tvbo 0.2.5

The Virtual Brain Ontology

The Virtual Brain Ontology

tvbo is a Python library to access the knowledge representation system (i.e., ontology) and data model for the neuroinformatics platform The Virtual Brain (TVB).

🚀 Installation

pip install tvbo

📖 Quick Start

Example: Lorenz Attractor Simulation

📝 Model Specification (YAML)

name: LorenzAttractor
parameters:
    sigma:
        value: 10
        label: Prandtl number
    rho:
        label: Rayleigh number
        value: 28
    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

🔧 Generate Code

from tvbo import Dynamics, SimulationExperiment

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"}},
    },
)

code = SimulationExperiment(local_dynamics=lorenz).render_code('jax')
print(code)

▶️ Run Simulation

from tvbo import Dynamics, SimulationExperiment

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"}},
    },
)

# Run simulation and plot results
SimulationExperiment(local_dynamics=lorenz).run(duration=1000).plot()

📚 Documentation

• Full Documentation
• Model Browser - Browse models, parameters, and equations
• Metadata Schema - Explore the TVB-O data model

🔬 Features

• 🧠 Access TVB ontology and knowledge base
• 📊 Define and simulate dynamical systems
• 🔄 Code generation for multiple backends (JAX, NumPy)
• 📈 Built-in visualization tools
• 🗃️ Structured metadata schema

📦 Installation Options

Standard Installation

pip install tvbo

With API Server Support

pip install tvbo[api]

With TVB Integration

pip install tvbo[tvb]

Full Installation (All Features)

pip install tvbo[all]

Note: The knowledge extra requires manual installation:

pip install git+https://github.com/neurommsig/neurommsig-knowledge.git

📄 License

Copyright © 2025 Charité Universitätsmedizin Berlin. This software is licensed under the terms of the European Union Public Licence (EUPL) version 1.2 or later.