ArticleBMC bioinformatics2010
An overview of the CellML API and its implementation.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed.
- NESTML: a generic modeling language and code generation tool for the simulation of spiking neural networks with advanced plasticity rules.Frontiers in neuroinformatics · 2025Article
- BioPAX in 2024: Where we are and where we are heading.Computational and structural biotechnology journal · 2024Review
- Guidelines for mechanistic modeling and analysis in cardiovascular research.American journal of physiology. Heart and circulatory physiology · 2024Review
- PyRates-A code-generation tool for modeling dynamical systems in biology and beyond.PLoS computational biology · 2023Article
- A novel modular modeling approach for understanding different electromechanics between left and right heart in rat.Frontiers in physiology · 2022Article
- Heart Rhythm Insights Into Structural Remodeling in Atrial Tissue: Timed Automata Approach.Frontiers in physiology · 2018Article
- MAGPIE: Simplifying access and execution of computational models in the life sciences.PLoS computational biology · 2017Article
- Reproducibility in Computational Neuroscience Models and Simulations.IEEE transactions on bio-medical engineering · 2016Article
- Challenges in horizontal model integration.BMC systems biology · 2016Article
- Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models.Biophysical journal · 2016Article
- JSBML 1.0: providing a smorgasbord of options to encode systems biology models.Bioinformatics (Oxford, England) · 2015Article
- OpenCOR: a modular and interoperable approach to computational biology.Frontiers in physiology · 2015Article
- Automatising the analysis of stochastic biochemical time-series.BMC bioinformatics · 2015Article
- Simulating physiological interactions in a hybrid system of mathematical models.Journal of clinical monitoring and computing · 2014Article
- SBML and CellML translation in antimony and JSim.Bioinformatics (Oxford, England) · 2014Article
- Using CellML with OpenCMISS to Simulate Multi-Scale Physiology.Frontiers in bioengineering and biotechnology · 2014Article
- Improving collaboration by standardization efforts in systems biology.Frontiers in bioengineering and biotechnology · 2014Review
- A single compartment model of pacemaking in dissasociated substantia nigra neurons: stability and energy analysis.Journal of computational neuroscience · 2013Article
- FieldML, a proposed open standard for the Physiome project for mathematical model representation.Medical & biological engineering & computing · 2013Article
- The systems biology simulation core algorithm.BMC systems biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
backgroundCellML is an XML based language for representing mathematical models, in a machine-independent form which is suitable for their exchange between different authors, and for archival in a model repository. Allowing for the exchange and archival of models in a computer readable form is a key strategic goal in bioinformatics, because of the associated improvements in scientific record accuracy, the faster iterative process of scientific development, and the ability to combine models into large integrative models.However, for CellML models to be useful, tools which can process them correctly are needed. Due to some of the more complex features present in CellML models, such as imports, developing code ab initio to correctly process models can be an onerous task. For this reason, there is a clear and pressing need for an application programming interface (API), and a good implementation of that API, upon which tools can base their support for CellML.
resultsWe developed an API which allows the information in CellML models to be retrieved and/or modified. We also developed a series of optional extension APIs, for tasks such as simplifying the handling of connections between variables, dealing with physical units, validating models, and translating models into different procedural languages.We have also provided a Free/Open Source implementation of this application programming interface, optimised to achieve good performance.
conclusionsTools have been developed using the API which are mature enough for widespread use. The API has the potential to accelerate the development of additional tools capable of processing CellML, and ultimately lead to an increased level of sharing of mathematical model descriptions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.