PEtab
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PEtab-dev
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
PEtab extensions were introduced in #537. We should be able to distinguish there between optional extensions and required extensions, i.e. those that modify the parameter estimation problem as such, and...
I.e. on https://petab.readthedocs.io/en/latest/documentation_data_format.html#condition-table The `NaN` case is listed for `speciesID` but not for `compartmentID` and `parameterID`. It is unclear what happens here, but I assume the initial values of the...
Hi all, in the condition table it should be clarified what happens if a parameter ID is provided for a parameter ID value: https://petab.readthedocs.io/en/latest/documentation_data_format.html#condition-table `${parameterId}` The values will override any...
**Which problem would you like to address? Please describe.** I often have simulation experiments where I not only have to change initial values but also values after a certain time....
**Which problem would you like to address? Please describe.** Parameters in SBML can be either `constant=True` or `constant=False`. In case of `constant=False` the parameter can be either governed by an...
At the moment, local parameters cannot be directly estimated within PEtab, as this requires unique parameter Ids. One would need to make them global parameters. Maybe instead we could use...
The current specifications describe re-initialization for species listed in the condition table. However, as noticed by @fbergmann, it is not clear how parameters that are targets of (implicitly or explicitly)...
Would be great if PEtab would be usable with non-SBML models. Formats to consider would include e.g. cellML, bngl, pysb, .... Personally interested in pysb support. Will be a significant...
so far we only allow for uniform, however, we should in my opinion distinguish between uniform and logUniform. in most cases we use actually log-uniform as we consider a uniform...
**Which problem would you like to address? Please describe.** Linting complains about invalid condition IDs. I believe the error is due to the fact that the condition id is numeric...
