From bdea7dcc84fbc1affde2282095a01e89ea64f17f Mon Sep 17 00:00:00 2001 From: dilpath Date: Mon, 15 Apr 2024 13:53:32 +0100 Subject: [PATCH] fix froehlich ref --- .../model_Froehlich_CellSystems2018.xml | 2 +- README.md | 69 ++++++++++--------- 2 files changed, 36 insertions(+), 35 deletions(-) diff --git a/Benchmark-Models/Froehlich_CellSystems2018/model_Froehlich_CellSystems2018.xml b/Benchmark-Models/Froehlich_CellSystems2018/model_Froehlich_CellSystems2018.xml index e95cdbe..1c34451 100644 --- a/Benchmark-Models/Froehlich_CellSystems2018/model_Froehlich_CellSystems2018.xml +++ b/Benchmark-Models/Froehlich_CellSystems2018/model_Froehlich_CellSystems2018.xml @@ -27,7 +27,7 @@ - + diff --git a/README.md b/README.md index 4b12012..e40e0c0 100644 --- a/README.md +++ b/README.md @@ -5,40 +5,41 @@ Contributions to the collection are very welcome. For this, please create a new ## Overview -| PEtab Problem ID | Conditions | Estimated Parameters | Events | Preequilibration | Postequilibration | Measurements | Observables | Noise distribution(s) | Species | References | SBML4Humans | -|:---------------------------------------------------------------------------------------------|-------------:|-----------------------:|---------:|-------------------:|--------------------:|---------------:|--------------:|:------------------------|----------:|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| [Alkan_SciSignal2018](Benchmark-Models/Alkan_SciSignal2018/) | 73 | 56 | 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/Benchmark-Models/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml) | -| [Bachmann_MSB2011](Benchmark-Models/Bachmann_MSB2011/) | 36 | 113 | 0 | 0 | 0 | 541 | 20 | normal; log10-normal | 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/Benchmark-Models/Bachmann_MSB2011/model_Bachmann_MSB2011.xml) | -| [Beer_MolBioSystems2014](Benchmark-Models/Beer_MolBioSystems2014/) | 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/Benchmark-Models/Beer_MolBioSystems2014/model_Beer_MolBioSystems2014.xml) | -| [Bertozzi_PNAS2020](Benchmark-Models/Bertozzi_PNAS2020/) | 2 | 3 | 0 | 0 | 0 | 138 | 1 | normal | 3 | [\[1\]](http://identifiers.org/pubmed/32616574) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Bertozzi_PNAS2020/model_Bertozzi_PNAS2020.xml) | -| [Blasi_CellSystems2016](Benchmark-Models/Blasi_CellSystems2016/) | 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/Benchmark-Models/Blasi_CellSystems2016/model_Blasi_CellSystems2016.xml) | -| [Boehm_JProteomeRes2014](Benchmark-Models/Boehm_JProteomeRes2014/) | 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/Benchmark-Models/Boehm_JProteomeRes2014/model_Boehm_JProteomeRes2014.xml) | -| [Borghans_BiophysChem1997](Benchmark-Models/Borghans_BiophysChem1997/) | 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/Benchmark-Models/Borghans_BiophysChem1997/model_Borghans_BiophysChem1997.xml) | -| [Brannmark_JBC2010](Benchmark-Models/Brannmark_JBC2010/) | 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/Benchmark-Models/Brannmark_JBC2010/model_Brannmark_JBC2010.xml) | -| [Bruno_JExpBot2016](Benchmark-Models/Bruno_JExpBot2016/) | 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/Benchmark-Models/Bruno_JExpBot2016/model_Bruno_JExpBot2016.xml) | -| [Chen_MSB2009](Benchmark-Models/Chen_MSB2009/) | 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/Benchmark-Models/Chen_MSB2009/model_Chen_MSB2009.xml) | -| [Crauste_CellSystems2017](Benchmark-Models/Crauste_CellSystems2017/) | 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/Benchmark-Models/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml) | -| [Elowitz_Nature2000](Benchmark-Models/Elowitz_Nature2000/) | 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/Benchmark-Models/Elowitz_Nature2000/model_Elowitz_Nature2000.xml) | -| [Fiedler_BMC2016](Benchmark-Models/Fiedler_BMC2016/) | 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/Benchmark-Models/Fiedler_BMC2016/model_Fiedler_BMC2016.xml) | -| [Froehlich_CellSystems2018](Benchmark-Models/Froehlich_CellSystems2018/) | 9169 | 4231 | 0 | 0 | 9169 | 9169 | 1 | normal | 1396 | [\[1\]](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/Benchmark-Models/Froehlich_CellSystems2018/model_Froehlich_CellSystems2018.xml) | -| [Fujita_SciSignal2010](Benchmark-Models/Fujita_SciSignal2010/) | 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/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml) | -| [Giordano_Nature2020](Benchmark-Models/Giordano_Nature2020/) | 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/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml) | -| [Isensee_JCB2018](Benchmark-Models/Isensee_JCB2018/) | 123 | 46 | 0 | 1 | 0 | 687 | 3 | normal | 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/Benchmark-Models/Isensee_JCB2018/model_Isensee_JCB2018.xml) | +| PEtab Problem ID | Conditions | Estimated Parameters | Events | Preequilibration | Postequilibration | Measurements | Observables | Noise