lanl/PyBNF

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An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuristic optimization algorithms, and an adaptive Markov chain Monte Carlo (MCMC) sampling algorithm.

Stars: 25
Forks: 25
Open beginner issues: 0
Indexed issues: 14
Avg merge: 2h 6m
Merged PRs (30d): 95

Dominant language: Python
License: No license data
Last GitHub push: Sep 19, 2026
Latest indexed: Sep 18, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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13 open issues indexed

config_keys.rst has fallen behind the grammar: 64 of 200 accepted keys have no entry, and config.rst still presents it as the complete list Open

Difficulty 3/5 1-2 days Newbie friendliness 74/100

lanl/PyBNF#765 · Opened Sep 18, 2026
adaptive MCMC carries a rolling-buffer design that was reduced to a single slot: arr_length is a constant 1, factor is never incremented, and five conditions are always true Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

lanl/PyBNF#764 · Opened Sep 18, 2026
PSO collision tie-break can loop forever: a fixed 1e-6 perturbation is below one ULP for a linear parameter above ~1e10 Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 78/100

lanl/PyBNF#721 · Opened Sep 16, 2026
Constraint gradient/Hessian use the raw sensitivity tensor while the penalty is scored on the normalized column, so the ADR-0053 chain rule is dropped Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 55/100

lanl/PyBNF#718 · 1 comment · Opened Sep 16, 2026
A positive-support prior family gets no wall at its support floor, so negative parameter values are accepted, simulated and scored Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 48/100

lanl/PyBNF#711 · Opened Sep 16, 2026
Parallel tempering rewinds the iteration counter after a replica exchange, so iteration exchange_every+1 is processed twice and can write two samples.txt rows for one iteration Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 82/100

lanl/PyBNF#710 · Opened Sep 16, 2026
Shrink the differential evolution population over the run, floored at the processor count (L-SHADE's population-size reduction) Open

enhancement gated

Difficulty 5/5 Over a week Newbie friendliness 35/100

lanl/PyBNF#699 · Opened Sep 14, 2026
Port the BNGL parameter-expression evaluator to libpetab-python's BnglModel, then delete the staging copy Open

low priority

Difficulty 5/5 Over a week Newbie friendliness 35/100

lanl/PyBNF#681 · 1 comment · Opened Sep 10, 2026
Experimental design should be able to average over an ensemble, not only compute at the best fit Open

exploratory

Difficulty 5/5 Over a week Newbie friendliness 25/100

lanl/PyBNF#669 · Opened Aug 25, 2026
Investigate synthetic likelihood as a principled objective for stochastic models Open

exploratory question

Difficulty 5/5 Over a week Newbie friendliness 38/100

lanl/PyBNF#665 · Opened Aug 25, 2026
Stop hopeless starts early in a multi-start fit instead of running every one to completion Open

enhancement exploratory

Difficulty 5/5 Over a week Newbie friendliness 45/100

lanl/PyBNF#662 · Opened Aug 25, 2026
Investigate: ADR-0059 rejects simulator-path HMC on an unmeasured cost model ("~1x a solve per leapfrog") — measure it against the bngsim JAX bridge, and settle it with numbers either way Open

exploratory

Difficulty 5/5 Over a week Newbie friendliness 35/100

lanl/PyBNF#576 · Opened Aug 14, 2026
Structural identifiability as a pre-fit gate: decide symbolically whether a parameter can EVER be identified from these observables, instead of inferring it numerically from a flat profile Open

exploratory

Difficulty 5/5 Over a week Newbie friendliness 35/100

lanl/PyBNF#575 · Opened Aug 14, 2026

lanl/PyBNF

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