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PEtab import: observableTransformation=log10 dropped in v1->v2 conversion → log10 observable imports as linear gaussian

Status: Open.

#499 In lanl/PyBNF;

· wshlavacek opened on Jul 18, 2026

Multi-start / restart for non-gradient optimizers (CMA-ES IPOP/BIPOP; generalize #386 beyond the gradient methods)

Status: Open.

#498 In lanl/PyBNF;

· wshlavacek opened on Jul 18, 2026

PEtab import: condition targetValue that is a parameter/expression (per-condition estimated IC) is rejected

enhancementNew feature or requestNew feature or request

Status: Open.

#496 In lanl/PyBNF;

· wshlavacek opened on Jul 18, 2026

PEtab import: observableParameters/noiseParameters placeholder mapping incomplete (scaling, per-obs sigma, affine noise)

bugSomething isn't workingSomething isn't working

enhancementNew feature or requestNew feature or request

Status: Open.

#495 In lanl/PyBNF;

· wshlavacek opened on Jul 18, 2026

PEtab import: ragged replicates (different observables per replicateId) crash replicate-.exp reconstruction

bugSomething isn't workingSomething isn't working

enhancementNew feature or requestNew feature or request

Status: Open.

#494 In lanl/PyBNF;

· wshlavacek opened on Jul 18, 2026

PEtab SBML import: observableFormula referencing an SBML assignmentRule variable is rejected as 'not a model entity'

bugSomething isn't workingSomething isn't working

enhancementNew feature or requestNew feature or request

Status: Open.

#493 In lanl/PyBNF;

· wshlavacek opened on Jul 18, 2026

Gradient fit aborts with AttributeError: NoneType.items when a simulation fails mid-fit (gradient_at doesn't guard res.simdata is None)

bugSomething isn't workingSomething isn't working

Status: Open.

#492 In lanl/PyBNF;

· wshlavacek opened on Jul 18, 2026

gntr assembles forward sensitivities twice per evaluation — DRY the gradient + Fisher-Hessian assemblers into one pass

Status: Open.

#488 In lanl/PyBNF;

· wshlavacek opened on Jul 17, 2026

Edition-2 one-model + condition: simulates the full {action}×{mutant} cross-product but scores only the diagonal — simulate only scored (action, condition) pairs

Status: Open.

#484 In lanl/PyBNF;

· wshlavacek opened on Jul 17, 2026

Add a small SSA end-to-end example to examples/real-world/ (fceri is cluster-scale)

Status: Open.

#472 In lanl/PyBNF;

· wshlavacek opened on Jul 11, 2026

Replace fixed 10-second waits during distributed-cluster startup and shutdown with real readiness checks

Status: Open.

#398 In lanl/PyBNF;

· wshlavacek opened on May 31, 2026