distribution(s) | Species | References | SBML4Humans | +|:---------------------------------------------------------------------------------------------|-------------:|-----------------------:|---------:|-------------------:|--------------------:|---------------:|--------------:|:------------------------|----------:|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| [Alkan_SciSignal2018](Benchmark-Models/Alkan_SciSignal2018/) | 73 | 56 | 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/Benchmark-Models/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml) | +| [Bachmann_MSB2011](Benchmark-Models/Bachmann_MSB2011/) | 36 | 113 | 0 | 0 | 0 | 541 | 20 | normal; log10-normal | 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/Benchmark-Models/Bachmann_MSB2011/model_Bachmann_MSB2011.xml) | +| [Beer_MolBioSystems2014](Benchmark-Models/Beer_MolBioSystems2014/) | 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/Benchmark-Models/Beer_MolBioSystems2014/model_Beer_MolBioSystems2014.xml) | +| [Bertozzi_PNAS2020](Benchmark-Models/Bertozzi_PNAS2020/) | 2 | 3 | 0 | 0 | 0 | 138 | 1 | normal | 3 | [\[1\]](http://identifiers.org/pubmed/32616574) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Bertozzi_PNAS2020/model_Bertozzi_PNAS2020.xml) | +| [Blasi_CellSystems2016](Benchmark-Models/Blasi_CellSystems2016/) | 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/Benchmark-Models/Blasi_CellSystems2016/model_Blasi_CellSystems2016.xml) | +| [Boehm_JProteomeRes2014](Benchmark-Models/Boehm_JProteomeRes2014/) | 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/Benchmark-Models/Boehm_JProteomeRes2014/model_Boehm_JProteomeRes2014.xml) | +| [Borghans_BiophysChem1997](Benchmark-Models/Borghans_BiophysChem1997/) | 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/Benchmark-Models/Borghans_BiophysChem1997/model_Borghans_BiophysChem1997.xml) | +| [Brannmark_JBC2010](Benchmark-Models/Brannmark_JBC2010/) | 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/Benchmark-Models/Brannmark_JBC2010/model_Brannmark_JBC2010.xml) | +| [Bruno_JExpBot2016](Benchmark-Models/Bruno_JExpBot2016/) | 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/Benchmark-Models/Bruno_JExpBot2016/model_Bruno_JExpBot2016.xml) | +| [Chen_MSB2009](Benchmark-Models/Chen_MSB2009/) | 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/Benchmark-Models/Chen_MSB2009/model_Chen_MSB2009.xml) | +| [Crauste_CellSystems2017](Benchmark-Models/Crauste_CellSystems2017/) | 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/Benchmark-Models/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml) | +| [Elowitz_Nature2000](Benchmark-Models/Elowitz_Nature2000/) | 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/Benchmark-Models/Elowitz_Nature2000/model_Elowitz_Nature2000.xml) | +| [Fiedler_BMC2016](Benchmark-Models/Fiedler_BMC2016/) | 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/Benchmark-Models/Fiedler_BMC2016/model_Fiedler_BMC2016.xml) | +| [Froehlich_CellSystems2018](Benchmark-Models/Froehlich_CellSystems2018/) | 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/Benchmark-Models/Froehlich_CellSystems2018/model_Froehlich_CellSystems2018.xml) | +| [Fujita_SciSignal2010](Benchmark-Models/Fujita_SciSignal2010/) | 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/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml) | +| [Giordano_Nature2020](Benchmark-Models/Giordano_Nature2020/) | 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/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml) | +| [Isensee_JCB2018](Benchmark-Models/Isensee_JCB2018/) | 123 | 46 | 0 | 1 | 0 | 687 | 3 | normal | 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/Benchmark-Models/Isensee_JCB2018/model_Isensee_JCB2018.xml) | | [Laske_PLOSComputBiol2019](Benchmark-Models/Laske_PLOSComputBiol2019/) | 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/Benchmark-Models/Laske_PLOSComputBiol2019/model_Laske_PLOSComputBiol2019.xml) | -| [Lucarelli_CellSystems2018](Benchmark-Models/Lucarelli_CellSystems2018/) | 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/Benchmark-Models/Lucarelli_CellSystems2018/model_Lucarelli_CellSystems2018.xml) | -| [Okuonghae_ChaosSolitonsFractals2020](Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/) | 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/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml) | -| [Oliveira_NatCommun2021](Benchmark-Models/Oliveira_NatCommun2021/) | 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/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml) | -| [Perelson_Science1996](Benchmark-Models/Perelson_Science1996/) | 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/Benchmark-Models/Perelson_Science1996/model_Perelson_Science1996.xml) | -| [Rahman_MBS2016](Benchmark-Models/Rahman_MBS2016/) | 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/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml) | -| [Raia_CancerResearch2011](Benchmark-Models/Raia_CancerResearch2011/) | 