mode 100644
index 00000000..9dab06a8
--- /dev/null
+++ b/notebooks/evaluation_2024.03/epi_scenario3/SEIR_scenario3_petrinet.json
@@ -0,0 +1,726 @@
+{
+ "header": {
+  "name": "SEIR Scenario 3",
+  "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.6/petrinet/petrinet_schema.json",
+  "schema_name": "petrinet",
+  "description": "SEIR Scenario 3",
+  "model_version": "0.1"
+ },
+ "properties": {},
+ "model": {
+  "states": [
+   {
+    "id": "S_y",
+    "name": "S_y",
+    "grounding": {
+     "identifiers": {
+      "ido": "0000514"
+     },
+     "modifiers": {
+      "status": "young"
+     }
+    },
+    "units": {
+     "expression": "person",
+     "expression_mathml": "<ci>person</ci>"
+    }
+   },
+   {
+    "id": "I_y",
+    "name": "I_y",
+    "grounding": {
+     "identifiers": {
+      "ido": "0000511"
+     },
+     "modifiers": {
+      "status": "young"
+     }
+    },
+    "units": {
+     "expression": "person",
+     "expression_mathml": "<ci>person</ci>"
+    }
+   },
+   {
+    "id": "E_y",
+    "name": "E_y",
+    "grounding": {
+     "identifiers": {
+      "apollosv": "00000154"
+     },
+     "modifiers": {
+      "status": "young"
+     }
+    },
+    "units": {
+     "expression": "person",
+     "expression_mathml": "<ci>person</ci>"
+    }
+   },
+   {
+    "id": "I_m",
+    "name": "I_m",
+    "grounding": {
+     "identifiers": {
+      "ido": "0000511"
+     },
+     "modifiers": {
+      "status": "middle"
+     }
+    },
+    "units": {
+     "expression": "person",
+     "expression_mathml": "<ci>person</ci>"
+    }
+   },
+   {
+    "id": "I_o",
+    "name": "I_o",
+    "grounding": {
+     "identifiers": {
+      "ido": "0000511"
+     },
+     "modifiers": {
+      "status": "old"
+     }
+    },
+    "units": {
+     "expression": "person",
+     "expression_mathml": "<ci>person</ci>"
+    }
+   },
+   {
+    "id": "S_m",
+    "name": "S_m",
+    "grounding": {
+     "identifiers": {
+      "ido": "0000514"
+     },
+     "modifiers": {
+      "status": "middle"
+     }
+    },
+    "units": {
+     "expression": "person",
+     "expression_mathml": "<ci>person</ci>"
+    }
+   },
+   {
+    "id": "E_m",
+    "name": "E_m",
+    "grounding": {
+     "identifiers": {
+      "apollosv": "00000154"
+     },
+     "modifiers": {
+      "status": "middle"
+     }
+    },
+    "units": {
+     "expression": "person",
+     "expression_mathml": "<ci>person</ci>"
+    }
+   },
+   {
+    "id": "S_o",
+    "name": "S_o",
+    "grounding": {
+     "identifiers": {
+      "ido": "0000514"
+     },
+     "modifiers": {
+      "status": "old"
+     }
+    },
+    "units": {
+     "expression": "person",
+     "expression_mathml": "<ci>person</ci>"
+    }
+   },
+   {
+    "id": "E_o",
+    "name": "E_o",
+    "grounding": {
+     "identifiers": {
+      "apollosv": "00000154"
+     },
+     "modifiers": {
+      "status": "old"
+     }
+    },
+    "units": {
+     "expression": "person",
+     "expression_mathml": "<ci>person</ci>"
+    }
+   },
+   {
+    "id": "R_y",
+    "name": "R_y",
+    "grounding": {
+     "identifiers": {
+      "ido": "0000592"
+     },
+     "modifiers": {
+      "status": "young"
+     }
+    },
+    "units": {
+     "expression": "person",
+     "expression_mathml": "<ci>person</ci>"
+    }
+   },
+   {
+    "id": "R_m",
+    "name": "R_m",
+    "grounding": {
+     "identifiers": {
+      "ido": "0000592"
+     },
+     "modifiers": {
+      "status": "middle"
+     }
+    },
+    "units": {
+     "expression": "person",
+     "expression_mathml": "<ci>person</ci>"
+    }
+   },
+   {
