BioModels

How can I quote BioModels?

Several papers about BioModels and related efforts have been published. Please see below for how to cite: BioModels | Reproducibility | BioModels Parameters | Path2Models | Associated services | Others.

For a more complete list, please refer to our Google Scholar profile.

BioModels

Rahuman S Malik-Sheriff, Mihai Glont, Tung V N Nguyen, Krishna Tiwari, Matthew G Roberts, Ashley Xavier, Manh T Vu, Jinghao Men, Matthieu Maire, Sarubini Kananathan, Emma L Fairbanks, Johannes P Meyer, Chinmay Arankalle, Thawfeek M Varusai, Vincent Knight-Schrijver, Lu Li, Corina Dueñas-Roca, Gaurhari Dass, Sarah M Keating, Young M Park, Nicola Buso, Nicolas Rodriguez, Michael Hucka, and Henning Hermjakob

BioModels — 15 years of sharing computational models in life science.

Nucl. Acids Res. 2020

[Nucl. Acids Res.] [ BibTeX entry]

        @article{BioModels2020,
        author = {Malik-Sheriff, Rahuman S and Glont, Mihai and Nguyen, Tung V N and Tiwari, Krishna and Roberts, Matthew G and Xavier, Ashley and Vu, Manh T and Men, Jinghao and Maire, Matthieu and Kananathan, Sarubini and Fairbanks, Emma L and Meyer, Johannes P and Arankalle, Chinmay and Varusai, Thawfeek M and Knight-Schrijver, Vincent and Li, Lu and Dueñas-Roca, Corina and Dass, Gaurhari and Keating, Sarah M and Park, Young M and Buso, Nicola and Rodriguez, Nicolas and Hucka, Michael and Hermjakob, Henning},
        title = "{BioModels — 15 years of sharing computational models in life science}",
        journal = {Nucleic Acids Research},
        volume = {48},
        number = {D1},
        pages = {D407-D415},
        year = {2020},
        month = {1},
        abstract = "{Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), a repository for mathematical models, was established in 2005. The current BioModels platform allows submission of models encoded in diverse modelling formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. The models submitted to BioModels are curated to verify the computational representation of the biological process and the reproducibility of the simulation results in the reference publication. The curation also involves encoding models in standard formats and annotation with controlled vocabularies following MIRIAM (minimal information required in the annotation of biochemical models) guidelines. BioModels now accepts large-scale submission of auto-generated computational models. With gradual growth in content over 15 years, BioModels currently hosts about 2000 models from the published literature. With about 800 curated models, BioModels has become the world’s largest repository of curated models and emerged as the third most used data resource after PubMed and Google Scholar among the scientists who use modelling in their research. Thus, BioModels benefits modellers by providing access to reliable and semantically enriched curated models in standard formats that are easy to share, reproduce and reuse.}",
        issn = {0305-1048},
        doi = {10.1093/nar/gkz1055},
        url = {https://doi.org/10.1093/nar/gkz1055},
        note = {gkz1055},
        eprint = {https://academic.oup.com/nar/article-pdf/48/D1/D407/31698010/gkz1055.pdff},
        }
        

Mihai Glont, Tung V N Nguyen, Martin Graesslin, Robert Hälke, Raza Ali, Jochen Schramm, Sarala M Wimalaratne, Varun B Kothamachu, Nicolas Rodriguez, Maciej J Swat, Jurgen Eils, Roland Eils, Camille Laibe, Rahuman S Malik-Sheriff, Vijayalakshmi Chelliah, Nicolas Le Novère, and Henning Hermjakob

BioModels: expanding horizons to include more modelling approaches and formats.

Nucl. Acids Res. 2018

[Nucl. Acids Res.] [ BibTeX entry]

            @ARTICLE{BioModels2018a,
            author  = {Glont, Mihai and Nguyen, Tung V N and Graesslin, Martin and Hälke, Robert and Ali, Raza and
            Schramm, Jochen and Wimalaratne, Sarala M and Kothamachu, Varun B and Rodriguez, Nicolas and
            Swat, Maciej J and Eils, Jurgen and Eils, Roland and Laibe, Camille and
            Malik-Sheriff, Rahuman S and Chelliah, Vijayalakshmi and Le Novère, Nicolas and Hermjakob, Henning},
            title   = {BioModels: expanding horizons to include more modelling approaches and formats},
            journal = {Nucleic Acids Research},
            volume  = {46},
            number  = {D1},
            pages   = {D1248–D1253},
            year    = {2018},
            doi     = {10.1093/nar/gkx1023},
            URL     = {https://dx.doi.org/10.1093/nar/gkx1023},
            eprint = {/oup/backfile/content_public/journal/nar/46/d1/10.1093_nar_gkx1023/2/gkx1023.pdf}
            }
        

