Comments (4)
When I import this model with my Petab problem using
pyPESTO
PEtab importer and compile to AMICI, it definesL_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.
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@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.
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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.
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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
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Related Issues (20)
- Clarification of condition table what happens if NaN is provided as a value
- Allow using observables in noiseFormula HOT 2
- Extensions: required/optional HOT 2
- Bounds documentation needs clairification HOT 2
- Specification of model time in observables file unclear HOT 2
- No Noise HOT 13
- Clarification/specification of order of condition changes required HOT 5
- Fix sphinx doc
- Add tool using PEtab
- Time-dependent changes in component values HOT 6
- PEtab extension for NLME HOT 15
- Update PETab to be model format agnostic HOT 4
- Allow species in `yValues` of the visualization table HOT 2
- Global vs local SBML parameters HOT 1
- No reference to paper in repository HOT 1
- Update editorial board page
- Allow formulas in condition table HOT 1
- Use somewhat normalized "experiments" table instead of conditions/timecourses HOT 16
- Long formats for conditions and experiments (timecourses) HOT 3
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