The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
The Physiome Model Repository 2
Abstract
Motivation: The Physiome Model Repository 2 (PMR2) software was created as part of the IUPS Physiome Project (Hunter and Borg, 2003), and today it serves as the foundation for the CellML model repository. Key advantages brought to the end user by PMR2 include: facilities for model exchange, enhanced collaboration and a detailed change history for each model. Availability: PMR2 is available under an open source license at http://www.cellml.org/tools/pmr/; a fully functional instance of this software can be accessed at http://models.physiomeproject.org/. Contact: tommy.yu@auckland.ac.nz
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Each is checked against this paper’s own text: does it say what the citing paper says it does?
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“Model repositories such as BioModels [10, 11], JWS Online [12], or the Physiome Model Repository 2 (PMR2) [13] provide different means to retrieve and use simulation models.”
From Relating simulation studies by provenance—Developing a family of Wnt signaling models (2021) · cites this paper as [13]
Citations
Cites
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Model Reproducibility: Overview
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Computational Modelling of Glucose Uptake in the Enterocyte
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Self-citationModel Reproducibility: Overview
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Computational Modelling of Glucose Uptake in the Enterocyte
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Self-citationLloyd, C. M. (2013) · Springer eBooks · doi:10.1007/978-1-4419-9863-7_1529
Self-citationYu, T., Britten, R. D., Nickerson, D. P., Hunter, P. J., & Nielsen, P. M. F. (2014) · Encyclopedia of Computational Neuroscience · doi:10.1007/978-1-4614-7320-6_168-1
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Self-citationYu, T., Britten, R. D., Nickerson, D. P., Hunter, P. J., & Nielsen, P. M. F. (2015) · Encyclopedia of Computational Neuroscience · doi:10.1007/978-1-4614-6675-8_168
Self-citationReproducibility study of the Fabbri et al. 2017 model of the human sinus node action potential
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Self-citationDatabases and Data Repositories in Computational Neuroscience: Overview
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Databases and Data Repositories in Computational Neuroscience: Overview
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Yu, T., Britten, R. D., Nickerson, D. P., Hunter, P. J., & Nielsen, P. M. F. (2022) · Encyclopedia of Computational Neuroscience · doi:10.1007/978-1-0716-1006-0_168
Self-citationModel Reproducibility: Overview
Crook, S. M. (2022) · Encyclopedia of Computational Neuroscience · doi:10.1007/978-1-0716-1006-0_763
Afshar, N., Safaei, S., Nickerson, D. P., Hunter, P. J., & Suresh, V. (2023) · Physiome · doi:10.36903/physiome.21708179
Self-citationAfshar, N., Safaei, S., Nickerson, D. P., Hunter, P. J., & Suresh, V. (2023) · Physiome · doi:10.36903/physiome.21708179.v1
Self-citationBioModels’ Model of the Year 2023
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Integrating Clustering with Overlaps into Intelligent Agent Systems
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Barral, Y.-S. H. M., Polonchuk, L., Clerx, M., Gavaghan, D. J., Mirams, G. R., & Wang, K. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.26.640287
Barral, Y.-S. H. M., Polonchuk, L., Clerx, M., Gavaghan, D. J., Mirams, G. R., & Wang, K. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012913
BioModels’ model of the year 2024
Malik‐Sheriff, R. S., Asari, H., Geris, L., Hermjakob, H., Raman, K., Shtylla, B., & Zimmermann‐Kogadeeva, M. (2026) · Frontiers in Systems Biology · doi:10.3389/fsysb.2026.1829848
FAIRsharing record for: BioModels
FAIRsharing Team (2015) · FAIRsharing.org · doi:10.25504/fairsharing.paz6mh
FAIRsharing record for: Human Physiome Field Markup Language
FAIRsharing Team (2015) · FAIRsharing.org · doi:10.25504/fairsharing.hbh5mk
FAIRsharing record for: COMODI
FAIRsharing Team (2018) · FAIRsharing.org · doi:10.25504/fairsharing.htq39f
Metadata
- Authors
- Yu, T., Lloyd, C. M., Nickerson, D. P., Cooling, M. T., Miller, A. K., Garny, A., Terkildsen, J. R., Lawson, J., Britten, R. D., Hunter, P. J., & Nielsen, P. M. F.
- Affiliations
- University of Auckland (NZ)
- Corresponding author
- Yu, Tommy
- ORCID
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-01-06
- Volume
- 27
- Issue
- 5
- Pages
- 743-744
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2171926758
- Cited by
- 169
- References
- 11
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 4 · 2023: 10 · 2022: 19 · 2021: 16 · 2020: 16 · 2019: 13 · 2018: 11 · 2017: 10 · 2016: 17 · 2015: 15 · 2014: 13 · 2013: 12 · 2012: 4
- FWCI
- 25.18
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- ResearchSpace (University of Auckland) (submittedVersion)
- Funders
- Wellcome Trust
- National Institute for Health and Care Research (NF-SI-0508-10212)
- British Heart Foundation
- Topics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- CellML, model repository, model exchange, model versioning, change history, open source software, computational physiology, model collaboration
- MeSH terms
- Models, Biological, Software, Databases, Factual, Computational Biology, Internet
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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