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Fixed PEtab parameters are treated as estimated if they don't exist in the SBML model #2184

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dilpath opened this issue Oct 27, 2023 · 0 comments
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enhancement PEtab PEtab-import related

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@dilpath
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dilpath commented Oct 27, 2023

What did you expect to happen?
A PEtab parameter with estimate=0 is treated as a fixed parameter during import.

The parameter is defined in the PEtab parameters table, then the initial condition species(t=0) = parameter is specified in the PEtab conditions table. The parameter does not exist in the SBML model.

What has happened instead?
The parameter is treated as estimated.
I also see the warning

- amici.petab_import - WARNING - Column 'initial_Susceptible' used in condition table but not entity with the corresponding ID exists. Ignoring.

To Reproduce
Compile the attached PEtab problem twice, with initial_Susceptible set to estimate=0 the first time, and estimate=1 the second time. The generated C++ are identical (the parameter isn't fixed in the first case).

AMICI version and system environment

  • OS and version: Ubuntu 22.04
  • AMICI interface: Python 3.10.12
  • AMICI version: after v0.19.0, c038ff5
  • Additional information: GNU 10.5.0

Bertozzi_PNAS2020.zip

@dilpath dilpath added the new Newly created label Oct 27, 2023
@dweindl dweindl added enhancement PEtab PEtab-import related and removed new Newly created labels Nov 29, 2023
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Labels
enhancement PEtab PEtab-import related
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