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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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Finish Raia model #58

Open LeonardSchmiester opened 4 years ago

LeonardSchmiester commented 4 years ago

Cannot validate the model with AMICI as the noise model is not supported yet.

dweindl commented 4 years ago

This was about state-dependent noise, right? (https://github.com/ICB-DCM/AMICI/issues/609)

LeonardSchmiester commented 4 years ago

It's observable-dependent noise I think

jvanhoefer commented 2 years ago

@LeonardSchmiester Would you have the PEtab tables around (i.e. at least the data)? I would be interested in using the raw data and would not need the model itself

dweindl commented 2 years ago

Here? https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/tree/model_Raia_CancerResearch2011/Benchmark-Models/Raia_CancerResearch2011

jvanhoefer commented 2 years ago

Ah, thank you, did not have a look at all the branches :)

dweindl commented 2 years ago

Cannot validate the model with AMICI as the noise model is not supported yet.

Supported by https://github.com/AMICI-dev/AMICI/pull/1692, in case somebody feels like finishing this one.

m-philipps commented 1 year ago

I finished it and also did optimization again, ended up with a different optimum than the one from the matlab BenchmarkCollection but the fit is slightly better for two and worse for one other observable so I left the nominalParameters that correspond to the other BenchmarkCollection.