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dweindldilpath
dweindl
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dilpath
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Overview table: link to respective publication (#149)
Add reference links to table based on SBML annotations. NOTE: Not all current models are properly annotated. Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
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‎Benchmark-Models/model_info.py‎

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"""Print some stats for each benchmark problem"""
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import os
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from typing import Dict
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from typing import Dict, List
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import libsbml
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import numpy as np
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import pandas as pd
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import petab
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markdown_columns = {
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'conditions': 'Conditions',
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'estimated_parameters': 'Estimated Parameters',
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'name': 'Model ID',
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'observables': 'Observables',
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'species': 'Species',
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'reference_uris': 'References',
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}
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index_column = 'name'
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len(problem.measurement_df[petab.OBSERVABLE_ID].unique()),
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'species':
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len(problem.sbml_model.getListOfSpecies()),
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'reference_uris':
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get_reference_uris(problem.sbml_model),
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}
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def get_reference_uris(sbml_model: libsbml.Model) -> List[str]:
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"""Get publication URIs from SBML is-described-by annotation"""
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cv_terms = sbml_model.getCVTerms()
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reference_uris = []
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for anno in cv_terms:
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if anno.getBiologicalQualifierType() != libsbml.BQB_IS_DESCRIBED_BY:
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continue
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resources = anno.getResources()
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for i in range(resources.getNumAttributes()):
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uri = resources.getValue(i)
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reference_uris.append(uri)
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return reference_uris
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def get_overview_table(path: str = None) -> pd.DataFrame:
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"""Get overview table with stats for all benchmark problems"""
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model_list = os.scandir(path=path)
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def main(
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markdown: bool = False,
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markdown: bool = False,
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):
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df = get_overview_table()
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pd.options.display.width = 0
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if markdown:
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# directory as markdown link
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df.rename(index=lambda x: f"[{x}](Benchmark-Models/{x}/)",
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inplace=True)
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# references to markdown links
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df['reference_uris'] = df['reference_uris'].apply(
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lambda x: " ".join([f"[\\[{i + 1}\\]]({uri})"
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for i, uri in enumerate(x)])
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)
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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())
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if __name__ == '__main__':
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import sys
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markdown = False
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if '--markdown' in sys.argv:
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markdown = True

‎README.md‎

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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](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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| Model ID | Conditions | Estimated Parameters | Events | Measurements | Observables | Species | References |
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|:---------------------------------------------------------------------------------------------|-------------:|-----------------------:|---------:|---------------:|--------------:|----------:|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| [Alkan_SciSignal2018](Benchmark-Models/Alkan_SciSignal2018/) | 73 | 56 | 0 | 1733 | 12 | 36 | [\[1\]](http://identifiers.org/doi/10.1126/scisignal.aat0229) |
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| [Bachmann_MSB2011](Benchmark-Models/Bachmann_MSB2011/) | 36 | 113 | 0 | 541 | 20 | 25 | [\[1\]](http://identifiers.org/doi/10.1038/msb.2011.50) |
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| [Beer_MolBioSystems2014](Benchmark-Models/Beer_MolBioSystems2014/) | 19 | 72 | 0 | 27132 | 2 | 4 | [\[1\]](http://identifiers.org/doi/10.1039/c3mb70594c) |
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| [Bertozzi_PNAS2020](Benchmark-Models/Bertozzi_PNAS2020/) | 2 | 3 | 0 | 138 | 1 | 3 | [\[1\]](http://identifiers.org/pubmed/32616574) |
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| [Blasi_CellSystems2016](Benchmark-Models/Blasi_CellSystems2016/) | 1 | 9 | 0 | 252 | 15 | 16 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2016.01.002) |
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| [Boehm_JProteomeRes2014](Benchmark-Models/Boehm_JProteomeRes2014/) | 1 | 9 | 0 | 48 | 3 | 8 | [\[1\]](http://identifiers.org/doi/10.1021/pr5006923) |
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| [Borghans_BiophysChem1997](Benchmark-Models/Borghans_BiophysChem1997/) | 1 | 23 | 0 | 111 | 1 | 3 | [\[1\]](http://identifiers.org/doi/10.1016/s0301-4622(97)00010-0) |
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| [Brannmark_JBC2010](Benchmark-Models/Brannmark_JBC2010/) | 8 | 22 | 0 | 43 | 3 | 9 | [\[1\]](http://identifiers.org/doi/10.1074/jbc.M110.106849) |
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| [Bruno_JExpBot2016](Benchmark-Models/Bruno_JExpBot2016/) | 6 | 13 | 0 | 77 | 5 | 7 | [\[1\]](http://identifiers.org/doi/10.1093/jxb/erw356) |
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| [Chen_MSB2009](Benchmark-Models/Chen_MSB2009/) | 4 | 155 | 0 | 120 | 3 | 500 | [\[1\]](http://identifiers.org/doi/10.1038/msb.2008.74) |
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| [Crauste_CellSystems2017](Benchmark-Models/Crauste_CellSystems2017/) | 1 | 12 | 0 | 21 | 4 | 5 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.01.014) |
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| [Elowitz_Nature2000](Benchmark-Models/Elowitz_Nature2000/) | 1 | 21 | 0 | 58 | 1 | 8 | [\[1\]](http://identifiers.org/doi/10.1038/35002125) |
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| [Fiedler_BMC2016](Benchmark-Models/Fiedler_BMC2016/) | 3 | 22 | 0 | 72 | 2 | 6 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-016-0319-7) |
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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 | [\[1\]](http://identifiers.org/pubmed/32322102) |
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| [Isensee_JCB2018](Benchmark-Models/Isensee_JCB2018/) | 123 | 46 | 0 | 687 | 3 | 25 | [\[1\]](http://identifiers.org/doi/10.1083/jcb.201708053) |
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| [Laske_PLOSComputBiol2019](Benchmark-Models/Laske_PLOSComputBiol2019/) | 3 | 13 | 0 | 42 | 13 | 41 | [\[1\]](http://identifiers.org/biomodels.db/BIOMD0000000463) [\[2\]](http://identifiers.org/biomodels.db/MODEL1307270000) [\[3\]](http://identifiers.org/pubmed/22593159) |
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| [Lucarelli_CellSystems2018](Benchmark-Models/Lucarelli_CellSystems2018/) | 16 | 84 | 0 | 1755 | 65 | 33 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.11.010) |
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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 | [\[1\]](http://identifiers.org/doi/10.1126/science.271.5255.1582) |
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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 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pone.0133653) |
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| [Sneyd_PNAS2002](Benchmark-Models/Sneyd_PNAS2002/) | 9 | 15 | 0 | 135 | 1 | 6 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.032281999) |
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| [Weber_BMC2015](Benchmark-Models/Weber_BMC2015/) | 2 | 36 | 0 | 135 | 8 | 7 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-015-0147-1) |
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| [Zhao_QuantBiol2020](Benchmark-Models/Zhao_QuantBiol2020/) | 7 | 28 | 0 | 82 | 1 | 5 | [\[1\]](http://identifiers.org/pubmed/32219006) |
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| [Zheng_PNAS2012](Benchmark-Models/Zheng_PNAS2012/) | 1 | 46 | 0 | 60 | 15 | 15 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.1201240109) |
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## License
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