From 70f812e3c8f3e33e579a9a32e0191bcdca64555c Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 12 Oct 2026 23:29:11 +0200 Subject: [PATCH] Fix SBML4Humans URLs sbml4humans.de no longer provides the `/model_url` route; reports are now served from `/report?url=...`. Update the URL generation in `bmp-create-overview` and the README overview table accordingly. Co-Authored-By: Claude Opus 5.5 --- README.md | 74 +++++++++---------- src/python/benchmark_models_petab/overview.py | 2 +- 2 files changed, 38 insertions(+), 38 deletions(-) diff --git a/README.md b/README.md index ffa5ca4..48ad16e 100644 --- a/README.md +++ b/README.md @@ -12,43 +12,43 @@ A sortable version of the table is available [here](https://benchmarking-initiative.github.io/Benchmark-Models-PEtab/). -| PEtab Problem ID | Conditions | Estimated Parameters | Events | Possible Discontinuities | Preequilibration | Postequilibration | Measurements | Observables | Noise distribution(s) | Objective prior distribution(s) | Species | References | SBML4Humans | -|:----------------------------------------------------------------------------------------|-------------:|-----------------------:|---------:|:---------------------------|-------------------:|--------------------:|---------------:|--------------:|:------------------------|:----------------------------------|----------:|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| [Alkan_SciSignal2018](problems/Alkan_SciSignal2018/v1/) | 73 | 44 | 0 | ✓ | 0 | 0 | 1733 | 12 | normal | | 36 | [\[1\]](http://identifiers.org/doi/10.1126/scisignal.aat0229) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Alkan_SciSignal2018/v1/model.xml) | -| [Armistead_CellDeathDis2024](problems/Armistead_CellDeathDis2024/v1/) | 2 | 14 | 0 | | 0 | 0 | 58 | 4 | normal | | 4 | [\[1\]](https://doi.org/10.1038/s41419-024-07134-2) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Armistead_CellDeathDis2024/v1/model.xml) | -| [Bachmann_MSB2011](problems/Bachmann_MSB2011/v1/) | 36 | 113 | 0 | | 0 | 0 | 541 | 20 | normal; log10-normal | parameterScaleNormal | 25 | [\[1\]](http://identifiers.org/doi/10.1038/msb.2011.50) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Bachmann_MSB2011/v1/model.xml) | -| [Beer_MolBioSystems2014](problems/Beer_MolBioSystems2014/v1/) | 19 | 72 | 0 | ✓ | 0 | 0 | 27132 | 2 | normal | | 4 | [\[1\]](http://identifiers.org/doi/10.1039/c3mb70594c) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Beer_MolBioSystems2014/v1/model.xml) | -| [Bertozzi_PNAS2020](problems/Bertozzi_PNAS2020/v1/) | 2 | 8 | 0 | | 0 | 0 | 22 | 2 | normal | | 3 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.2006520117) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Bertozzi_PNAS2020/v1/model.xml) | -| [Blasi_CellSystems2016](problems/Blasi_CellSystems2016/v1/) | 1 | 9 | 0 | | 0 | 1 | 252 | 15 | log-normal | | 16 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2016.01.002) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Blasi_CellSystems2016/v1/model.xml) | -| [Boehm_JProteomeRes2014](problems/Boehm_JProteomeRes2014/v1/) | 1 | 9 | 0 | | 0 | 0 | 48 | 3 | normal | | 8 | [\[1\]](http://identifiers.org/doi/10.1021/pr5006923) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Boehm_JProteomeRes2014/v1/model.xml) | -| [Borghans_BiophysChem1997](problems/Borghans_BiophysChem1997/v1/) | 1 | 23 | 0 | | 0 | 0 | 111 | 1 | log10-normal | | 3 | [\[1\]](http://identifiers.org/doi/10.1016/s0301-4622(97)00010-0) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Borghans_BiophysChem1997/v1/model.xml) | -| [Brannmark_JBC2010](problems/Brannmark_JBC2010/v1/) | 