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CellML: its future, present and past
Open accessAbstract
Advances in biotechnology and experimental techniques have lead to the elucidation of vast amounts of biological data. Mathematical models provide a method of analysing this data; however, there are two issues that need to be addressed: (1) the need for standards for defining cell models so they can, for example, be exchanged across the World Wide Web, and also read into simulation software in a consistent format and (2) eliminating the errors which arise with the current method of model publication. CellML has evolved to meet these needs of the modelling community. CellML is a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. In this paper we summarise the structure of CellML, its current applications (including biological pathway and electrophysiological models), and its future development--in particular, the development of toolsets and the integration of ontologies.
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“BioPAX does not support this, but coordinates with the SBML and CellML mathematical modeling languages55,56 and a growing software toolset supporting biological process simulation57 which cover these aspects.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [55]
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Denham, S. L. (2015) · Springer eBooks · doi:10.1007/978-1-4614-6675-8_764 · Cited by 1
Modular model buildingPreprint
Mallavarapu, A., Thomson, M., Ullian, B., & Gunawardena, J. (2007) · arXiv (Cornell University) · doi:10.48550/arxiv.0710.3421 · Cited by 1
Modelling Bacterial Regulatory Networks with Petri Nets
Shaw, O. (2007) · OpenGrey (Institut de l'Information Scientifique et Technique) · doi:10.25405/ncl.34130109 · Cited by 1
Metadata
- Authors
- Lloyd, C. M., Halstead, M. D. B., & Nielsen, P. F.
- Affiliations
- University of Auckland (NZ)
- Corresponding author
- Lloyd, Catherine M.
- Venue
- Progress in Biophysics and Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2004-06
- Volume
- 85
- Issue
- 2-3
- Pages
- 433-450
- ISSN
- 0079-6107 (ISSN-L)
- OpenAlex
- W2042880070
- Cited by
- 499
- References
- 27
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 12 · 2023: 4 · 2022: 12 · 2021: 10 · 2020: 17 · 2019: 10 · 2018: 12 · 2017: 10 · 2016: 18 · 2015: 24 · 2014: 24 · 2013: 28 · 2012: 28
- FWCI
- 14.55
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Progress in Biophysics and Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Directorate for Biological Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Physical Sciences › Mathematics › Modeling and Simulation › Modeling and Simulation Systems
- Keywords
- CellML, electrophysiological model, ontology integration
- MeSH terms
- Algorithms, Animals, Cell Physiological Phenomena, Computer Simulation, Humans, Models, Biological, Programming Languages, Software, Information Storage and Retrieval, Hypermedia
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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