bngsim

Embeddable simulation engine for biochemical reaction networks.

bngsim is a high-performance C++ simulation kernel with Python bindings that replaces BioNetGen's subprocess-based run_network driver. The library also includes two network-free simulators. It loads BioNetGen .net and .xml files, runs deterministic and stochastic simulations in-process, and returns results as NumPy arrays — no file I/O, no subprocess spawning, no Perl dependency.

Highlights

Fast — in-process execution with the GIL released during simulation; thread-parallel batch sweeps
No toolchain at runtime — import bngsim; no compilers, no BNGPATH, no Perl
Modern SUNDIALS — v7.x CVODE/CVODES with re-entrant SUNContext
Multi-format — loads BioNetGen .net and .xml, Antimony (.ant), and SBML (.xml) models SBML Test Suite results, plus rule-based BNGL (.bngl) via BNG2.pl with bngsim[bngl]
Rich results — NumPy arrays, named observable access, pandas/xarray, HDF5 save/load
Standards interchange — .net/cBNGL ⇄ SBML and SED-ML + OMEX packaging, every conversion verified faithful
Gradient-ready — CVODES forward sensitivities, Fisher information
Validated — matches run_network to ~10⁻¹² (ODE) and cross-checked against RoadRunner and the SBML semantic test suite

Installation

pip install bngsim

Prebuilt wheels ship for common platforms; large models may benefit from the optional sparse (KLU) solver. See the installation guide for source builds, the KLU dependency, and optional extras.

Quickstart

import bngsim

# Load a model (BioNetGen .net/.xml, Antimony, or SBML) and run an ODE simulation
model = bngsim.Model.from_net("model.net")
sim = bngsim.Simulator(model, method="ode")
result = sim.run(t_span=(0.0, 100.0), n_points=1001)

result.time               # (1001,) NumPy array of time points
result.observables["A"]   # trajectory of observable "A"
result.dataframe          # pandas DataFrame of time + all observables

Other formats load through the sibling constructors — Model.from_sbml, Model.from_antimony, and their *_string variants.

Stochastic (method="ssa" / "psa"), network-free (NFsim / RuleMonkey), sensitivity analysis, steady-state, and events are all covered in the quickstart and user guide.

Documentation

Full documentation is hosted at bngsim.readthedocs.io and lives in docs/:

Installation · Quickstart
User guide — loading models, simulation, network-free, results, events, sensitivities, steady state, compiled RHS and its artifact cache, SBML/SED-ML/OMEX interchange
Reference — API · expression language
Architecture · benchmarks & validation

The package ships one console script, bngsim-cache (equivalently python -m bngsim.cache): it reports on and prunes the compiled-artifact cache that codegen fills, which nothing empties on its own. See managing the artifact cache.

Benchmarks & validation

bngsim beats run_network on every SSA/PSA model measured (geometric-mean speedup ~8.7× SSA), agrees with libRoadRunner across the full BioModels ODE corpus, and scores 1577 Match on the SBML semantic test suite with zero wrong-but-plausible answers. The numbers, methodology, and reproducible harnesses are in benchmarks & validation, with the committed cross-engine snapshots under parity_checks/. To re-run the suites and reproduce the numbers — the pinned-fetch model, corpus provenance, tool versions, and a no-download smoke path — see REPRODUCING.md. The supported-construct matrix is in SUPPORT_MATRIX.md.

Contributing

Build-from-source, test, and CI instructions are in CONTRIBUTING.md and the development docs. Release history is in CHANGELOG.md.

License

MIT. See LICENSE for the full text and the Triad/LANL copyright notice.

Third-party code and model/test-data corpora that BNGsim redistributes are listed, with their licenses, in NOTICE.

Citation

If you use bngsim in your research, please cite:

Preprint coming soon!

Acknowledgments

BNGsim was developed and validated against RoadRunner, AMICI, COPASI, BioNetGen, and the SBML/DSMTS test suites. See ACKNOWLEDGMENTS.md for citations.

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bngsim 0.14.0

bngsim

Highlights

Installation

Quickstart

Documentation

Benchmarks & validation

Contributing

License

Citation

Acknowledgments

Project links

Key dates

1 maintainer

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GitHub Statistics

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