overview

name	overview
description	What TVBO is — the three pillars (LinkML datamodel, ontology, Python package) plus the Odoo platform. Use when working with the tvbo library or deciding whether to reach for it.

TVBO Overview

TVBO (The Virtual Brain Ontology) is a knowledge-representation and simulation toolkit for large-scale brain network models. It consists of three pillars plus a platform.

Pillar 1 — LinkML datamodel

schema/*.yaml defines the structured metadata for SimulationExperiment, SimulationStudy, Dynamics, Network, Atlas, and friends. The Python types in tvbo/datamodel/ are generated from this schema. Users consume them through the higher-level classes in tvbo/classes/.

Pillar 2 — Ontology

tvb-o.owl and the TTL/SHACL files in ontology/ carry the axioms about:

• SimulationExperiment and SimulationStudy
• Network and DynamicalSystem
• Software used to specify and run Dynamical Network Models

Loaded via owlready2 from tvbo.ontology.

Pillar 3 — Python package

The tvbo Python package does four things:

1. Specifies models — Dynamics, Equation, Network, etc. as Python objects or YAML files.
2. Loads SimulationExperiments, SimulationStudys, and all other ontology-backed classes.
3. Generates code for all supported backends (JAX, NumPy, TVB, Julia/DifferentialEquations.jl, PyRates, ModelingToolkit, NetworkDynamics, NeuroML, …).
4. Executes the generated code and runs experiments against the chosen backend.

Entry points: from tvbo import Dynamics, SimulationExperiment. See the writing-models and running-simulations skills for the everyday workflows.

Platform — tvbo.charite.de

An Odoo-based management layer over the ontology. Users can:

• Display knowledge stored in the ontology and the curated models.
• Retrieve knowledge programmatically.
• Set up their own models, store and share SimulationExperiments / SimulationStudys (public by default; private with an API key).
• Load shared experiments back into Python.

A discussion / Q&A layer for the community is on the roadmap. See the platform skill for client-side usage.

When to use TVBO

• You want to describe a neural-mass / dynamical-network model once and run it on multiple simulator backends.
• You want your models to be machine-readable, citable, and shareable (the ontology + LinkML schema make this possible).
• You want a structured way to bundle experiments and studies for reproducibility.

Installation

pip install tvbo            # core
pip install tvbo[jax]       # JAX backend
pip install tvbo[tvb]       # The Virtual Brain backend
pip install tvbo[pyrates]   # PyRates backend
pip install tvbo[julia]     # juliacall + Julia backends
pip install tvbo[all]       # everything

Documentation: https://virtual-twin.github.io/tvbo/