8 | 22 | 0 | ✓ | 1 | 0 | 43 | 3 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1074/jbc.M110.106849) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Brannmark_JBC2010/v1/model.xml) | -| [Bruno_JExpBot2016](problems/Bruno_JExpBot2016/v1/) | 6 | 13 | 0 | | 0 | 0 | 77 | 5 | normal | | 7 | [\[1\]](http://identifiers.org/doi/10.1093/jxb/erw356) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Bruno_JExpBot2016/v1/model.xml) | -| [Chen_MSB2009](problems/Chen_MSB2009/v1/) | 4 | 155 | 0 | ✓ | 0 | 0 | 120 | 3 | normal | | 500 | [\[1\]](http://identifiers.org/doi/10.1038/msb.2008.74) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Chen_MSB2009/v1/model.xml) | -| [Crauste_CellSystems2017](problems/Crauste_CellSystems2017/v1/) | 1 | 12 | 0 | | 0 | 0 | 21 | 4 | normal | | 5 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.01.014) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Crauste_CellSystems2017/v1/model.xml) | -| [Elowitz_Nature2000](problems/Elowitz_Nature2000/v1/) | 1 | 21 | 0 | | 0 | 0 | 58 | 1 | log10-normal | | 8 | [\[1\]](http://identifiers.org/doi/10.1038/35002125) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Elowitz_Nature2000/v1/model.xml) | -| [Fiedler_BMCSystBiol2016](problems/Fiedler_BMCSystBiol2016/v1/) | 3 | 22 | 0 | | 0 | 0 | 72 | 2 | normal | | 6 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-016-0319-7) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Fiedler_BMCSystBiol2016/v1/model.xml) | -| [Froehlich_CellSystems2018](problems/Froehlich_CellSystems2018/v1/) | 9169 | 4231 | 0 | | 0 | 9169 | 9169 | 1 | normal | | 1396 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2018.10.013) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Froehlich_CellSystems2018/v1/model.xml) | -| [Fujita_SciSignal2010](problems/Fujita_SciSignal2010/v1/) | 6 | 19 | 0 | ✓ | 0 | 0 | 144 | 3 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1126/scisignal.2000810) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Fujita_SciSignal2010/v1/model.xml) | -| [Giordano_Nature2020](problems/Giordano_Nature2020/v1/) | 1 | 50 | 0 | ✓ | 0 | 0 | 313 | 7 | normal | | 13 | [\[1\]](http://identifiers.org/pubmed/32322102) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Giordano_Nature2020/v1/model.xml) | -| [Isensee_JCB2018](problems/Isensee_JCB2018/v1/) | 123 | 46 | 0 | ✓ | 1 | 0 | 687 | 3 | normal | parameterScaleNormal | 25 | [\[1\]](http://identifiers.org/doi/10.1083/jcb.201708053) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Isensee_JCB2018/v1/model.xml) | -| [Lang_PLOSComputBiol2024](problems/Lang_PLOSComputBiol2024/v1/) | 1 | 294 | 0 | | 0 | 0 | 9600 | 16 | normal | laplace; uniform | 124 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pcbi.1011151) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Lang_PLOSComputBiol2024/v1/model.xml) | -| [Laske_PLOSComputBiol2019](problems/Laske_PLOSComputBiol2019/v1/) | 3 | 13 | 0 | | 0 | 0 | 42 | 13 | normal; log-normal | | 41 | [\[1\]](http://identifiers.org/biomodels.db/BIOMD0000000463) [\[2\]](http://identifiers.org/biomodels.db/MODEL1307270000) [\[3\]](http://identifiers.org/doi/10.1371/journal.pcbi.1006944) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Laske_PLOSComputBiol2019/v1/model.xml) | -| [Liu_IFACPapersOnLine2025](problems/Liu_IFACPapersOnLine2025/v1/) | 2 | 9 | 1 | ✓ | 0 | 0 | 100 | 1 | normal | | 0 | [\[1\]](http://identifiers.org/doi/10.1016/j.ifacol.2025.07.160) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Liu_IFACPapersOnLine2025/v1/model.xml) | -| [Lucarelli_CellSystems2018](problems/Lucarelli_CellSystems2018/v1/) | 