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OpenCor – Cardiac Regulation

To illustrate MAP-CORE – SIM-CORE integration, a Study has been realized, that is accessed through a SPARC Portal map (but can also be accessed through the Portal computational Study section). After selecting the relevant nodes in a flat-map, a user can specify simulation parameters within the flat-map and launch the OpenCOR simulation for execution within o²S²PARC. The results can be visualized in o²S²PARC and (soon) also within the flat-map.

OpenCOR is a software projects aimed at providing a modelling environment for CellML models, such as those developed as part of the Physiome Initiative and within SPARC.

Usage

The workflow is as follows:

  1. To begin, open the o²S²PARC platform in your browser by going to https://osparc.io/ and log in. This will then take you to your Dashboard. From the Dashboard click on the Templates tab on the top menu to see Template Studies available to you and then click on the [ISAN] osparc-opencor Template card.

  2. After creating your own instance of the OpenCOR Template or access it through a MAP-CORE map, you will see a simple flowchart consisting of two Services. The o²S²PARC-opencor Service will do the full simulation with your own input parameters.

    opencor_flow

  3. The input parameters you can choose will be the type of stimulation and normalized amplitude. You can access these by clicking on the osparc-opencor Service.

  4. You can get a little more information about the inputs by hovering over the value adjustment arrows on the right of each field.

    opencor_settings

  5. After you have chosen your preferred parameters, click Run at the top left corner of the Pipeline Workspace.

  6. When the osparc-opencor Service shows Success, all processes have completed. Double click on the 2D plot Service to switch to the Interactive View of the Workbench to plot the simulation outputs.

  7. Scrolling to the bottom of the 2D Plot Interactive View, you will see options for plotting with Rawgraph and various data inputs for plots. Select o²S²PARC inputs. There should be two files available for to plot in the 2D plot settings: “Membrane Potential and Heart rate” and “Membrane Potential (CSV-format)”.

  8. Choose the CSV-formatted file under the field o²S²PARC inputs.

    opecorinputs

  9. After loading the data, you can scroll down to see a line plot of the simulated transmembrane potential as a result of your chosen stimulus.

    opencor_spike