PyRates Integration

Bidirectional interoperability with PyRates dynamical systems toolbox

Overview

PyRates is a Python framework for numerical simulation and analysis of dynamical systems. TVBO provides full round-trip interoperability:

Direction	Method	Use Case
TVBO → PyRates	`model.to_yaml(format="pyrates")`	Use PyRates analysis tools
PyRates → TVBO	`Dynamics.from_pyrates()`	Use TVBO simulation/export

Tutorials

Tutorial	Description
PyRates Overview	Basic round-trip interoperability
Analysis	Time series analysis and visualization
Bifurcation	Bifurcation diagram analysis
Heterogeneous Networks	Spatially varying parameters

Quick Start

Export TVBO Model to PyRates

from tvbo import Dynamics

# Load a TVBO model
model = Dynamics.from_file("database/models/JansenRit.yaml")

# Export to PyRates YAML format
model.to_yaml(format="pyrates", path="jr_pyrates.yaml")

Import PyRates Model to TVBO

from tvbo import Dynamics

# Import from PyRates YAML
model = Dynamics.from_pyrates("pyrates_model.yaml")

# Use with TVBO simulation
print(model.equations)

Feature Mapping

Feature	TVBO	PyRates
Differential equations	`equation.rhs` attribute	`var' = rhs` syntax
Initial values	`initial_value` attribute	`variable(value)`
Parameters	`Parameter` objects	Numeric values
State variables	`StateVariable` objects	Variables in equations
Coupling	`CouplingFunction`	Operator connections

Use Cases

Bifurcation Analysis

PyRates provides tools for computing bifurcation diagrams. Export your TVBO model to analyze stability:

from tvbo import Dynamics

model = Dynamics.from_file("JansenRit.yaml")
model.to_yaml(format="pyrates", path="jr.yaml")

# Use PyRates continuation tools
from pyrates.utility.bifurcation import PyCoBi
# ... bifurcation analysis

Parameter Sweeps

Run systematic parameter explorations:

from tvbo import Dynamics

model = Dynamics.from_file("WilsonCowan.yaml")
pyrates_yaml = model.to_yaml(format="pyrates")

# Use PyRates parameter sweep
from pyrates import grid_search
# ... parameter sweep

See Also