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Overview table: link to respective directory (#148)
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‎Benchmark-Models/model_info.py‎

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pd.options.display.width = 0
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if markdown:
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df.rename(index=lambda x: f"[{x}](Benchmark-Models/{x}/)",
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inplace=True)
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df.index.rename(markdown_columns[index_column], inplace=True)
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df.rename(columns=markdown_columns, inplace=True)
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print(df.to_markdown())

‎README.md‎

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@@ -4,37 +4,37 @@ A collection of mathematical models with experimental data in the [PEtab](https:
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Contributions to the collection are very welcome. For this, please create a new branch, 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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## Overview
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| Model ID | Conditions | Estimated Parameters | Events | Measurements | Observables | Species |
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|:------------------------------------|-------------:|-----------------------:|---------:|---------------:|--------------:|----------:|
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| Alkan_SciSignal2018 | 73 | 56 | 0 | 1733 | 12 | 36 |
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| Bachmann_MSB2011 | 36 | 113 | 0 | 541 | 20 | 25 |
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| Beer_MolBioSystems2014 | 19 | 72 | 0 | 27132 | 2 | 4 |
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| Bertozzi_PNAS2020 | 2 | 3 | 0 | 138 | 1 | 3 |
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| Blasi_CellSystems2016 | 1 | 9 | 0 | 288 | 16 | 16 |
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| Boehm_JProteomeRes2014 | 1 | 9 | 0 | 48 | 3 | 8 |
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| Borghans_BiophysChem1997 | 1 | 23 | 0 | 111 | 1 | 3 |
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| Brannmark_JBC2010 | 8 | 22 | 0 | 43 | 3 | 9 |
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| Bruno_JExpBot2016 | 6 | 13 | 0 | 77 | 5 | 7 |
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| Chen_MSB2009 | 4 | 155 | 0 | 120 | 3 | 500 |
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| Crauste_CellSystems2017 | 1 | 12 | 0 | 21 | 4 | 5 |
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| Elowitz_Nature2000 | 1 | 21 | 0 | 58 | 1 | 8 |
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| Fiedler_BMC2016 | 3 | 22 | 0 | 72 | 2 | 6 |
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| Fujita_SciSignal2010 | 6 | 19 | 0 | 144 | 3 | 9 |
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| Giordano_Nature2020 | 1 | 50 | 0 | 313 | 7 | 13 |
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| Isensee_JCB2018 | 120 | 46 | 0 | 687 | 6 | 25 |
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| Laske_PLOSComputBiol2019 | 3 | 13 | 0 | 42 | 13 | 41 |
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| Lucarelli_CellSystems2018 | 16 | 84 | 0 | 1755 | 43 | 33 |
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| Okuonghae_ChaosSolitonsFractals2020 | 1 | 16 | 0 | 92 | 2 | 9 |
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| Oliveira_NatCommun2021 | 1 | 12 | 0 | 120 | 2 | 9 |
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| Perelson_Science1996 | 1 | 3 | 0 | 16 | 1 | 4 |
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| Rahman_MBS2016 | 1 | 9 | 0 | 23 | 1 | 7 |
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| Raimundez_PCB2020 | 170 | 136 | 0 | 627 | 79 | 22 |
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| SalazarCavazos_MBoC2020 | 4 | 6 | 0 | 18 | 3 | 75 |
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| Schwen_PONE2014 | 19 | 30 | 0 | 286 | 4 | 11 |
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| Sneyd_PNAS2002 | 9 | 15 | 0 | 135 | 1 | 6 |
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| Weber_BMC2015 | 2 | 39 | 0 | 135 | 8 | 7 |
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| Zhao_QuantBiol2020 | 7 | 28 | 0 | 82 | 1 | 5 |
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| Zheng_PNAS2012 | 1 | 46 | 0 | 60 | 15 | 15 |
