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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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Multiple models in publication #27

Open yannikschaelte opened 5 years ago

yannikschaelte commented 5 years ago

@LeonardSchmiester @PhilippStaedter please add details.

We should discuss what to do when we have multiple models in one publication. Say all use the same data and experimental conditions. So the models describe the same stuff, but maybe in more or less detail or alternative networks.

One could put all such models in the same folder and just enumerate / make the names unique. Alternative suggestions?

yannikschaelte commented 5 years ago

see also LeonardSchmiester/Benchmark-Models#43

LeonardSchmiester commented 5 years ago

In these cases parameters are seperated individually for every model right? But we also have cases, with different models but all in one parameter estimation (e.g. Becker)?

Maybe use subfolders for individual optimizations within the same publication?

yannikschaelte commented 5 years ago

good point. I guess in this case some of the parameters coincide, while others are model specific. thus one could do subfolders, or just separate folders on the global level, à la Kouril2021Model1, 2.

LeonardSchmiester commented 5 years ago

In favor of subfolders as it might get crowded for publications with a lot of models. Might also be easier, if you want to specify model selection.

yannikschaelte commented 5 years ago

yeah sounds about right. then we would have different cases in one AuthorYEAR folder: When all parameters coincide and we just have different models, we have all in one folder level, and when it's different parameterization problems, then we have subfolders. would make sense.