+    "id": "R_o",
+    "name": "R_o",
+    "grounding": {
+     "identifiers": {
+      "ido": "0000592"
+     },
+     "modifiers": {
+      "status": "old"
+     }
+    },
+    "units": {
+     "expression": "person",
+     "expression_mathml": "<ci>person</ci>"
+    }
+   }
+  ],
+  "transitions": [
+   {
+    "id": "t1",
+    "input": [
+     "I_y",
+     "S_y"
+    ],
+    "output": [
+     "I_y",
+     "E_y"
+    ],
+    "properties": {
+     "name": "t1"
+    }
+   },
+   {
+    "id": "t2",
+    "input": [
+     "I_m",
+     "S_y"
+    ],
+    "output": [
+     "I_m",
+     "E_y"
+    ],
+    "properties": {
+     "name": "t2"
+    }
+   },
+   {
+    "id": "t3",
+    "input": [
+     "I_o",
+     "S_y"
+    ],
+    "output": [
+     "I_o",
+     "E_y"
+    ],
+    "properties": {
+     "name": "t3"
+    }
+   },
+   {
+    "id": "t4",
+    "input": [
+     "I_y",
+     "S_m"
+    ],
+    "output": [
+     "I_y",
+     "E_m"
+    ],
+    "properties": {
+     "name": "t4"
+    }
+   },
+   {
+    "id": "t5",
+    "input": [
+     "I_m",
+     "S_m"
+    ],
+    "output": [
+     "I_m",
+     "E_m"
+    ],
+    "properties": {
+     "name": "t5"
+    }
+   },
+   {
+    "id": "t6",
+    "input": [
+     "I_o",
+     "S_m"
+    ],
+    "output": [
+     "I_o",
+     "E_m"
+    ],
+    "properties": {
+     "name": "t6"
+    }
+   },
+   {
+    "id": "t7",
+    "input": [
+     "I_y",
+     "S_o"
+    ],
+    "output": [
+     "I_y",
+     "E_o"
+    ],
+    "properties": {
+     "name": "t7"
+    }
+   },
+   {
+    "id": "t8",
+    "input": [
+     "I_m",
+     "S_o"
+    ],
+    "output": [
+     "I_m",
+     "E_o"
+    ],
+    "properties": {
+     "name": "t8"
+    }
+   },
+   {
+    "id": "t9",
+    "input": [
+     "I_o",
+     "S_o"
+    ],
+    "output": [
+     "I_o",
+     "E_o"
+    ],
+    "properties": {
+     "name": "t9"
+    }
+   },
+   {
+    "id": "t10",
+    "input": [
+     "E_y"
+    ],
+    "output": [
+     "I_y"
+    ],
+    "properties": {
+     "name": "t10"
+    }
+   },
+   {
+    "id": "t11",
+    "input": [
+     "E_m"
+    ],
+    "output": [
+     "I_m"
+    ],
+    "properties": {
+     "name": "t11"
+    }
+   },
+   {
+    "id": "t12",
+    "input": [
+     "E_o"
+    ],
+    "output": [
+     "I_o"
+    ],
+    "properties": {
+     "name": "t12"
+    }
+   },
+   {
+    "id": "t13",
+    "input": [
+     "I_y"
+    ],
+    "output": [
+     "R_y"
+    ],
+    "properties": {
+     "name": "t13"
+    }
+   },
+   {
+    "id": "t14",
+    "input": [
+     "I_m"
+    ],
+    "output": [
+     "R_m"
+    ],
+    "properties": {
+     "name": "t14"
+    }
+   },
+   {
+    "id": "t15",
+    "input": [
+     "I_o"
+    ],
+    "output": [
+     "R_o"
+    ],
+    "properties": {
+     "name": "t15"
+    }
+   }
+  ]
+ },
+ "semantics": {
+  "ode": {
+   "rates": [
+    {
+     "target": "t1",
+     "expression": "I_y*Myy*S_y*beta*(-mcw*mew + 1)/N",
+     "expression_mathml": "<apply><divide/><apply><times/><ci>I_y</ci><ci>Myy</ci><ci>S_y</ci><ci>beta</ci><apply><plus/><apply><minus/><apply><times/><ci>mcw</ci><ci>mew</ci></apply></apply><cn>1</cn></apply></apply><ci>N</ci></apply>"
+    },
+    {
+     "target": "t2",
+     "expression": "I_m*Mym*S_y*beta*(-mcw*mew + 1)/N",
+     "expression_mathml": "<apply><divide/><apply><times/><ci>I_m</ci><ci>Mym</ci><ci>S_y</ci><ci>beta</ci><apply><plus/><apply><minus/><apply><times/><ci>mcw</ci><ci>mew</ci></apply></apply><cn>1</cn></apply></apply><ci>N</ci></apply>"
+    },
+    {
+     "target": "t3",
+     "expression": "I_o*Myo*S_y*beta*(-mcw*mew + 1)/N",
