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Benchmarking-Initiative / Benchmark-Models-PEtab

A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling
BSD 3-Clause "New" or "Revised" License
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Add priors to Schwen Model, fixes #139 #141

Closed FFroehlich closed 2 years ago

FFroehlich commented 2 years ago

Adds missing parameter priors to the schwen model

dilpath commented 2 years ago

Looks fine to me, but difficult to review, as I'm not sure where to find the source of this information (e.g. can't see it in a general info file [1], or in the original publication).

[1] https://github.com/LeonardSchmiester/Benchmark-Models/blob/hackathon/Benchmark-Models/Schwen_PONE2014/General_info.xlsx

Do you know where the parameter vector in this table is from (publication or optimization with our tools)? If the latter, then it should be updated to match the best result obtained with the updated problem (and then, simulation data should be updated as well).

FFroehlich commented 2 years ago

Looks fine to me, but difficult to review, as I'm not sure where to find the source of this information (e.g. can't see it in a general info file [1], or in the original publication).

Priors were added based on d2d Example implementation. I am not sure whether there is a published study describing the calibration of the model. The d2d Readme states that it is a combination of data from the original publication and additional data (which is partly available from Clemens Kreutz thesis).

[1] https://github.com/LeonardSchmiester/Benchmark-Models/blob/hackathon/Benchmark-Models/Schwen_PONE2014/General_info.xlsx

Do you know where the parameter vector in this table is from (publication or optimization with our tools)? If the latter, then it should be updated to match the best result obtained with the updated problem (and then, simulation data should be updated as well).

As far as I can tell the nominal parameter values are exactly the same as in [1] (and generally think it would be helpful to add a text file to every benchmark containing this information).

dweindl commented 2 years ago

and generally think it would be helpful to add a text file to every benchmark containing this information

We could consider adding some annotations to the yaml files. (Could also put it into the SBML model, but not sure if that's best place to describe the data.)

dilpath commented 2 years ago

and generally think it would be helpful to add a text file to every benchmark containing this information

We could consider adding some annotations to the yaml files. (Could also put it into the SBML model, but not sure if that's best place to describe the data.)

The result format for PEtab would be sufficient when it's ready