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
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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
(1994) · Cited by 21,711
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg015 · Cited by 3,060
Self-citationLi, C., Donizelli, M., Rodríguez, N., Dharuri, H. K., Endler, L., Chelliah, V., Li, L., He, E., Henry, A., Stefan, M. I., et al. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-92 · Cited by 561
Integration from proteins to organs: the Physiome Project
Hunter, P. J., & Borg, T. K. (2003) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1054 · Cited by 486
Self-citationLibSBML: an API Library for SBML
Bornstein, B. J., Keating, S. M., Jouraku, A., & Hucka, M. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn051 · Cited by 373
An Overview of CellML 1.1, a Biological Model Description Language
Cuellar, A. A., Lloyd, C. M., Nielsen, P. F., Bullivant, D. P., Nickerson, D. P., & Hunter, P. J. (2003) · SIMULATION · doi:10.1177/0037549703040939 · Cited by 345
Self-citationWeb-based kinetic modelling using JWS Online
Olivier, B. G., & Snoep, J. L. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth200 · Cited by 326
Lloyd, C. M., Lawson, J. R., Hunter, P. J., & Nielsen, P. F. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn390 · Cited by 276
Self-citationFieldML: concepts and implementation
Christie, G. R., Nielsen, P. M. F., Blackett, S. A., Bradley, C. P., & Hunter, P. J. (2009) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2009.0025 · Cited by 102
Self-citationAn overview of the CellML API and its implementation
Miller, A. K., Marsh, J., Reeve, A. M., Garny, A., Britten, R. D., Halstead, M. D. B., Cooper, J., Nickerson, D. P., & Nielsen, P. F. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-178 · Cited by 81
Self-citation
Research works printed but not linked: 2
- Aspeli, 2007, Professional Plone Development.
- Baiju, 2009, A Comprehensive Guide to Zope Component Architecture.
Cited by
Sorted by citations
BioModels—15 years of sharing computational models in life science
Malik-Sheriff, R. S., Glont, M., Nguyen, T. V. N., Tiwari, K., Roberts, M. G., Xavier, A., Vu, M. T., Men, J., Maire, M., Kananathan, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1055 · Cited by 361
The openCARP simulation environment for cardiac electrophysiology
Plank, G., Loewe, A., Neic, A., Augustin, C. M., Huang, Y.-L., Gsell, M. A. F., Karabelas, E., Nothstein, M., Prassl, A. J., Sánchez, J., et al. (2021) · Computer Methods and Programs in Biomedicine · doi:10.1016/j.cmpb.2021.106223 · Cited by 277
Proceedings of the 2017 Winter Simulation Conference
Chan, W.-M., D’Ambrogio, A., Zacharewicz, G., Mustafee, N., Wainer, G., & Page, E. (2017) · HAL · Cited by 251
Chase, J. G., Preiser, J., Dickson, J. L., Pironet, A., Chiew, Y. S., Pretty, C. G., Shaw, G. M., Benyó, B. I., Möeller, K., Safaei, S., et al. (2018) · BioMedical Engineering OnLine · doi:10.1186/s12938-018-0455-y · Cited by 191
Self-citationJohnstone, R. H., Chang, E. T. Y., Bardenet, R., de Boer, T. P., Gavaghan, D. J., Pathmanathan, P., Clayton, R. H., & Mirams, G. R. (2015) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2015.11.018 · Cited by 134
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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