+     "expression_mathml": "<apply><divide/><apply><times/><ci>I_o</ci><ci>Myo</ci><ci>S_y</ci><ci>beta</ci><apply><plus/><apply><minus/><apply><times/><ci>mcw</ci><ci>mew</ci></apply></apply><cn>1</cn></apply></apply><ci>N</ci></apply>"
+    },
+    {
+     "target": "t4",
+     "expression": "I_y*Mmy*S_m*beta*(-mcw*mew + 1)/N",
+     "expression_mathml": "<apply><divide/><apply><times/><ci>I_y</ci><ci>Mmy</ci><ci>S_m</ci><ci>beta</ci><apply><plus/><apply><minus/><apply><times/><ci>mcw</ci><ci>mew</ci></apply></apply><cn>1</cn></apply></apply><ci>N</ci></apply>"
+    },
+    {
+     "target": "t5",
+     "expression": "I_m*Mmm*S_m*beta*(-mcw*mew + 1)/N",
+     "expression_mathml": "<apply><divide/><apply><times/><ci>I_m</ci><ci>Mmm</ci><ci>S_m</ci><ci>beta</ci><apply><plus/><apply><minus/><apply><times/><ci>mcw</ci><ci>mew</ci></apply></apply><cn>1</cn></apply></apply><ci>N</ci></apply>"
+    },
+    {
+     "target": "t6",
+     "expression": "I_o*Mmo*S_m*beta*(-mcw*mew + 1)/N",
+     "expression_mathml": "<apply><divide/><apply><times/><ci>I_o</ci><ci>Mmo</ci><ci>S_m</ci><ci>beta</ci><apply><plus/><apply><minus/><apply><times/><ci>mcw</ci><ci>mew</ci></apply></apply><cn>1</cn></apply></apply><ci>N</ci></apply>"
+    },
+    {
+     "target": "t7",
+     "expression": "I_y*Moy*S_o*beta*(-mcw*mew + 1)/N",
+     "expression_mathml": "<apply><divide/><apply><times/><ci>I_y</ci><ci>Moy</ci><ci>S_o</ci><ci>beta</ci><apply><plus/><apply><minus/><apply><times/><ci>mcw</ci><ci>mew</ci></apply></apply><cn>1</cn></apply></apply><ci>N</ci></apply>"
+    },
+    {
+     "target": "t8",
+     "expression": "I_m*Mom*S_o*beta*(-mcw*mew + 1)/N",
+     "expression_mathml": "<apply><divide/><apply><times/><ci>I_m</ci><ci>Mom</ci><ci>S_o</ci><ci>beta</ci><apply><plus/><apply><minus/><apply><times/><ci>mcw</ci><ci>mew</ci></apply></apply><cn>1</cn></apply></apply><ci>N</ci></apply>"
+    },
+    {
+     "target": "t9",
+     "expression": "I_o*Moo*S_o*beta*(-mcw*mew + 1)/N",
+     "expression_mathml": "<apply><divide/><apply><times/><ci>I_o</ci><ci>Moo</ci><ci>S_o</ci><ci>beta</ci><apply><plus/><apply><minus/><apply><times/><ci>mcw</ci><ci>mew</ci></apply></apply><cn>1</cn></apply></apply><ci>N</ci></apply>"
+    },
+    {
+     "target": "t10",
+     "expression": "E_y*r_EI",
+     "expression_mathml": "<apply><times/><ci>E_y</ci><ci>r_EI</ci></apply>"
+    },
+    {
+     "target": "t11",
+     "expression": "E_m*r_EI",
+     "expression_mathml": "<apply><times/><ci>E_m</ci><ci>r_EI</ci></apply>"
+    },
+    {
+     "target": "t12",
+     "expression": "E_o*r_EI",
+     "expression_mathml": "<apply><times/><ci>E_o</ci><ci>r_EI</ci></apply>"
+    },
+    {
+     "target": "t13",
+     "expression": "I_y*r_IR",
+     "expression_mathml": "<apply><times/><ci>I_y</ci><ci>r_IR</ci></apply>"
+    },
+    {
+     "target": "t14",
+     "expression": "I_m*r_IR",
+     "expression_mathml": "<apply><times/><ci>I_m</ci><ci>r_IR</ci></apply>"
+    },
+    {
+     "target": "t15",
+     "expression": "I_o*r_IR",
+     "expression_mathml": "<apply><times/><ci>I_o</ci><ci>r_IR</ci></apply>"
+    }
+   ],
+   "initials": [
+    {
+     "target": "S_y",
+     "expression": "10305660.0",
+     "expression_mathml": "<cn>10305660.0</cn>"
+    },
+    {
+     "target": "I_y",
+     "expression": "50.0",
+     "expression_mathml": "<cn>50.0</cn>"
+    },
+    {
+     "target": "E_y",
+     "expression": "50.0",
+     "expression_mathml": "<cn>50.0</cn>"
+    },
+    {
+     "target": "I_m",
+     "expression": "50.0",
+     "expression_mathml": "<cn>50.0</cn>"
+    },
+    {
+     "target": "I_o",
+     "expression": "50.0",
