About · The Virtual Brain Ontology
An executable knowledge framework for brain-network modeling
TVB-O represents a whole-brain model and the experiment that runs it as one typed, ontology-grounded object. From that single source, one compiler generates runnable code and a methods report, and a four-domain ontology makes models comparable across the literature. It aligns to and extends the EBRAINS ecosystem rather than replacing it.
The gap
No shared representation of what a model is
A published brain model is usually bespoke code. It can drift from the equations in the paper, is often shared with missing parameters, and stays hard to run because results depend on software versions and execution environments — so results are difficult to reproduce and compare.
Underneath lies a single absence: no shared, machine-readable representation of what a model is, or of the whole simulation experiment around it — its network, inputs, execution and analyses. TVB-O supplies that representation, following the example set by SBML and BioModels in systems biology.
Anatomy of the framework
Three pillars and a platform
LinkML data model
A minimal, human- and machine-readable schema for everything needed to reproduce an experiment. The typed Python classes are generated from it, so the specification and the code never diverge.
Ontology
The formal, machine-readable backbone: shared terms and logical axioms with stable identifiers under w3id.org/tvbo, aligned to external ontologies for physics, biology, anatomy and clinical domains.
Python package · tvbo
Specify a model once as YAML or Python objects, load curated entries from the database, generate code across backends, then run, fit and analyse — with a CLI for HPC workflows.
The platform
A web layer over the ontology and curated database: browse the knowledge graph, assemble experiments in the builder, and retrieve everything through a REST API — for people and AI agents.
Prior work
Where TVB-O fits
Capabilities read down the left; tools across the top. No existing standard fills every row — the closest come from two directions, and only TVB-O's column is complete.
Row 4 is the crux: only TVB-O grounds a model's entities in all four domains at once — physical units, biological process, brain anatomy, and clinical disorder — and it is the only tool that is executable, whole-brain, four-domain-grounded, curated and interoperable together.
Relationship to TVB
Built with The Virtual Brain, not instead of it
TVB-O is not a fork of The Virtual Brain. It is a specification and knowledge layer that treats TVB as one of several execution backends. The same types describe any dynamical system on any network — a single Lorenz attractor, a lattice of oscillators, or a power grid — so the framework reaches beyond whole-brain simulation while remaining native to it.
It aligns to and extends EBRAINS resources such as openMINDS and the Model Catalog, and interoperates with NeuroML/LEMS, BIDS and SBML rather than competing with them.
Who builds it
Developed at Charité and the BIH
TVB-O is developed in the Brain Simulation Section at Charité — Universitätsmedizin Berlin and the Berlin Institute of Health (BIH), the group behind The Virtual Brain.
Start with the Python package
Install with pip install tvbo, load a model from the database, and generate runnable code in a few lines.