Interoperability

TVBO integrations with external tools and standards

TVBO provides seamless interoperability with various neuroimaging tools, optimization frameworks, and metadata standards. This enables researchers to leverage specialized capabilities from different ecosystems while maintaining a unified model representation.

Integration Overview

flowchart LR
    subgraph TVBO["TVBO Core"]
        D[Dynamics]
        S[SimulationExperiment]
        N[Network]
    end
    
    subgraph Optimization["Optimization"]
        O[tvboptim]
    end
    
    subgraph Analysis["Analysis"]
        P[PyRates]
    end
    
    subgraph Standards["Standards"]
        B[BIDS]
        M[OpenMINDS]
    end
    
    TVBO <--> O
    TVBO <--> P
    TVBO --> B
    TVBO --> M

Available Integrations

Integration	Direction	Description
tvboptim	Bidirectional	JAX-based optimization and parameter fitting
PyRates	Bidirectional	Dynamical systems analysis and bifurcation
BIDS	Export	Brain Imaging Data Structure (BEP034)
OpenMINDS	Export	EBRAINS Knowledge Graph metadata

Quick Start

Optimization with tvboptim

from tvbo import SimulationExperiment

# Load experiment and run optimization
exp = SimulationExperiment.from_file("experiment.yaml")
results = exp.run()

# Access optimization results
print(results.optimization.fic.history)

Analysis with PyRates

from tvbo import Dynamics

# Export TVBO model to PyRates
model = Dynamics.from_file("JansenRit.yaml")
model.to_yaml(format="pyrates")

Export to BIDS

from tvbo import SimulationExperiment

exp = SimulationExperiment.from_file("experiment.yaml")
exp.to_bids("output/bids")

Export to OpenMINDS

from tvbo import SimulationExperiment

exp = SimulationExperiment.from_file("experiment.yaml")
exp.to_openminds("output/openminds.jsonld")