+     "expression_mathml": "<cn>50.0</cn>"
+    },
+    {
+     "target": "S_m",
+     "expression": "15281905.0",
+     "expression_mathml": "<cn>15281905.0</cn>"
+    },
+    {
+     "target": "E_m",
+     "expression": "50.0",
+     "expression_mathml": "<cn>50.0</cn>"
+    },
+    {
+     "target": "S_o",
+     "expression": "12154442.0",
+     "expression_mathml": "<cn>12154442.0</cn>"
+    },
+    {
+     "target": "E_o",
+     "expression": "50.0",
+     "expression_mathml": "<cn>50.0</cn>"
+    },
+    {
+     "target": "R_y",
+     "expression": "0.0",
+     "expression_mathml": "<cn>0.0</cn>"
+    },
+    {
+     "target": "R_m",
+     "expression": "0.0",
+     "expression_mathml": "<cn>0.0</cn>"
+    },
+    {
+     "target": "R_o",
+     "expression": "0.0",
+     "expression_mathml": "<cn>0.0</cn>"
+    }
+   ],
+   "parameters": [
+    {
+     "id": "Myy",
+     "value": 38.62,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "N",
+     "value": 37742307.0,
+     "units": {
+      "expression": "person",
+      "expression_mathml": "<ci>person</ci>"
+     }
+    },
+    {
+     "id": "beta",
+     "value": 0.2,
+     "distribution": {
+      "type": "StandardUniform1",
+      "parameters": {
+       "minimum": 0.05,
+       "maximum": 0.8
+      }
+     },
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "mcw",
+     "value": 0.0,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "mew",
+     "value": 0.0,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "Mym",
+     "value": 20.56,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "Myo",
+     "value": 6.12,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "Mmy",
+     "value": 20.56,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "Mmm",
+     "value": 28.22,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "Mmo",
+     "value": 11.6,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "Moy",
+     "value": 6.12,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "Mom",
+     "value": 11.6,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "Moo",
+     "value": 20.01,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "r_EI",
+     "value": 0.08,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
+    {
+     "id": "r_IR",
+     "value": 0.06,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    }
+   ],
+   "observables": [
+    {
+     "id": "susceptible",
+     "name": "susceptible",
+     "expression": "S_m + S_o + S_y",
+     "expression_mathml": "<apply><plus/><ci>S_m</ci><ci>S_o</ci><ci>S_y</ci></apply>"
+    },
+    {
+     "id": "exposed",
+     "name": "exposed",
+     "expression": "E_m + E_o + E_y",
+     "expression_mathml": "<apply><plus/><ci>E_m</ci><ci>E_o</ci><ci>E_y</ci></apply>"
+    },
+    {
+     "id": "infected",
+     "name": "infected",
+     "expression": "I_m + I_o + I_y",
+     "expression_mathml": "<apply><plus/><ci>I_m</ci><ci>I_o</ci><ci>I_y</ci></apply>"
+    },
+    {
+     "id": "recovered",
+     "name": "recovered",
+     "expression": "R_m + R_o + R_y",
+     "expression_mathml": "<apply><plus/><ci>R_m</ci><ci>R_o</ci><ci>R_y</ci></apply>"
+    }
+   ],
+   "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": []
+  }
+ }
+}
\ No newline at end of file
diff --git a/notebooks/evaluation_2024.03/epi_scenario3/epi_eval_sc3_seir.ipynb b/notebooks/evaluation_2024.03/epi_scenario3/epi_eval_sc3_seir.ipynb
new file mode 100644
index 00000000..c4717d93
--- /dev/null
+++ b/notebooks/evaluation_2024.03/epi_scenario3/epi_eval_sc3_seir.ipynb
@@ -0,0 +1,455 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "14d9fa23-f229-4499-889f-8b84bf790223",
