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Benchmark Problems for Dynamic Modeling of Intracellular Processes

A collection of ODE models with experimental data as benchmark problems in order to evaluate new and existing methodologies for data-based modeling. The introduction and analysis of the benchmark problem collection is published in Bioinformatics:

Hass, H., Loos, C., Raimúndez-Álvarez, E., Timmer, J., Hasenauer, J., Kreutz, C. Benchmark problems for dynamic modeling of intracellular processes, Bioinformatics, btz020.

The benchmark models were export from Data2Dynamics (https://github.com/Data2Dynamics/d2d), version of Aug 17th 2018, commit tag f27f9fd554fd23f9c048239172fafc6686a27fe0. Export can be repeated by compiling the respective model within the 'Example' folder, followed by call of arExportBenchmark

We provide descriptions about using the benchmark models in the Wiki (https://github.com/Benchmarking-Initiative/Benchmark-Models/wiki) in this github repository.

Contributions to the collection are very welcome. For this, please fork the repository, add your model and test your files with the provided functions, and start a pull request. We will then check your model and merge it into the collection. We are continuously working on the extension of the collection.

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A collection of ODE models with experimental data as benchmark problems in order to evaluate new and existing methodologies for data-based modelling

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