writing-models

name	writing-models
description	How to specify a Dynamics in TVBO — the YAML and Python forms, parameter / state-variable / equation conventions, and common pitfalls.

Writing Models in TVBO

A Dynamics is the smallest building block: a set of named parameters and state variables governed by ODE equations. It can be written as YAML or constructed directly in Python.

YAML form

name: LorenzAttractor
parameters:
    sigma:
        value: 10
        label: Prandtl number
    rho:
        value: 28
        label: Rayleigh number
    beta:
        value: 2.6666666666666665
state_variables:
    X:
        equation:
            lhs: \dot{X}
            rhs: sigma * (Y - X)
    Y:
        equation:
            lhs: \dot{Y}
            rhs: X * (rho - Z) - Y
    Z:
        equation:
            lhs: \dot{Z}
            rhs: X * Y - beta * Z

Python form

from tvbo import Dynamics

lorenz = Dynamics(
    parameters={
        "sigma": {"value": 10.0},
        "rho": {"value": 28.0},
        "beta": {"value": 8 / 3},
    },
    state_variables={
        "X": {"equation": {"rhs": "sigma * (Y - X)"}},
        "Y": {"equation": {"rhs": "X * (rho - Z) - Y"}},
        "Z": {"equation": {"rhs": "X * Y - beta * Z"}},
    },
)

Loading a curated model from a source

TVBO components are declarative: a Dynamics is either specified inline (as above), loaded from YAML, or pointed at semantically via an iri. The IRI's prefix names the source — tvbo: for the built-in ontology, but the same mechanism is intended to dispatch to other prefixes (e.g. neuroml:) that resolve from other ontologies / data sources.

# Direct construction (Python API)
dyn = Dynamics.from_db("ReducedWongWangExcInh")

# As a semantic pointer inside a SimulationExperiment dict
dynamics = {"name": "ReducedWongWang", "iri": "tvbo:ReducedWongWangExcInh"}

A bare name string (dynamics="ReducedWongWangExcInh") is not a semantic pointer — there's no prefix, so the resolver cannot tell which source to query. Always include the iri.

Conventions and pitfalls

• lhs is LaTeX, not Python. \dot{X} for a time-derivative. Omit lhs to default to \dot{<state>}.
• rhs is a SymPy-parseable expression. Names must match parameters and state variables. Greek letters as full words: sigma, not σ.
• label on a parameter is human-readable metadata (renders in the platform browser). Keep name machine-friendly.
• Parameters carry values; state variables carry equations. Don't put a value on a state variable.
• Don't hand-edit tvbo/datamodel/** — that's generated from schema/*.yaml. Use the Dynamics class.
• Trust the slots. Never assign a raw {} / [] to a LinkML slot — a JsonObj in your data is the symptom of mis-configured YAML / a Python object leaking into the schema. The active datamodel (tvbo/datamodel/schema.py) is the jsonasobj2 / YAMLRoot dataclass form. Inlined dicts/lists are coerced into typed classes only in __post_init__ (i.e. at construction). Mutating a slot afterwards does not re-run that coercion:
  • Multivalued slots (dict- or list-backed: parameters, dynamics, coupling, nodes, edges, transforms, …) → mutate the existing container in place: .update(...) / container["X"] = ... for dict slots, .append(...) for list slots. To get a typed entry, insert a constructed class: net.dynamics["X"] = Dynamics(...).
    • ❌ net.dynamics = {...} — a raw dict goes through jsonasobj2's JsonObj.__setattr__, which wraps it in a bare JsonObj (it later breaks .items() / .values() on round-trip).
    • ❌ net.nodes = [{...}] — a raw list isn't wrapped in JsonObj, but its entries stay uncoerced plain dicts, never Node instances.
    • ⚠️ .update({...}) / ["X"] = {...} avoids the JsonObj, but a raw dict still isn't normalized — prefer inserting a constructed class instance.
  • Single-valued slots → plain = is correct. Assign a scalar directly (net.number_of_nodes = 76); for a nested-object slot assign a constructed LinkML class instance (net.coordinate_space = CommonCoordinateSpace(...)), never a raw {} (which becomes a bare JsonObj).
  • Best of all: pass everything at construction (Network(dynamics={...}, nodes=[...])) so __post_init__ normalizes it into typed classes for you.
• Never change a datatype; only assign valid LinkML class instances. If a slot expects a class, construct that class — don't pass a bare dict or an ad-hoc object.

  This holds as long as the active datamodel is the dataclass/YAMLRoot one. If TVBO switches to the pydantic datamodel (tvbo/datamodel/pydantic.py), dict-assignment may become valid (pydantic validates/coerces) — unverified.

Beyond ODEs

• Stochastic terms via tvbo.classes.noise.
• Discrete events via tvbo.classes.event.
• Perturbations / stimulation via tvbo.classes.perturbation.
• Network coupling via tvbo.classes.coupling + tvbo.classes.network.
• Continuation (bifurcation analysis) via tvbo.classes.continuation.

See the running-simulations skill for what to do once you have a Dynamics.