16 | 84 | 0 | | 0 | 0 | 1755 | 65 | normal; log10-normal | | 33 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.11.010) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Lucarelli_CellSystems2018/v1/model.xml) | -| [Okuonghae_ChaosSolitonsFractals2020](problems/Okuonghae_ChaosSolitonsFractals2020/v1/) | 1 | 16 | 0 | | 0 | 0 | 92 | 2 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1016/j.chaos.2020.110032) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Okuonghae_ChaosSolitonsFractals2020/v1/model.xml) | -| [Oliveira_NatCommun2021](problems/Oliveira_NatCommun2021/v1/) | 1 | 12 | 0 | ✓ | 0 | 0 | 120 | 2 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1038/s41467-020-19798-3) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Oliveira_NatCommun2021/v1/model.xml) | -| [Perelson_Science1996](problems/Perelson_Science1996/v1/) | 1 | 3 | 0 | | 0 | 0 | 16 | 1 | log10-normal | | 4 | [\[1\]](http://identifiers.org/doi/10.1126/science.271.5255.1582) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Perelson_Science1996/v1/model.xml) | -| [Rahman_MBS2016](problems/Rahman_MBS2016/v1/) | 1 | 9 | 0 | | 0 | 0 | 23 | 1 | normal | | 7 | [\[1\]](http://identifiers.org/doi/10.1016/j.mbs.2016.07.009) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Rahman_MBS2016/v1/model.xml) | -| [Raia_CancerResearch2011](problems/Raia_CancerResearch2011/v1/) | 4 | 39 | 0 | | 0 | 0 | 205 | 8 | normal | | 14 | [\[1\]](http://identifiers.org/doi/10.1158/0008-5472.CAN-10-2987) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Raia_CancerResearch2011/v1/model.xml) | -| [Raimundez_PCB2020](problems/Raimundez_PCB2020/v1/) | 170 | 136 | 0 | ✓ | 4 | 0 | 627 | 79 | normal | parameterScaleNormal; laplace | 22 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pcbi.1007147) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Raimundez_PCB2020/v1/model.xml) | -| [SalazarCavazos_MBoC2020](problems/SalazarCavazos_MBoC2020/v1/) | 4 | 6 | 0 | | 0 | 0 | 18 | 3 | normal | | 75 | [\[1\]](http://identifiers.org/doi/10.1091/mbc.E19-09-0548) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/SalazarCavazos_MBoC2020/v1/model.xml) | -| [Schwen_PONE2014](problems/Schwen_PONE2014/v1/) | 19 | 30 | 0 | | 0 | 0 | 286 | 4 | log10-normal | parameterScaleNormal | 11 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pone.0133653) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Schwen_PONE2014/v1/model.xml) | -| [Smith_BMCSystBiol2013](problems/Smith_BMCSystBiol2013/v1/) | 35 | 25 | 3 | ✓ | 0 | 0 | 62 | 9 | normal | | 133 | [\[1\]](http://identifiers.org/doi/10.1186/1752-0509-7-41) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Smith_BMCSystBiol2013/v1/model.xml) | -| [Sneyd_PNAS2002](problems/Sneyd_PNAS2002/v1/) | 9 | 15 | 0 | | 0 | 0 | 135 | 1 | normal | | 6 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.032281999) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Sneyd_PNAS2002/v1/model.xml) | -| [Weber_BMC2015](problems/Weber_BMC2015/v1/) | 2 | 36 | 0 | ✓ | 1 | 0 | 135 | 8 | normal | | 7 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-015-0147-1) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Weber_BMC2015/v1/model.xml) | -| [Zhao_QuantBiol2020](problems/Zhao_QuantBiol2020/v1/) | 7 | 28 | 0 | | 0 | 0 | 82 | 1 | normal | | 5 | [\[1\]](http://identifiers.org/pubmed/32219006) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Zhao_QuantBiol2020/v1/model.xml) | -| [Zheng_PNAS2012](problems/Zheng_PNAS2012/v1/) | 1 | 46 | 0 | | 1 | 0 | 60 | 15 | normal | | 15 