+   "metadata": {},
+   "source": [
+    "# Scenario 3: Causal Reasoning with Interventions"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "80f64161-69df-41c6-a014-3dcd1afbdcb3",
+   "metadata": {},
+   "source": [
+    "### Load MIRA dependencies"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "id": "efd146e7-0742-4e39-a374-39fe931df029",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import json\n",
+    "import sympy\n",
+    "\n",
+    "from mira.metamodel import *\n",
+    "from mira.examples.concepts import susceptible, exposed, infected, recovered\n",
+    "from mira.modeling import Model\n",
+    "from mira.modeling.amr.petrinet import AMRPetriNetModel, template_model_to_petrinet_json\n",
+    "from mira.sources.amr.petrinet import template_model_from_amr_json\n",
+    "from mira.metamodel.io import model_to_json_file, model_from_json_file"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "82328f7c-76da-4eb1-8241-fe0e23b58683",
+   "metadata": {},
+   "source": [
+    "## Build SEIR model"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4f42f426-67a8-4ff8-87ae-22dc95e2bbbe",
+   "metadata": {},
+   "source": [
+    "### Define units"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "id": "f8d81322-226a-4676-a0b8-923e7220e10d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "person_units = lambda: Unit(expression=sympy.Symbol('person'))\n",
+    "day_units = lambda: Unit(expression=sympy.Symbol('day'))\n",
+    "per_day_units = lambda: Unit(expression=1/sympy.Symbol('day'))\n",
+    "dimensionless_units = lambda: Unit(expression=sympy.Integer('1'))\n",
+    "per_day_per_person_units = lambda: Unit(expression=1/(sympy.Symbol('day')*sympy.Symbol('person')))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6900e964-edb2-4427-bab1-d2c9dcdabc82",
+   "metadata": {},
+   "source": [
+    "# Define and stratify model concepts"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "id": "5e2c1d9f-51a9-46a4-aa06-5aa862b8b081",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "_susceptible = Concept(name='S', units=person_units(), identifiers={'ido': '0000514'})\n",
+    "_exposed = Concept(name='E', units=person_units(), identifiers={'apollosv': '00000154'})\n",
+    "_infected = Concept(name='I', units=person_units(), identifiers={'ido': '0000511'})\n",
+    "_recovered = Concept(name='R', units=person_units(), identifiers={'ido': '0000592'})\n",
+    "\n",
+    "c = {\n",
+    "    'S_y': _susceptible.with_context(status=\"young\"),\n",
+    "    'S_m': _susceptible.with_context(status=\"middle\"),\n",
+    "    'S_o': _susceptible.with_context(status=\"old\"),\n",
+    "    'E_y': _exposed.with_context(status=\"young\"),\n",
+    "    'E_m': _exposed.with_context(status=\"middle\"),\n",
+    "    'E_o': _exposed.with_context(status=\"old\"),\n",
+    "    'I_y': _infected.with_context(status=\"young\"),\n",
+    "    'I_m': _infected.with_context(status=\"middle\"),\n",
+    "    'I_o': _infected.with_context(status=\"old\"),\n",
+    "    'R_y': _recovered.with_context(status=\"young\"),\n",
+    "    'R_m': _recovered.with_context(status=\"middle\"),\n",
+    "    'R_o': _recovered.with_context(status=\"old\"),\n",
+    "}\n",
+    "\n",
+    "for concept in c:\n",
+    "    c[concept].name = concept"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4792ddd4-f7bd-43e5-8cc7-a729573b39eb",
+   "metadata": {},
+   "source": [
+    "### Define parameters with uncertainty"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "id": "b4774d31-1ad4-4027-a82b-6bee06907e03",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# To add a small distribution around parameters (for Terarium)\n",
