ArticleFrontiers in physiology2015
OpenCOR: a modular and interoperable approach to computational biology.
Article in Frontiers in physiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- A Modular Computational Approach for Assessing Active and Passive Force Contributions in Interstitial Lymphatic Fluid Uptake.Annals of biomedical engineering · 2026Article
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- Understanding the hemodynamic changes in fetuses with coarctation of the aorta using a lumped model of fetal circulation.PLoS computational biology · 2025Article
- Numerical accuracy of closed-loop steady state in a zero-dimensional cardiovascular model.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2025Article
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- Neural network emulation of the human ventricular cardiomyocyte action potential: a tool for more efficient computation in pharmacological studies.bioRxiv : the preprint server for biology · 2023Article
- Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model.PLoS computational biology · 2023Article
- Analysis of noisy transient signals based on Gaussian process regression.Biophysical journal · 2023Article
- Linking cortex and contraction-Integrating models along the corticomuscular pathway.Frontiers in physiology · 2023Article
- CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities.Frontiers in bioinformatics · 2023Article
- Alternative strategies in cardiac preclinical research and new clinical trial formats.Cardiovascular research · 2022Review
- Automated model calibration with parallel MCMC: Applications for a cardiovascular system model.Frontiers in physiology · 2022Article
- A novel modular modeling approach for understanding different electromechanics between left and right heart in rat.Frontiers in physiology · 2022Article
- NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories.Frontiers in physiology · 2022Article
- Modular assembly of dynamic models in systems biology.PLoS computational biology · 2021Article
- Contribution of HCN1 variant to sinus bradycardia: A case report.Journal of arrhythmia · 2021Article
- RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.Nucleic acids research · 2021Article
- Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective.NPJ systems biology and applications · 2021Article
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2 authors.
Funding
Abstract
Computational biologists have been developing standards and formats for nearly two decades, with the aim of easing the description and exchange of experimental data, mathematical models, simulation experiments, etc. One of those efforts is CellML (cellml.org), an XML-based markup language for the encoding of mathematical models. Early CellML-based environments include COR and OpenCell. However, both of those tools have limitations and were eventually replaced with OpenCOR (opencor.ws). OpenCOR is an open source modeling environment that is supported on Windows, Linux and OS X. It relies on a modular approach, which means that all of its features come in the form of plugins. Those plugins can be used to organize, edit, simulate and analyze models encoded in the CellML format. We start with an introduction to CellML and two of its early adopters, which limitations eventually led to the development of OpenCOR. We then go onto describing the general philosophy behind OpenCOR, as well as describing its openness and its development process. Next, we illustrate various aspects of OpenCOR, such as its user interface and some of the plugins that come bundled with it (e.g., its editing and simulation plugins). Finally, we discuss some of the advantages and limitations of OpenCOR before drawing some concluding remarks.
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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.