ArticleFrontiers in bioengineering and biotechnology2014
Using CellML with OpenCMISS to Simulate Multi-Scale Physiology.
Article in Frontiers in bioengineering and biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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Who cites it
13 citing papers in PubMed.
- A novel modular modeling approach for understanding different electromechanics between left and right heart in rat.Frontiers in physiology · 2022Article
- A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows.PLoS computational biology · 2019Article
- Assessing Cardiomyocyte Excitation-Contraction Coupling Site Detection From Live Cell Imaging Using a Structurally-Realistic Computational Model of Calcium Release.Frontiers in physiology · 2019Article
- Computational Modeling of Glucose Uptake in the Enterocyte.Frontiers in physiology · 2019Article
- Next-generation, personalised, model-based critical care medicine: a state-of-the art review of in silico virtual patient models, methods, and cohorts, and how to validation them.Biomedical engineering online · 2018Review
- Meeting the multiscale challenge: representing physiology processes over ApiNATOMY circuits using bond graphs.Interface focus · 2018Article
- Roadmap for cardiovascular circulation model.The Journal of physiology · 2016Article
- The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.Interface focus · 2016Review
- Requirements for the formal representation of pathophysiology mechanisms by clinicians.Interface focus · 2016Article
- Multiscale musculoskeletal modelling, data-model fusion and electromyography-informed modelling.Interface focus · 2016Article
- Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data.GigaScience · 2016Review
- OpenCOR: a modular and interoperable approach to computational biology.Frontiers in physiology · 2015Article
- The virtual intestine: in silico modeling of small intestinal electrophysiology and motility and the applications.Wiley interdisciplinary reviews. Systems biology and medicineReview
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
OpenCMISS is an open-source modeling environment aimed, in particular, at the solution of bioengineering problems. OpenCMISS consists of two main parts: a computational library (OpenCMISS-Iron) and a field manipulation and visualization library (OpenCMISS-Zinc). OpenCMISS is designed for the solution of coupled multi-scale, multi-physics problems in a general-purpose parallel environment. CellML is an XML format designed to encode biophysically based systems of ordinary differential equations and both linear and non-linear algebraic equations. A primary design goal of CellML is to allow mathematical models to be encoded in a modular and reusable format to aid reproducibility and interoperability of modeling studies. In OpenCMISS, we make use of CellML models to enable users to configure various aspects of their multi-scale physiological models. This avoids the need for users to be familiar with the OpenCMISS internal code in order to perform customized computational experiments. Examples of this are: cellular electrophysiology models embedded in tissue electrical propagation models; material constitutive relationships for mechanical growth and deformation simulations; time-varying boundary conditions for various problem domains; and fluid constitutive relationships and lumped-parameter models. In this paper, we provide implementation details describing how CellML models are integrated into multi-scale physiological models in OpenCMISS. The external interface OpenCMISS presents to users is also described, including specific examples exemplifying the extensibility and usability these tools provide the physiological modeling and simulation community. We conclude with some thoughts on future extension of OpenCMISS to make use of other community developed information standards, such as FieldML, SED-ML, and BioSignalML. Plans for the integration of accelerator code (graphical processing unit and field programmable gate array) generated from CellML models is also discussed.
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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.