+    "def unif_distribution_create(value: float):\n",
+    "    return Distribution(\n",
+    "        type=\"StandardUniform1\",\n",
+    "        parameters={\"minimum\": value, \"maximum\": value + max(0.01*value,0.1)},\n",
+    "    )"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "id": "a902e806-0dad-4bf6-a264-0172324257b0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "parameters = {\n",
+    "    'beta': Parameter(name='beta', value=sympy.Float(0.2), units=per_day_units(),\n",
+    "                      distribution=Distribution(type='StandardUniform1',\n",
+    "                                                parameters={'minimum': 0.05,\n",
+    "                                                            'maximum': 0.8})),  # Infection rate\n",
+    "    'N': Parameter(name='total_population', value=sympy.Float(37742307.0), units=person_units()),  # Total population\n",
+    "    'mew': Parameter(name='mew', value=sympy.Float(0.0), units=per_day_units()),  # Mask efficacy\n",
+    "    'mcw': Parameter(name='mcw', value=sympy.Float(0.0), units=per_day_units()),  # Mask compliance\n",
+    "    'r_EI': Parameter(name='r_EI', value=sympy.Float(0.08), units=per_day_units()),  # Rate of progressing E -> I\n",
+    "    'r_IR': Parameter(name='r_IR', value=sympy.Float(0.06), units=per_day_units()),  # Rate of progressing I -> R\n",
+    "    'Myy': Parameter(name='Myy', value=sympy.Float(38.62), units=per_day_units()),  # Contact rate young -> young\n",
+    "    'Mym': Parameter(name='Mym', value=sympy.Float(20.56), units=per_day_units()),  # Contact rate young -> middle\n",
+    "    'Myo': Parameter(name='Myo', value=sympy.Float(6.12), units=per_day_units()),  # Contact rate young -> old\n",
+    "    'Mmy': Parameter(name='Mmy', value=sympy.Float(20.56), units=per_day_units()),  # Contact rate middle -> young\n",
+    "    'Mmm': Parameter(name='Mmm', value=sympy.Float(28.22), units=per_day_units()),  # Contact rate middle -> middle\n",
+    "    'Mmo': Parameter(name='Mmo', value=sympy.Float(11.6), units=per_day_units()),  # Contact rate middle -> old\n",
+    "    'Moy': Parameter(name='Moy', value=sympy.Float(6.12), units=per_day_units()),  # Contact rate old -> young\n",
+    "    'Mom': Parameter(name='Mom', value=sympy.Float(11.6), units=per_day_units()),  # Contact rate old -> middle\n",
+    "    'Moo': Parameter(name='Moo', value=sympy.Float(20.01), units=per_day_units()),  # Contact rate old -> old\n",
+    "}"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e0e7b89c-8d24-42b2-afe1-e3bddf0bfc5c",
+   "metadata": {},
+   "source": [
+    "### Define variables"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "id": "802ce5dd-9f50-43c3-8d0b-f1e7a692d7b0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "S_y, S_m, S_o, E_y, E_m, E_o, I_y, I_m, I_o, R_y, R_m, R_o, beta, N, mew, mcw, r_EI, r_IR, Myy, Mym, Myo, Mmy, Mmm, Mmo, Moy, Mom, Moo = \\\n",
+    "    sympy.symbols(\n",
+    "        'S_y S_m S_o E_y E_m E_o I_y I_m I_o R_y R_m R_o beta N mew mcw r_EI r_IR Myy Mym Myo Mmy Mmm Mmo Moy Mom Moo'\n",
+    "    )"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8d3dceac-1113-4c55-92a3-3b5ab34ee960",
+   "metadata": {},
+   "source": [
+    "### Set initial values"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "id": "f892e033-55da-44c6-b309-459dee0cae1a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "initials = {\n",
+    "    \"S_y\": Initial(concept=c[\"S_y\"], expression=10305660.0),\n",