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.1205707109) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Zheng_PNAS2012/v1/model.xml) | +| PEtab Problem ID | Conditions | Estimated Parameters | Events | Possible Discontinuities | Preequilibration | Postequilibration | Measurements | Observables | Noise distribution(s) | Objective prior distribution(s) | Species | References | SBML4Humans | +|:----------------------------------------------------------------------------------------|-------------:|-----------------------:|---------:|:---------------------------|-------------------:|--------------------:|---------------:|--------------:|:------------------------|:----------------------------------|----------:|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| [Alkan_SciSignal2018](problems/Alkan_SciSignal2018/v1/) | 73 | 44 | 0 | ✓ | 0 | 0 | 1733 | 12 | normal | | 36 | [\[1\]](http://identifiers.org/doi/10.1126/scisignal.aat0229) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Alkan_SciSignal2018/v1/model.xml) | +| [Armistead_CellDeathDis2024](problems/Armistead_CellDeathDis2024/v1/) | 2 | 14 | 0 | | 0 | 0 | 58 | 4 | normal | | 4 | [\[1\]](https://doi.org/10.1038/s41419-024-07134-2) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Armistead_CellDeathDis2024/v1/model.xml) | +| [Bachmann_MSB2011](problems/Bachmann_MSB2011/v1/) | 36 | 113 | 0 | | 0 | 0 | 541 | 20 | normal; log10-normal | parameterScaleNormal | 25 | [\[1\]](http://identifiers.org/doi/10.1038/msb.2011.50) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Bachmann_MSB2011/v1/model.xml) | +| [Beer_MolBioSystems2014](problems/Beer_MolBioSystems2014/v1/) | 19 | 72 | 0 | ✓ | 0 | 0 | 27132 | 2 | normal | | 4 | [\[1\]](http://identifiers.org/doi/10.1039/c3mb70594c) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Beer_MolBioSystems2014/v1/model.xml) | +| [Bertozzi_PNAS2020](problems/Bertozzi_PNAS2020/v1/) | 2 | 8 | 0 | | 0 | 0 | 22 | 2 | normal | | 3 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.2006520117) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Bertozzi_PNAS2020/v1/model.xml) | +| [Blasi_CellSystems2016](problems/Blasi_CellSystems2016/v1/) | 1 | 9 | 0 | | 0 | 1 | 252 | 15 | log-normal | | 16 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2016.01.002) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Blasi_CellSystems2016/v1/model.xml) | +| [Boehm_JProteomeRes2014](problems/Boehm_JProteomeRes2014/v1/) | 1 | 9 | 0 | | 0 | 0 | 48 | 3 | normal | | 8 | [\[1\]](http://identifiers.org/doi/10.1021/pr5006923) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Boehm_JProteomeRes2014/v1/model.xml) | +| [Borghans_BiophysChem1997](problems/Borghans_BiophysChem1997/v1/) | 1 | 23 | 0 | | 0 | 0 | 111 | 1 | log10-normal | | 3 | [\[1\]](http://identifiers.org/doi/10.1016/s0301-4622(97)00010-0) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Borghans_BiophysChem1997/v1/model.xml) | +| [Brannmark_JBC2010](problems/Brannmark_JBC2010/v1/) | 8 | 22 | 0 | ✓ | 1 | 0 | 43 | 3 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1074/jbc.M110.106849) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Brannmark_JBC2010/v1/model.xml) | +| [Bruno_JExpBot2016](problems/Bruno_JExpBot2016/v1/) | 6 | 13 | 0 | | 0 | 0 | 77 | 5 | normal | | 7 | [\[1\]](http://identifiers.org/doi/10.1093/jxb/erw356) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Bruno_JExpBot2016/v1/model.xml) | +| [Chen_MSB2009](problems/Chen_MSB2009/v1/) | 4 | 155 | 0 | ✓ | 0 | 0 | 120 | 3 | normal | | 500 | [\[1\]](http://identifiers.org/doi/10.1038/msb.2008.74) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Chen_MSB2009/v1/model.xml) | +| [Crauste_CellSystems2017](problems/Crauste_CellSystems2017/v1/) | 