Handling of events on parameters that are subject to condition specific values.

[leodarrigade]

Handling of events on parameters that are subject to condition specific values.

[dweindl]

When I import this model with my Petab problem using pyPESTO PEtab importer and compile to AMICI, it defines L_0 as a StateId of the AMICI model

Hi, that is correct / intended. In AMICI, parameters are constant (unlike in SBML). Any target of an event assignment, assignment rule, or rate rule will be a state variable in the AMICI model.

[leodarrigade]

@dweindl Thanks for the precision.

@dilpath Thank you, it is working fine with your solution. I think it could be useful to include in the PEtab documentation that parameters in the condition table cannot change values over time and be subject of event.

[dilpath]

Hi,
I would suggest rewriting your PEtab problem to remove L_0 from the condition table, which should only include values/variables that are constant throughout time.

Instead, rename L_0 to L_0_conc in your condition table, and add an initialAssignmentRule in your SBML model that sets L_0(t=0) = L_0_conc. You will need to add an SBML parameter for L_0_conc. Let me know if the issue persists.

[dilpath]

Great!

Agreed, currently there is ambiguity in the current version of the spec, and behavior could be tool-specific. The spec will be updated to specify how to handle "time-dependent" parameters, in the next version of PEtab. The issue is tracked at #513