+    "    \"S_m\": Initial(concept=c[\"S_m\"], expression=15281905.0),\n",
+    "    \"S_o\": Initial(concept=c[\"S_o\"], expression=12154442.0),\n",
+    "    \"E_y\": Initial(concept=c[\"E_y\"], expression=50.0),\n",
+    "    \"E_m\": Initial(concept=c[\"E_m\"], expression=50.0),\n",
+    "    \"E_o\": Initial(concept=c[\"E_o\"], expression=50.0),\n",
+    "    \"I_y\": Initial(concept=c[\"I_y\"], expression=50.0),\n",
+    "    \"I_m\": Initial(concept=c[\"I_m\"], expression=50.0),\n",
+    "    \"I_o\": Initial(concept=c[\"I_o\"], expression=50.0),\n",
+    "    \"R_y\": Initial(concept=c[\"R_y\"], expression=0.0),\n",
+    "    \"R_m\": Initial(concept=c[\"R_m\"], expression=0.0),\n",
+    "    \"R_o\": Initial(concept=c[\"R_o\"], expression=0.0),\n",
+    "}"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "51ea2d61-7dc7-4aa3-849e-9817708158cc",
+   "metadata": {},
+   "source": [
+    "### Define templates"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "id": "5f186c10-7b95-4678-8737-ebca86c1f856",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "##### S -> E\n",
+    "# Sy -> Ey by Iy\n",
+    "syeyiy = ControlledConversion(\n",
+    "    subject=c['S_y'],\n",
+    "    outcome=c['E_y'],\n",
+    "    controller=c['I_y'],\n",
+    "    rate_law=beta*S_y*(1 - mew*mcw)*(Myy*I_y) / N\n",
+    ")\n",
+    "# Sy -> Ey by Im\n",
+    "syeyim = ControlledConversion(\n",
+    "    subject=c['S_y'],\n",
+    "    outcome=c['E_y'],\n",
+    "    controller=c['I_m'],\n",
+    "    rate_law=beta*S_y*(1 - mew*mcw)*(Mym*I_m) / N\n",
+    ")\n",
+    "# Sy -> Ey by Io\n",
+    "syeyio = ControlledConversion(\n",
+    "    subject=c['S_y'],\n",
+    "    outcome=c['E_y'],\n",
+    "    controller=c['I_o'],\n",
+    "    rate_law=beta*S_y*(1 - mew*mcw)*(Myo*I_o) / N\n",
+    ")\n",
+    "\n",
+    "# Sm -> Em by Iy\n",
+    "smemiy = ControlledConversion(\n",
+    "    subject=c['S_m'],\n",
+    "    outcome=c['E_m'],\n",
+    "    controller=c['I_y'],\n",
+    "    rate_law=beta*S_m*(1 - mew*mcw)*(Mmy*I_y) / N\n",
+    ")\n",
+    "# Sm -> Em by Im\n",
+    "smemim = ControlledConversion(\n",
+    "    subject=c['S_m'],\n",
+    "    outcome=c['E_m'],\n",
+    "    controller=c['I_m'],\n",
+    "    rate_law=beta*S_m*(1 - mew*mcw)*(Mmm*I_m) / N\n",
+    ")\n",
+    "# Sm -> Em by Io\n",
+    "smemio = ControlledConversion(\n",
+    "    subject=c['S_m'],\n",
+    "    outcome=c['E_m'],\n",
+    "    controller=c['I_o'],\n",
+    "    rate_law=beta*S_m*(1 - mew*mcw)*(Mmo*I_o) / N\n",
+    ")\n",
+    "\n",
+    "# So -> Eo by Iy\n",
+    "soeoiy = ControlledConversion(\n",
+    "    subject=c['S_o'],\n",
+    "    outcome=c['E_o'],\n",
+    "    controller=c['I_y'],\n",
+    "    rate_law=beta*S_o*(1 - mew*mcw)*(Moy*I_y) / N\n",
+    ")\n",
+    "# So -> Eo by Im\n",
+    "soeoim = ControlledConversion(\n",
+    "    subject=c['S_o'],\n",
+    "    outcome=c['E_o'],\n",
+    "    controller=c['I_m'],\n",
+    "    rate_law=beta*S_o*(1 - mew*mcw)*(Mom*I_m) / N\n",
+    ")\n",
+    "# So -> Eo by Io\n",
+    "soeoio = ControlledConversion(\n",
+    "    subject=c['S_o'],\n",
+    "    outcome=c['E_o'],\n",
+    "    controller=c['I_o'],\n",
+    "    rate_law=beta*S_o*(1 - mew*mcw)*(Moo*I_o) / N\n",
+    ")\n",
+    "\n",
+    "#### E -> I\n",
+    "# Ey -> Iy\n",
+    "eyiy = NaturalConversion(\n",
+    "    subject=c['E_y'],\n",
+    "    outcome=c['I_y'],\n",
+    "    rate_law=r_EI*E_y\n",
+    ")\n",
+    "# Em -> Im\n",
+    "emim = NaturalConversion(\n",
+    "    subject=c['E_m'],\n",
+    "    outcome=c['I_m'],\n",
+    "    rate_law=r_EI*E_m\n",
+    ")\n",
