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When having dedicated writer functions such as `petab.conditions.write_condition_df` etc, I would actually expect that they perform some kind of sanity check on the output. Having pretty bare wrappers…
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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, a…
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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 a unique na…
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**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…
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The format documentation often refers to "optimization", while "estimation" would probably be more general. PEtab is designed to also work with non-optimization based methods such as sampling, right?
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Hi, I have a following setup:
- A single model and two experimental conditions - healthy (H) and patient (P)
- The model has 92 parameters and one of them is fixed. And other two are shared among H …
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**Is your feature request related to a problem? Please describe.**
Sometimes when parameter estimating ODE-models, or when importing a model in the SBML format, event time-points are dependent on m…
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Have there been any plans for a command-line interface for pypesto, e.g. `pypesto-optimize --problem=petab:problem.yaml --config=optimization_options.yaml --output=hdf5:results.h5`? I'd find that conv…
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e.g. the Chen model has specified noiseParameters in the measurement data, and no replicate measurement data is available. (so, standard deviation cant be calculated from replicates)
For plotting the…
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If there is only a single data point associated with a scaling parameter, drop that data point and scaling parameter (and report).