1 | 12 | 0 | | 0 | 0 | 21 | 4 | normal | | 5 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.01.014) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Crauste_CellSystems2017/v1/model.xml) | +| [Elowitz_Nature2000](problems/Elowitz_Nature2000/v1/) | 1 | 21 | 0 | | 0 | 0 | 58 | 1 | log10-normal | | 8 | [\[1\]](http://identifiers.org/doi/10.1038/35002125) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Elowitz_Nature2000/v1/model.xml) | +| [Fiedler_BMCSystBiol2016](problems/Fiedler_BMCSystBiol2016/v1/) | 3 | 22 | 0 | | 0 | 0 | 72 | 2 | normal | | 6 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-016-0319-7) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Fiedler_BMCSystBiol2016/v1/model.xml) | +| [Froehlich_CellSystems2018](problems/Froehlich_CellSystems2018/v1/) | 9169 | 4231 | 0 | | 0 | 9169 | 9169 | 1 | normal | | 1396 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2018.10.013) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Froehlich_CellSystems2018/v1/model.xml) | +| [Fujita_SciSignal2010](problems/Fujita_SciSignal2010/v1/) | 6 | 19 | 0 | ✓ | 0 | 0 | 144 | 3 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1126/scisignal.2000810) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Fujita_SciSignal2010/v1/model.xml) | +| [Giordano_Nature2020](problems/Giordano_Nature2020/v1/) | 1 | 50 | 0 | ✓ | 0 | 0 | 313 | 7 | normal | | 13 | [\[1\]](http://identifiers.org/pubmed/32322102) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Giordano_Nature2020/v1/model.xml) | +| [Isensee_JCB2018](problems/Isensee_JCB2018/v1/) | 123 | 46 | 0 | ✓ | 1 | 0 | 687 | 3 | normal | parameterScaleNormal | 25 | [\[1\]](http://identifiers.org/doi/10.1083/jcb.201708053) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Isensee_JCB2018/v1/model.xml) | +| [Lang_PLOSComputBiol2024](problems/Lang_PLOSComputBiol2024/v1/) | 1 | 294 | 0 | | 0 | 0 | 9600 | 16 | normal | laplace; uniform | 124 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pcbi.1011151) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Lang_PLOSComputBiol2024/v1/model.xml) | +| [Laske_PLOSComputBiol2019](problems/Laske_PLOSComputBiol2019/v1/) | 3 | 13 | 0 | | 0 | 0 | 42 | 13 | normal; log-normal | | 41 | [\[1\]](http://identifiers.org/biomodels.db/BIOMD0000000463) [\[2\]](http://identifiers.org/biomodels.db/MODEL1307270000) [\[3\]](http://identifiers.org/doi/10.1371/journal.pcbi.1006944) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Laske_PLOSComputBiol2019/v1/model.xml) | +| [Liu_IFACPapersOnLine2025](problems/Liu_IFACPapersOnLine2025/v1/) | 2 | 9 | 1 | ✓ | 0 | 0 | 100 | 1 | normal | | 0 | [\[1\]](http://identifiers.org/doi/10.1016/j.ifacol.2025.07.160) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Liu_IFACPapersOnLine2025/v1/model.xml) | +| [Lucarelli_CellSystems2018](problems/Lucarelli_CellSystems2018/v1/) | 16 | 84 | 0 | | 0 | 0 | 1755 | 65 | normal; log10-normal | | 33 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.11.010) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Lucarelli_CellSystems2018/v1/model.xml) | +| [Okuonghae_ChaosSolitonsFractals2020](problems/Okuonghae_ChaosSolitonsFractals2020/v1/) | 1 | 16 | 0 | | 0 | 0 | 92 | 2 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1016/j.chaos.2020.110032) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Okuonghae_ChaosSolitonsFractals2020/v1/model.xml) | +| [Oliveira_NatCommun2021](problems/Oliveira_NatCommun2021/v1/) | 1 | 12 | 0 | ✓ | 0 | 0 | 120 | 2 