Reproducibility

Krishna Tiwari, Sarubini Kananathan, Matthew G Roberts, Johannes P Meyer, Mohammad Umer Sharif Shohan, Ashley Xavier, Matthieu Maire, Ahmad Zyoud, Jinghao Men, Szeyi Ng, Tung V N Nguyen, Mihai Glont, Henning Hermjakob, Rahuman S Malik‐Sheriff

Reproducibility in systems biology modelling

Molecular Systems Biology 2021

[Molecular Systems Biology] [ BibTeX entry]

        @article{https://doi.org/10.15252/msb.20209982,
            author = {Tiwari, Krishna and Kananathan, Sarubini and Roberts, Matthew G and Meyer, Johannes P and Sharif Shohan, Mohammad Umer and Xavier, Ashley and Maire, Matthieu and Zyoud, Ahmad and Men, Jinghao and Ng, Szeyi and Nguyen, Tung V N and Glont, Mihai and Hermjakob, Henning and Malik-Sheriff, Rahuman S},
            title = {Reproducibility in systems biology modelling},
            journal = {Molecular Systems Biology},
            volume = {17},
            number = {2},
            pages = {e9982},
            doi = {https://doi.org/10.15252/msb.20209982},
            url = {https://www.embopress.org/doi/abs/10.15252/msb.20209982},
            eprint = {https://www.embopress.org/doi/pdf/10.15252/msb.20209982},
            abstract = {Reproducibility of scientific results is a key element of science and credibility. The lack of reproducibility across many scientific fields has emerged as an important concern. In this piece, we assess mathematical model reproducibility and propose a scorecard for improving reproducibility in this field.},
            year = {2021}
        }
        

BioModels Parameters

Mihai Glont, Chinmay Arankalle, Krishna Tiwari, Tung V N Nguyen, Henning Hermjakob, Rahuman S Malik Sheriff

BioModels Parameters: a treasure trove of parameter values from published systems biology models

Bioinformatics 2020

[Bioinformatics] [ BibTeX entry]

        @article{10.1093/bioinformatics/btaa560,
        author = {Glont, Mihai and Arankalle, Chinmay and Tiwari, Krishna and Nguyen, Tung V N and Hermjakob, Henning and Malik Sheriff, Rahuman S},
        title = "{BioModels Parameters: a treasure trove of parameter values from published systems biology models}",
        journal = {Bioinformatics},
        year = {2020},
        month = {06},
        abstract = "{One of the major bottlenecks in building systems biology models is identification and estimation of model parameters for model calibration. Searching for model parameters from published literature and models is an essential, yet laborious task.We have developed a new service, BioModels Parameters, to facilitate search and retrieval of parameter values from the SBML models stored in BioModels. Modelers can now directly search for a model entity (e.g. a protein or drug) to retrieve the rate equations describing it; the associated parameter values (e.g. degradation rate, production rate, Kcat, Michaelis-Menten constant, etc) and the initial concentrations. Currently, BioModels Parameters contains entries from over 75,000 reactions and 60 different taxa with cross-references. The retrieved rate equations and parameters can be used for scanning parameter ranges, model fitting and model extension. Thus, BioModels Parameters will be a valuable service for systems biology modelers.The data is accessible via web interface and API. BioModels Parameters is free to use and is publicly available at https://www.ebi.ac.uk/biomodels/parameterSearch.}",
        issn = {1367-4803},
        doi = {10.1093/bioinformatics/btaa560},
        url = {https://doi.org/10.1093/bioinformatics/btaa560},
        note = {btaa560},
        eprint = {https://academic.oup.com/bioinformatics/article-pdf/doi/10.1093/bioinformatics/btaa560/33420759/btaa560.pdf},
        }
        

Other publications

Vijayalakshmi Chelliah, Nick Juty, Ishan Ajmera, Raza Ali, Marine Dumousseau, Mihai Glont, Michael Hucka, Gaël Jalowicki, Sarah Keating, Vincent Knight-Schrijver, Audald Lloret-Villas, Kedar Nath Natarajan, Jean-Baptiste Pettit, Nicolas Rodriguez, Michael Schubert, Sarala M. Wimalaratne, Yangyang Zhao, Henning Hermjakob, Nicolas Le Novère and Camille Laibe

BioModels: ten-year anniversary.

