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PEtab-dev / PEtab

PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
https://petab.readthedocs.io
MIT License
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Global vs local SBML parameters #570

Closed leodarrigade closed 8 months ago

leodarrigade commented 8 months ago

Which problem would you like to address? Please describe. From my experience, PETab does not support SBML local parameters (for details on local vs global parameters, see for example p.53 of SBML 2 specification here).

Describe the solution you would like It would be nice if the PEtab documentation could mention that all parameters must be declared globally.

matthiaskoenig commented 8 months ago

Just to comment for anybody wanting to use local parameters. You can easily convert local into global parameters via the libsbml local to global converter: https://sbml.org/software/libsbml/5.18.0/docs/formatted/cpp-api/class_s_b_m_l_local_parameter_converter.html

This is a simple SBML converter you would run over the SBML model to get a new SBML model with global instead of local parameters.