running-simulations

name	running-simulations
description	How to run a SimulationExperiment in TVBO — choosing a backend, calling run/plot, and what each optional extra (jax, tvb, pyrates, julia) provides.

Running Simulations

Once you have a Dynamics (see the writing-models skill), wrap it in a SimulationExperiment and run it.

The quick path

from tvbo import Dynamics, SimulationExperiment

experiment = SimulationExperiment(dynamics=my_dynamics)
experiment.run(duration=1000).plot()

run() returns a result container; plot() is built-in. For details see tvbo/run/, tvbo/plot/, tvbo/analysis/.

Declarative sourcing: inline vs YAML vs IRI

TVBO is declarative about where each component comes from. A SimulationExperiment section is always one of:

1. Fully inline — a Python instance or a dict containing every field.
2. From YAML — SimulationExperiment.from_file(...) / from_string(...).
3. Semantic pointer — a dict with an iri CURIE. The prefix selects the source (tvbo: for the built-in ontology; in principle other prefixes like neuroml: can resolve from other sources); remaining fields are backfilled from that source.

A bare name string is not a semantic pointer — it has no prefix, so the resolver cannot tell which source to query. Use the iri form:

exp = SimulationExperiment(
    dynamics={"name": "ReducedWongWang", "iri": "tvbo:ReducedWongWangExcInh"},
    coupling={"name": "Linear", "iri": "tvbo:Linear"},
    network={
        "parcellation": {"atlas": {"name": "DesikanKilliany",
                                    "iri": "tvbo:DesikanKilliany"}},
        "tractogram":   {"name": "dTOR", "iri": "tvbo:dTOR"},
    },
    integration={"method": "Heun", "duration": 10_000, "noise": None},
)

coupling additionally accepts a bare string as a tvbo:-prefixed shorthand, but prefer the explicit iri form for clarity and to avoid coupling docs to the default namespace.

Picking a backend

The default backend is JAX. Switch via render_code('<backend>') for export, or pass backend=... to SimulationExperiment.

Backend	Extras to install	Use when
jax	pip install tvbo[jax] (already in core)	Default; differentiable; fast on GPU/TPU
tvb	pip install tvbo[tvb]	You need TVB's curated set of neural-mass models
pyrates	pip install tvbo[pyrates]	Rate-coded brain network models + numerical continuation
julia	pip install tvbo[julia]	DifferentialEquations.jl, ModelingToolkit, NetworkDynamics
neuroml	pip install tvbo[neuroml]	Multi-compartment models via NEURON/LEMS
tvboptim	pip install tvbo[tvboptim]	JAX-based optimisation / parameter fitting

Render-only (no execution)

code = experiment.render_code('jax')
print(code)

Useful for inspecting the generated code or running it outside TVBO.

Studies

A SimulationStudy aggregates multiple experiments (e.g. parameter sweeps). See tvbo/classes/study.py.

Pitfalls

• Intel Mac: TVBO pins numba<0.60 and llvmlite<0.44 on darwin/x86_64. JAX is pinned to 0.4.28 (last Intel-Mac release). If installation complains, check pyproject.toml's platform conditionals.
• TVB extra: pulls numba transitively; the same Intel-Mac caps apply.
• Julia extra: requires a working Julia runtime. juliacall will download one on first import if absent.
• --run-slow is a pytest flag, not a TVBO option. It controls which tests run, not which simulations.