Nucl. Acids Res. 2015

[Nucl. Acids Res.] [ BibTeX entry]

            @ARTICLE{BioModels2015a,
            author  = {Chelliah, Vijayalakshmi and Juty, Nick and Ajmera, Ishan and Ali, Raza and Dumousseau, Marine and Glont, Mihai
            and Hucka, Michael and Jalowicki, Ga{\"e}l and Keating, Sarah and Knight-Schrijver, Vincent and Lloret-Villas, Audald
            and Nath Natarajan, Kedar and Pettit, Jean-Baptiste and Rodriguez, Nicolas and Schubert, Michael
            and Wimalaratne, Sarala M. and Zhao, Yangyang and Hermjakob, Henning and Le Nov{\`e}re, Nicolas and Laibe, Camille},
            title   = {{BioModels: ten-year anniversary.}},
            journal = {Nucl. Acids Res.},
            year    = {2015},
            doi     = {10.1093/nar/gku1181}}
        

A Lloret‐Villas, TM Varusai, N Juty, C Laibe, N Le Novère, H Hermjakob and V Chelliah

The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions.

CPT: Pharmacometrics & Systems Pharmacology 2017

[ CPT: Pharmacometrics & Systems Pharmacology] [ BibTeX entry]

            @ARTICLE{BioModels2017a,
            author  = {A Lloret‐Villas and TM Varusai and N Juty and C Laibe and N Le Novère and H Hermjakob and V Chelliah},
            title   = {The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying
            Neurodegeneration: Evolving Dimensions and Future Directions},
            journal = {CPT: Pharmacometrics & Systems Pharmacology},
            volume  = {6},
            number  = {2},
            pages   = {73-86},
            year    = {2017},
            doi     = {10.1002/psp4.12155},
            URL     = {https://ascpt.onlinelibrary.wiley.com/doi/abs/10.1002/psp4.12155}
            }
        

Nick Juty, Raza Ali, Mihai Glont, Sarah Keating, Nicolas Rodriguez, Maciej J. Swat, Sarala M. Wimalaratne, Henning Hermjakob, Nicolas Le Novère, Camille Laibe and Vijayalakshmi Chelliah

BioModels: Content, Features, Functionality and Use.

CPT: Pharmacometrics & Systems Pharmacology 2015

[CPT: Pharmacometrics & Systems Pharmacology] [ BibTeX entry]

            @ARTICLE{BioModels2015b,
            author  = {Juty, Nick and Ali, Raza and Glont, Mihai and Keating, Sarah and Rodriguez, Nicolas and Swat, Maciej J.
            and Wimalaratne, Sarala M. and  Hermjakob, Henning and Le Nov{\`e}re, Nicolas and Laibe, Camille and Chelliah, Vijayalakshmi},
            title   = {{BioModels: Content, Features, Functionality and Use.}},
            journal = {CPT: Pharmacometrics & Systems Pharmacology},
            year    = {2015},
            doi     = {10.1002/psp4.3}
            }
        

Nicolas Le Novère, Benjamin Bornstein, Alexander Broicher, Mélanie Courtot, Marco Donizelli, Harish Dharuri, Lu Li, Herbert Sauro, Maria Schilstra, Bruce Shapiro, Jacky L. Snoep and Michael Hucka

BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems.

Nucleic Acids Research 2006, 34(Database issue):D689-91

[Europe PMC] [Nucleic Acids Res] [ BibTeX entry]

            @ARTICLE{BioModels2006,
            author  = {Le Nov{\`e}re, Nicolas and Bornstein, Benjamin and Broicher, Alexander and Courtot, M{\'e}lanie
            and Donizelli, Marco and Dharuri, Harish and Li, Lu and Sauro, Herbert and Schilstra, Maria
            and Shapiro, Bruce and Snoep, Jacky L. and Hucka, Michael},
            title   = {{BioModels Database}: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems},
            journal = {Nucleic Acids Research},
            year    = {2006},
            month   = {Jan},
            volume  = {34},
            pages   = {D689--D691},
            number  = {Database issue},
            pmid    = {16381960}
            }
        

Vijayalakshmi Chelliah, Camille Laibe, Nicolas Le Novère

BioModels Database: A Repository of Mathematical Models of Biological Processes.