4 | 39 | 0 | 0 | 0 | 205 | 8 | normal | 14 | [\[1\]](https://doi.org/10.1158/0008-5472.CAN-10-2987) "MedB-1 model" | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml) | -| [Raimundez_PCB2020](Benchmark-Models/Raimundez_PCB2020/) | 170 | 136 | 0 | 4 | 0 | 627 | 79 | normal | 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/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml) | -| [SalazarCavazos_MBoC2020](Benchmark-Models/SalazarCavazos_MBoC2020/) | 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/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml) | -| [Schwen_PONE2014](Benchmark-Models/Schwen_PONE2014/) | 19 | 30 | 0 | 0 | 0 | 286 | 4 | log10-normal | 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/Benchmark-Models/Schwen_PONE2014/model_Schwen_PONE2014.xml) | -| [Smith_BMCSystBiol2013](Benchmark-Models/Smith_BMCSystBiol2013/) | 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/Benchmark-Models/Smith_BMCSystBiol2013/model_Smith_BMCSystBiol2013.xml) | -| [Sneyd_PNAS2002](Benchmark-Models/Sneyd_PNAS2002/) | 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/Benchmark-Models/Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml) | -| [Weber_BMC2015](Benchmark-Models/Weber_BMC2015/) | 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/Benchmark-Models/Weber_BMC2015/model_Weber_BMC2015.xml) | -| [Zhao_QuantBiol2020](Benchmark-Models/Zhao_QuantBiol2020/) | 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/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml) | -| [Zheng_PNAS2012](Benchmark-Models/Zheng_PNAS2012/) | 1 | 46 | 0 | 1 | 0 | 60 | 15 | normal | 15 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.1201240109) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml) | +| [Lucarelli_CellSystems2018](Benchmark-Models/Lucarelli_CellSystems2018/) | 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/Benchmark-Models/Lucarelli_CellSystems2018/model_Lucarelli_CellSystems2018.xml) | +| [Okuonghae_ChaosSolitonsFractals2020](Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/) | 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/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml) | +| [Oliveira_NatCommun2021](Benchmark-Models/Oliveira_NatCommun2021/) | 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/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml) | +| [Perelson_Science1996](Benchmark-Models/Perelson_Science1996/) | 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/Benchmark-Models/Perelson_Science1996/model_Perelson_Science1996.xml) | +| [Rahman_MBS2016](Benchmark-Models/Rahman_MBS2016/) | 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/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml) | +| [Raia_CancerResearch2011](Benchmark-Models/Raia_CancerResearch2011/) | 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/Benchmark-Models/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml) | +| [Raimundez_PCB2020](Benchmark-Models/Raimundez_PCB2020/) | 170 | 136 | 0 | 4 | 0 | 627 | 79 | normal | 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/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml) | +| [SalazarCavazos_MBoC2020](Benchmark-Models/SalazarCavazos_MBoC2020/) | 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/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml) | +| [Schwen_PONE2014](Benchmark-Models/Schwen_PONE2014/) | 19 | 30 | 0 | 0 | 0 | 286 | 4 | log10-normal | 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/Benchmark-Models/Schwen_PONE2014/model_Schwen_PONE2014.xml) | +| [Smith_BMCSystBiol2013](Benchmark-Models/Smith_BMCSystBiol2013/) | 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/Benchmark-Models/Smith_BMCSystBiol2013/model_Smith_BMCSystBiol2013.xml) | +| [Sneyd_PNAS2002](Benchmark-Models/Sneyd_PNAS2002/) | 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/Benchmark-Models/Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml) | +| [Weber_BMC2015](Benchmark-Models/Weber_BMC2015/) | 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/Benchmark-Models/Weber_BMC2015/model_Weber_BMC2015.xml) | +| [Zhao_QuantBiol2020](Benchmark-Models/Zhao_QuantBiol2020/) | 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/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml) | +| [Zheng_PNAS2012](Benchmark-Models/Zheng_PNAS2012/) | 1 | 46 | 0 | 1 | 0 | 60 | 15 | normal | 15 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.1201240109) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml) | + ## License @@ -58,4 +59,4 @@ When using this work, please cite an appropriate version on Zenodo: https://doi. The model collection has been used in multiple [publications](src/benchmark_refs.bib). -If you used the benchmark problems in your work and your publication is missing, please let us know via a new GitHub issue. \ No newline at end of file +If you used the benchmark problems in your work and your publication is missing, please let us know via a new GitHub issue.