TVB-O API Documentation

Adapters

This module contains adapters for different simulation backends:

adapters	Backend adapters for SimulationExperiment.
base	Base adapter for processing SimulationExperiment metadata.
bids	BIDS BEP034 Export Module
bifurcationkit	BifurcationKit.jl backend adapter for SimulationExperiment.
diffeq	DifferentialEquations.jl backend adapter for SimulationExperiment.
julia	Python ↔︎ Julia bridge using juliacall (PythonCall.jl).
modelingtoolkit	Standalone ModelingToolkit.jl backend adapter for SimulationExperiment.
networkdynamics	NetworkDynamics.jl backend adapter for SimulationExperiment.
neuroml	NeuroML/LEMS adapter for SimulationExperiment.
openminds	OpenMINDS JSON-LD conversion utilities for TVBO.
pyrates	PyRates backend adapter for SimulationExperiment.
pyrates_bifurcation	PyRates/PyCoBi bifurcation analysis backend adapter for SimulationExperiment.
tvb	TVB (The Virtual Brain) adapter for tvbo.

Analysis

Houses analysis result container classes (e.g., BifurcationResult) and related

analysis	Analysis subpackage.
bifurcation	Bifurcation analysis result objects and helpers.

API

This module provides the API for the TVB Ontology.

api	TVB-O API
direct_ontology_api	Direct RDF/SPARQL-based ontology API.
dynamics_api	Dynamics model API — serves neural mass models from the tvbo database.
experiment_api	Experiment API — serves simulation experiments from the tvbo database.
main
network_api	Network retrieval API — serves normative connectomes from the tvbo database.
ontology_api	This module provides a set of methods, through the OntologyAPI interface, which

Classes

Core simulation classes: dynamics, coupling, noise, continuation, observation, perturbation, equation, functions, experiment, study, network, and atlas.

classes	tvbo.classes
atlas
continuation	Continuation
coupling	TVB-O wrapper for Coupling functions
dynamics
equation	# Handling Equations and Expressions
experiment
function	Function Classes
network
noise
observation
parcellation	This module provides functions for loading and accessing parcellation data.
perturbation
study

TVB-O Code Generation

Template rendering, code printing, and backend-specific code generation.

codegen	TVB-O Code Generation
code
cuda	CUDA Adapter for TVBO
functions	Function Code Generation
lems	# LEMS-Generator
pyrates	PyRates Integration Module
templater

Data

Access and manage TVB-O data.

data	Data Module
converters	Format converters: BEP017 export.
matrix_io	Low-level matrix read/write for HDF5 groups and Zarr groups.
network_io	High-level Network I/O. Dispatches by companion file extension.
registry	Canonical database registry — resolves short names to YAML file paths.
types

Data Model

Auto-generated from LinkML schema. Usage: from tvbo.datamodel.schema import Dynamics, Parameter, Equation from tvbo.datamodel.pydantic import Dynamics as PydanticDynamics

datamodel	TVB-O Data Model
pydantic
schema

Export

Non-code exports: reports, metadata standards (OpenMINDS).

export	TVB-O Export
report	Report Module

TVB-O Ontology

OWL ontology access, query, and configuration.

ontology	TVB-O Ontology
config	TVB-O Model Configuration Module
constants	Constants
db
graph	# Graph-based representation of the ontology.
owl	—
query

Atlas

atlas
freesurfer

Semantic Web

semanticweb
tvbgo	TVB-GO Module

Parse

TVB-O Parse

parse	TVB-O Parse
expression
lems_loader	This module deals with loading elements from LEMS-generated files.
tvb_converter	Convert TVB simulator objects to tvbo datamodel instances.

Plot

This module contains utilities for plotting TVB-O models. {python} from tvbo import plot plot.ontology.plot_model('JansenRit')

plot	TVB-O’s plotting utilities
analysis
animate	Animation utilities for SimulationResult.
bifurcation_diagram
functions
network	Network graph plotting utilities.
network_graph	Network graph plotting utilities.
ontology	Plotting functions for visualizing networks
phase	Phase-space trajectory and vector-field plots for SimulationResult.
timeseries	Time-series, EEG, and power-spectrum plotting for SimulationResult.
utils

Run

run
compgraph
graph
julia	Low-level Julia execution utilities for running generated Julia code.

RateML

rateml
utils

tvboptim

Mako templates for generating tvboptim network dynamics code from TVBO models.

tvboptim	# TVB-Optim Templates
utils	TVB-Optim Template Utilities

Utilities

Core utilities: Bunch container, PyTree formatting, YAML I/O, and metadata traversal helpers. Plotting utilities (colors, colormaps, multiview) have moved to tvbo.plot.utils and are re-exported here for backward compatibility. Analysis functions (per_window_fc, ttest_correlation_strength) have moved to tvbo.analysis.

utils	Utilities Module for TVB-O
report	Report Module
units	Unit and Dimension Utilities