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| Model ID | Conditions | Estimated Parameters | Events | Measurements | Observables | Species |
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|:---------------------------------------------------------------------------------------------|-------------:|-----------------------:|---------:|---------------:|--------------:|----------:|
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| [Alkan_SciSignal2018](Benchmark-Models/Alkan_SciSignal2018/) | 73 | 56 | 0 | 1733 | 12 | 36 |
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| [Bachmann_MSB2011](Benchmark-Models/Bachmann_MSB2011/) | 36 | 113 | 0 | 541 | 20 | 25 |
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| [Beer_MolBioSystems2014](Benchmark-Models/Beer_MolBioSystems2014/) | 19 | 72 | 0 | 27132 | 2 | 4 |
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| [Bertozzi_PNAS2020](Benchmark-Models/Bertozzi_PNAS2020/) | 2 | 3 | 0 | 138 | 1 | 3 |
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| [Blasi_CellSystems2016](Benchmark-Models/Blasi_CellSystems2016/) | 1 | 9 | 0 | 252 | 15 | 16 |
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| [Boehm_JProteomeRes2014](Benchmark-Models/Boehm_JProteomeRes2014/) | 1 | 9 | 0 | 48 | 3 | 8 |
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| [Borghans_BiophysChem1997](Benchmark-Models/Borghans_BiophysChem1997/) | 1 | 23 | 0 | 111 | 1 | 3 |
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| [Brannmark_JBC2010](Benchmark-Models/Brannmark_JBC2010/) | 8 | 22 | 0 | 43 | 3 | 9 |
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| [Bruno_JExpBot2016](Benchmark-Models/Bruno_JExpBot2016/) | 6 | 13 | 0 | 77 | 5 | 7 |
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| [Chen_MSB2009](Benchmark-Models/Chen_MSB2009/) | 4 | 155 | 0 | 120 | 3 | 500 |
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| [Crauste_CellSystems2017](Benchmark-Models/Crauste_CellSystems2017/) | 1 | 12 | 0 | 21 | 4 | 5 |
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| [Elowitz_Nature2000](Benchmark-Models/Elowitz_Nature2000/) | 1 | 21 | 0 | 58 | 1 | 8 |
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| [Fiedler_BMC2016](Benchmark-Models/Fiedler_BMC2016/) | 3 | 22 | 0 | 72 | 2 | 6 |
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| [Fujita_SciSignal2010](Benchmark-Models/Fujita_SciSignal2010/) | 6 | 19 | 0 | 144 | 3 | 9 |
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| [Giordano_Nature2020](Benchmark-Models/Giordano_Nature2020/) | 1 | 50 | 0 | 313 | 7 | 13 |
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| [Isensee_JCB2018](Benchmark-Models/Isensee_JCB2018/) | 123 | 46 | 0 | 687 | 3 | 25 |
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| [Laske_PLOSComputBiol2019](Benchmark-Models/Laske_PLOSComputBiol2019/) | 3 | 13 | 0 | 42 | 13 | 41 |
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| [Lucarelli_CellSystems2018](Benchmark-Models/Lucarelli_CellSystems2018/) | 16 | 84 | 0 | 1755 | 65 | 33 |
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| [Okuonghae_ChaosSolitonsFractals2020](Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/) | 1 | 16 | 0 | 92 | 2 | 9 |
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| [Oliveira_NatCommun2021](Benchmark-Models/Oliveira_NatCommun2021/) | 1 | 12 | 0 | 120 | 2 | 9 |
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| [Perelson_Science1996](Benchmark-Models/Perelson_Science1996/) | 1 | 3 | 0 | 16 | 1 | 4 |
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| [Rahman_MBS2016](Benchmark-Models/Rahman_MBS2016/) | 1 | 9 | 0 | 23 | 1 | 7 |
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| [Raimundez_PCB2020](Benchmark-Models/Raimundez_PCB2020/) | 170 | 136 | 0 | 627 | 79 | 22 |
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| [SalazarCavazos_MBoC2020](Benchmark-Models/SalazarCavazos_MBoC2020/) | 4 | 6 | 0 | 18 | 3 | 75 |
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| [Schwen_PONE2014](Benchmark-Models/Schwen_PONE2014/) | 19 | 30 | 0 | 286 | 4 | 11 |
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| [Sneyd_PNAS2002](Benchmark-Models/Sneyd_PNAS2002/) | 9 | 15 | 0 | 135 | 1 | 6 |
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| [Weber_BMC2015](Benchmark-Models/Weber_BMC2015/) | 2 | 36 | 0 | 135 | 8 | 7 |
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| [Zhao_QuantBiol2020](Benchmark-Models/Zhao_QuantBiol2020/) | 7 | 28 | 0 | 82 | 1 | 5 |
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| [Zheng_PNAS2012](Benchmark-Models/Zheng_PNAS2012/) | 1 | 46 | 0 | 60 | 15 | 15 |
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## License
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