OpenCOR: a modular and interoperable approach to computational biology

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.

Myokit: A simple interface to cardiac cellular electrophysiology

“…A good example of a GUI-based tool is OpenCOR (Garny and Hunter, 2015), a merger of the older tools COR and OpenCell/ PCEnv. It provides an interface through which CellML models can be loaded, single-cell simulations are run and the results may be visualized.…”

LongQt: A cardiac electrophysiology simulation platform

“…However, increasing complexity of models and programming expertise required to use these models is still a research barrier. A number of simulation platforms and model repositories have been developed to facilitate electrophysiology computer simulation and visualization, including OpenCOR, CESE Plus 2.0, Myokit and more [19], [21], [22], [23]. However, there remains a great need to bridge experimental and theoretical worlds in electrophysiology research.…”

The Virtual Physiological Human: Ten Years After

“…An Application Programming Interface (API) is available but more user-friendly software called OpenCOR 15 , developed to create, edit and run CellML models is also available (16). A related XML standard, designed specifically for biochemical reactions and developed by the systems biology community, called SBML 16 , has many alternative software platforms.…”

“…A related XML standard, designed specifically for biochemical reactions and developed by the systems biology community, called SBML 16 , has many alternative software platforms.…”