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1038/s41467-020-19798-3) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Oliveira_NatCommun2021/v1/model.xml) | +| [Perelson_Science1996](problems/Perelson_Science1996/v1/) | 1 | 3 | 0 | | 0 | 0 | 16 | 1 | log10-normal | | 4 | [\[1\]](http://identifiers.org/doi/10.1126/science.271.5255.1582) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Perelson_Science1996/v1/model.xml) | +| [Rahman_MBS2016](problems/Rahman_MBS2016/v1/) | 1 | 9 | 0 | | 0 | 0 | 23 | 1 | normal | | 7 | [\[1\]](http://identifiers.org/doi/10.1016/j.mbs.2016.07.009) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Rahman_MBS2016/v1/model.xml) | +| [Raia_CancerResearch2011](problems/Raia_CancerResearch2011/v1/) | 4 | 39 | 0 | | 0 | 0 | 205 | 8 | normal | | 14 | [\[1\]](http://identifiers.org/doi/10.1158/0008-5472.CAN-10-2987) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Raia_CancerResearch2011/v1/model.xml) | +| [Raimundez_PCB2020](problems/Raimundez_PCB2020/v1/) | 170 | 136 | 0 | ✓ | 4 | 0 | 627 | 79 | normal | parameterScaleNormal; laplace | 22 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pcbi.1007147) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Raimundez_PCB2020/v1/model.xml) | +| [SalazarCavazos_MBoC2020](problems/SalazarCavazos_MBoC2020/v1/) | 4 | 6 | 0 | | 0 | 0 | 18 | 3 | normal | | 75 | [\[1\]](http://identifiers.org/doi/10.1091/mbc.E19-09-0548) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/SalazarCavazos_MBoC2020/v1/model.xml) | +| [Schwen_PONE2014](problems/Schwen_PONE2014/v1/) | 19 | 30 | 0 | | 0 | 0 | 286 | 4 | log10-normal | parameterScaleNormal | 11 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pone.0133653) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Schwen_PONE2014/v1/model.xml) | +| [Smith_BMCSystBiol2013](problems/Smith_BMCSystBiol2013/v1/) | 35 | 25 | 3 | ✓ | 0 | 0 | 62 | 9 | normal | | 133 | [\[1\]](http://identifiers.org/doi/10.1186/1752-0509-7-41) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Smith_BMCSystBiol2013/v1/model.xml) | +| [Sneyd_PNAS2002](problems/Sneyd_PNAS2002/v1/) | 9 | 15 | 0 | | 0 | 0 | 135 | 1 | normal | | 6 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.032281999) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Sneyd_PNAS2002/v1/model.xml) | +| [Weber_BMC2015](problems/Weber_BMC2015/v1/) | 2 | 36 | 0 | ✓ | 1 | 0 | 135 | 8 | normal | | 7 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-015-0147-1) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Weber_BMC2015/v1/model.xml) | +| [Zhao_QuantBiol2020](problems/Zhao_QuantBiol2020/v1/) | 7 | 28 | 0 | | 0 | 0 | 82 | 1 | normal | | 5 | [\[1\]](http://identifiers.org/pubmed/32219006) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Zhao_QuantBiol2020/v1/model.xml) | +| [Zheng_PNAS2012](problems/Zheng_PNAS2012/v1/) | 1 | 46 | 0 | | 1 | 0 | 60 | 15 | normal | | 15 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.1205707109) | [\[1\]](https://sbml4humans.de/report?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/problems/Zheng_PNAS2012/v1/model.xml) | ## License diff --git a/src/python/benchmark_models_petab/overview.py b/src/python/benchmark_models_petab/overview.py index 35759c9..b146975 100644 --- a/src/python/benchmark_models_petab/overview.py +++ b/src/python/benchmark_models_petab/overview.py @@ -118,7 +118,7 @@ def get_sbml4humans_urls(petab_problem_id: str) -> List[str]: f"{repo_root}/{PROBLEMS_DIRNAME}/{petab_problem_id}" f"/{V1_DIRNAME}/{model_filename}" ) - urls.append(f"https://sbml4humans.de/model_url?url={gh_raw_url}") + urls.append(f"https://sbml4humans.de/report?url={gh_raw_url}") return urls