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OpenCOR: a modular and interoperable approach to computational biology.

Garny A, Hunter PJ - Front Physiol (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Auckland Bioengineering Institute, The University of Auckland Auckland, New Zealand.

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.

No MeSH data available.


Graphical user interface. The graphical user interface consists of a central area where files are loaded and rendered (the OpenCOR logo is shown, if no files are opened). The rendering of a file depends on the selected view (to the right of the central area). In the case of the Editing mode (to the left of the central area), the views currently available are the CellML Annotation view, the Raw view and the Raw CellML view. Several windows (the CellML Model Repository window, the File Browser window, the File Organiser window and the Help window) are also available. By default, they are docked around the central area, but they can also be hidden or undocked.
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Figure 1: Graphical user interface. The graphical user interface consists of a central area where files are loaded and rendered (the OpenCOR logo is shown, if no files are opened). The rendering of a file depends on the selected view (to the right of the central area). In the case of the Editing mode (to the left of the central area), the views currently available are the CellML Annotation view, the Raw view and the Raw CellML view. Several windows (the CellML Model Repository window, the File Browser window, the File Organiser window and the Help window) are also available. By default, they are docked around the central area, but they can also be hidden or undocked.

Mentions: Figure 1 shows what the GUI version of OpenCOR looks like when started for the very first time (opencor.ws/user/userInterfaces/graphicalUserInterface.html). Initially, no files are opened, so the OpenCOR logo is shown in the central area of the GUI. Upon opening a file, the logo is replaced with a rendering of the file. The rendering is based on the selected mode and view (to the left and to the right of the central area, respectively). There are currently two modes available: Editing and Simulation. Each mode offers one or several views. In the case of the Editing mode, those views are the CellML Annotation view, the Raw view and the Raw CellML view.


OpenCOR: a modular and interoperable approach to computational biology.

Garny A, Hunter PJ - Front Physiol (2015)

Graphical user interface. The graphical user interface consists of a central area where files are loaded and rendered (the OpenCOR logo is shown, if no files are opened). The rendering of a file depends on the selected view (to the right of the central area). In the case of the Editing mode (to the left of the central area), the views currently available are the CellML Annotation view, the Raw view and the Raw CellML view. Several windows (the CellML Model Repository window, the File Browser window, the File Organiser window and the Help window) are also available. By default, they are docked around the central area, but they can also be hidden or undocked.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4319394&req=5

Figure 1: Graphical user interface. The graphical user interface consists of a central area where files are loaded and rendered (the OpenCOR logo is shown, if no files are opened). The rendering of a file depends on the selected view (to the right of the central area). In the case of the Editing mode (to the left of the central area), the views currently available are the CellML Annotation view, the Raw view and the Raw CellML view. Several windows (the CellML Model Repository window, the File Browser window, the File Organiser window and the Help window) are also available. By default, they are docked around the central area, but they can also be hidden or undocked.
Mentions: Figure 1 shows what the GUI version of OpenCOR looks like when started for the very first time (opencor.ws/user/userInterfaces/graphicalUserInterface.html). Initially, no files are opened, so the OpenCOR logo is shown in the central area of the GUI. Upon opening a file, the logo is replaced with a rendering of the file. The rendering is based on the selected mode and view (to the left and to the right of the central area, respectively). There are currently two modes available: Editing and Simulation. Each mode offers one or several views. In the case of the Editing mode, those views are the CellML Annotation view, the Raw view and the Raw CellML view.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Auckland Bioengineering Institute, The University of Auckland Auckland, New Zealand.

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.

No MeSH data available.