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Michaelis-Menten: the compiled RHS has no sFree clamp, so it contradicts both the interpreted RHS and its own emitted Jacobian

bugSomething isn't workingSomething isn't working

Status: Open.

#93 In lanl/bngsim;

· wshlavacek opened on Jul 28, 2026

The sensitivity df/dp path has no #95 derivation budget, so a genome-scale Functional model can hang the build instead of declining

Status: Open.

#90 In lanl/bngsim;

· wshlavacek opened on Jul 28, 2026

MIR JIT: a Functional model with sensitivity_params fails to compile (c2mir rejects bngsim_codegen_output_sens)

bugSomething isn't workingSomething isn't working

Status: Open.

#85 In lanl/bngsim;

· wshlavacek opened on Jul 27, 2026

Forward-sensitivity integration exhausts mxstep at a fitted if(t>=...) switch time, killing gradient fits of models with moving discontinuities

Status: Open.

#82 In lanl/bngsim;

· wshlavacek opened on Jul 27, 2026

No way to carry forward sensitivities through a pre-equilibration into a scored parameter scan (blocks gradient fitting of pre-equilibrated dose-response)

Status: Open.

#81 In lanl/bngsim;

· wshlavacek opened on Jul 27, 2026

Model.set_param does not rebuild a species initial condition that references the parameter (species_ic_param_refs recorded, ic_state_dirty never set)

Status: Open.

#79 In lanl/bngsim;

· wshlavacek opened on Jul 27, 2026

steady_state(method="newton") can return the saddle on a bistable model and report converged

Status: Open.

#78 In lanl/bngsim;

· wshlavacek opened on Jul 27, 2026

Steady-state FD ∂f/∂p uses an absolute step floor, so a small rate constant is probed at 1500% (15.9x error on before_bunching)

Status: Open.

#76 In lanl/bngsim;

· wshlavacek opened on Jul 27, 2026

Steady-state d(func)/dp still finite-differences: route it through the compiled bngsim_codegen_output_sens

enhancementNew feature or requestNew feature or request

Status: Open.

#75 In lanl/bngsim;

· wshlavacek opened on Jul 27, 2026

steady_state(): no way to exclude write-only accumulator species from the convergence test

Status: Open.

#74 In lanl/bngsim;

· wshlavacek opened on Jul 27, 2026

Analytic sensitivity RHS for Functional rate laws (df/dp), so forward sensitivity leaves the CVODES difference-quotient path

enhancementNew feature or requestNew feature or request

Status: Open.

#55 In lanl/bngsim;

· wshlavacek opened on Jul 26, 2026

Forward sensitivity w.r.t. a switch time encoded as an SBML event (event-time sensitivity dt*/dp != 0)

enhancementNew feature or requestNew feature or request

Status: Open.

#49 In lanl/bngsim;

· wshlavacek opened on Jul 25, 2026