Methods in Molecular Biology 2013, 1021:189-199

[Europe PMC] [Springer] [ BibTeX entry]

            @ARTICLE{BioModels2013,
            author  = {Chelliah, Vijayalakshmi and Laibe, Camille and Le Nov{\`e}re, Nicolas},
            title   = {BioModels Database: A Repository of Mathematical Models of Biological Processes.},
            journal = {Methods Mol Biol},
            year    = {2013},
            volume  = {1021},
            pages   = {189--199},
            pmid    = {23715986},
            }
        

Chen Li, Marco Donizelli, Nicolas Rodriguez, Harish Dharuri, Lukas Endler, Vijayalakshmi Chelliah, Lu Li, Enuo He, Arnaud Henry, Melanie I. Stefan, Jacky L. Snoep, Michael Hucka, Nicolas Le Novère and Camille Laibe

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.

BMC Systems Biology 2010, 4:92

[Europe PMC] [BMC Sys Bio] [ BibTeX entry]

            @ARTICLE{BioModels2010,
            author  = {Li, Chen and Donizelli, Marco and Rodriguez, Nicolas and Dharuri, Harish and Endler, Lukas and Chelliah, Vijayalakshmi
            and Li, Lu and He, Enuo and Henry, Arnaud and Stefan, Melanie I. and Snoep, Jacky L. and Hucka, Michael
            and Le Nov{\`e}re, Nicolas and Laibe, Camille},
            title   = {{BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.}},
            journal = {BMC Systems Biology},
            year    = {2010},
            month   = {Jun},
            volume  = {4},
            pages   = {92},
            pmid    = {20587024}
            }
        

Path2Models

Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Laibe, Camille, Andreas Dräger and Nicolas Le Novère

Path2Models: large-scale generation of computational models from biochemical pathway maps.

BMC Systems Biology 2013, 7:116

[Europe PMC] [BMC Sys Bio] [ BibTeX entry]

@ARTICLE{BioModels2010,
  author  = {B{\"u}chel, Finja and Rodriguez, Nicolas and Swainston, Neil and Wrzodek, Clemens and Czauderna, Tobias and Keller, Roland
            and Mittag, Florian and Schubert, Michael and Glont, Mihai and Golebiewski, Martin and van Iersel, Martijn and Keating, Sarah
            and Rall, Matthias and Wybrow, Michael and Hermjakob, Henning and Hucka, Michael and Kell, Douglas B and M{\"u}ller, Wolfgang
            and Mendes, Pedro and Zell, Andreas and Chaouiya, Claudine and Saez-Rodriguez, Julio and Schreiber, Falk and Laibe, Camille
            and Dr{\"a}ger, Andreas and Le Nov{\`e}re, Nicolas},
  title   = {{Path2Models: large-scale generation of computational models from biochemical pathway maps.}},
  journal = {BMC Systems Biology},
  year    = {2013},
  month   = {Nov},
  volume  = {7},
  pages   = {116},
  pmid    = {24180668}
}

Associated services

Sarala M Wimalaratne, Pierre Grenon, Henning Hermjakob, Nicolas Le Novère and Camille Laibe

BioModels linked dataset.

BMC Systems Biology 2014, 8(1):91

[Europe PMC] [BMC Sys Bio] [ BibTeX entry]

@ARTICLE{Wimalaratne2014,
	Title   = {BioModels linked dataset},
	Author  = {Wimalaratne, Sarala M and Grenon, Pierre and Hermjakob, Henning and Le Nov{\`e}re, Nicolas and Laibe, Camille},
	DOI     = {10.1186/s12918-014-0091-5},
        pmid    = {25182954},
	Number  = {1},
	Volume  = {8},
	Month   = {August},
	Year    = {2014},
	Journal = {BMC systems biology},
	ISSN    = {1752-0509},
	Pages   = {91}
}

Chen Li, Mélanie Courtot, Nicolas Le Novère and Camille Laibe

BioModels.net Web Services, a free and integrated toolkit for computational modelling software.

Briefings in Bioinformatics 2010, 11:270-277

[Europe PMC] [Brief Bioinform] [ BibTeX entry]

            @ARTICLE{BioModelsWebServices2010,
            author  = {Li, Chen and Courtot, M{\'e}lanie and Le Nov{\`e}re, Nicolas and Laibe, Camille},
            title   = {BioModels.net Web Services, a free and integrated toolkit for computational modelling software.},
            journal = {Brief Bioinform},
            year    = {2010},
            volume  = {11},
            pages   = {270--277},
            number  = {3},
            month   = {May},
            pmid    = {19939940}
            }