+    "# Eo -> Io\n",
+    "eoio = NaturalConversion(\n",
+    "    subject=c['E_o'],\n",
+    "    outcome=c['I_o'],\n",
+    "    rate_law=r_EI*E_o\n",
+    ")\n",
+    "\n",
+    "#### I -> R\n",
+    "# Iy -> Ry\n",
+    "iyry = NaturalConversion(\n",
+    "    subject=c['I_y'],\n",
+    "    outcome=c['R_y'],\n",
+    "    rate_law=r_IR*I_y\n",
+    ")\n",
+    "# Im -> Rm\n",
+    "imrm = NaturalConversion(\n",
+    "    subject=c['I_m'],\n",
+    "    outcome=c['R_m'],\n",
+    "    rate_law=r_IR*I_m\n",
+    ")\n",
+    "# Io -> Ro\n",
+    "ioro = NaturalConversion(\n",
+    "    subject=c['I_o'],\n",
+    "    outcome=c['R_o'],\n",
+    "    rate_law=r_IR*I_o\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a845f3f9-fe95-4931-9a4b-c3800774f940",
+   "metadata": {},
+   "source": [
+    "### Define observables"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "id": "38e21c50-8b53-4288-a8ef-73f6e02ac63a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "observables_seir = {\n",
+    "    'susceptible': Observable(name='susceptible', expression=S_y+S_m+S_o),\n",
+    "    'exposed': Observable(name='exposed', expression=E_y+E_m+E_o),\n",
+    "    'infected': Observable(name='infected', expression=I_y+I_m+I_o),\n",
+    "    'recovered': Observable(name='recovered', expression=R_y+R_m+R_o),\n",
+    "}"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e0a0a040-600d-45f4-bc68-be57074b6cac",
+   "metadata": {},
+   "source": [
+    "### Define template model and save as petrinet AMR"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "id": "4c523830-dfc3-4b8a-b584-5dad7f95c729",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "seir_model = TemplateModel(\n",
+    "    templates=[\n",
+    "        syeyiy,\n",
+    "        syeyim,\n",
+    "        syeyio,\n",
+    "        smemiy,\n",
+    "        smemim,\n",
+    "        smemio,\n",
+    "        soeoiy,\n",
+    "        soeoim,\n",
+    "        soeoio,\n",
+    "        eyiy,\n",
+    "        emim,\n",
+    "        eoio,\n",
+    "        iyry,\n",
+    "        imrm,\n",
+    "        ioro,\n",
+    "    ],\n",
+    "    parameters=parameters,\n",
+    "    initials=initials,\n",
+    "    time=Time(name='t', units=day_units()),\n",
+    "    observables=observables_seir,\n",
+    "    annotations=Annotations(name='SEIR Scenario 3')\n",
+    ")\n",
+    "\n",
+    "# Save as JSON\n",
+    "with open(\"SEIR_scenario3_petrinet.json\", 'w') as fh:\n",
+    "    json.dump(template_model_to_petrinet_json(seir_model), fh, indent=1)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "cedfa54c-a1c6-4eb5-9674-9ac17d823fb3",
+   "metadata": {},
+   "source": [
+    "## Change parameter values and uncertainty from the AMR"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "id": "12219f8d-566f-466d-b35e-6bb70af5cea7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "filename = \"SEIR_scenario3_petrinet.json\"\n",
+    "with open(filename, 'r') as fh:\n",
+    "    tm = template_model_from_amr_json(json.load(fh))\n",
+    "\n",
+    "# Change `Myy` parameter value\n",
+    "tm.parameters[\"Myy\"].value = 50.0\n",
+    "\n",
+    "# Change `Myy` distribution\n",
+    "tm.parameters[\"Myy\"].distribution = Distribution(type='StandardUniform1',\n",
+    "                                                 parameters={'minimum': 40.0, 'maximum': 80.0})\n",
+    "\n",
+    "# Save as updated AMR\n",
+    "with open('update_parameters_example.json', 'w') as fh:\n",
+    "    json.dump(template_model_to_petrinet_json(tm), fh, indent=1)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}