viva-tellurium

Process-bigraph wrapper for Tellurium / libroadrunner, exposing any SBML or Antimony kinetic model as a process-bigraph Process so it can be composed with other simulators in a bigraph document.

View Interactive Demo Report — Lotka-Volterra predator-prey, Elowitz-Leibler repressilator, and Gillespie stochastic dimerization with Plotly time series, phase portraits, reaction-rate charts, and bigraph architecture diagrams.

Installation

uv venv .venv && source .venv/bin/activate
uv pip install -e .

Quick Start

from process_bigraph import Composite, allocate_core, gather_emitter_results
from process_bigraph.emitter import RAMEmitter
from viva_tellurium import TelluriumProcess, make_tellurium_document

ANTIMONY = """
model decay
  S1 = 10; S2 = 0
  S1 -> S2; k*S1; k = 0.3
end
"""

core = allocate_core()
core.register_link('TelluriumProcess', TelluriumProcess)
core.register_link('ram-emitter', RAMEmitter)

doc = make_tellurium_document(model=ANTIMONY, interval=1.0)
sim = Composite({'state': doc}, core=core)
sim.run(10.0)

print(gather_emitter_results(sim)[('emitter',)][-1]['species'])

API

TelluriumProcess (Process)

Time-driven bridge wrapping a RoadRunner instance. Lazy init; each update() advances by interval.

Config (all optional, one of model/model_file required): model, model_format ('antimony'/'sbml'), model_file, integrator ('cvode'/'gillespie'), absolute_tolerance, relative_tolerance, seed, species_overrides, parameter_overrides, reset_on_init.

TelluriumStep (Step)

One-shot trajectory Step. Extra config: start_time, end_time, n_points. Outputs: time_series (list), species_trajectories (map[list]).

make_tellurium_document(...)

Ready-to-run composite document wiring a TelluriumProcess to a stores dict and a RAM emitter.

Demo & Tests

python demo/demo_report.py   # regenerates demo/report.html, opens in Safari
pytest tests/                # 17 offline tests