Convention B: dict-of-formulas

Convention B is the clearest format for reproducible model exchange inside Python.

Example file

Create decay_dict.py:

model = {
    "species": {
        "x": 1.0,
    },
    "parameters": {
        "k": 0.2,
    },
    "parameter_units": {
        "k": "per_second",
    },
    "odes": {
        "x": "-k*x",
    },
    "compartments": {
        "cell": 1.0,
    },
}

Convert

ode2sbml convert decay_dict.py --output decay.xml --format sbml

Add assignment rules

model = {
    "species": {"S": 10.0, "P": 0.0},
    "parameters": {"k": 0.1},
    "odes": {
        "S": "-flux",
        "P": "flux",
    },
    "assignment_rules": {
        "flux": "k*S",
    },
}

Add events

model = {
    "species": {"x": 0.0},
    "parameters": {"k": 1.0},
    "odes": {"x": "k"},
    "events": [
        {
            "trigger": "x >= 10",
            "assignments": {"x": "0"},
            "delay": 0.0,
        }
    ],
}

Best default

Use Convention B for published examples, tests, and tutorials. It is explicit, readable, and avoids AST parsing ambiguity.