Developing the Virtual Physiological Human

This tutorial will demonstrate tools, techniques and best practices that aid scientists in the development and application of computational models and simulation experiments in their work toward the creation of a virtual physiological human. The Physiome Model Repository (PMR) provides a framework for the storage, curation and exchange of data. By using standards suitable to their data, scientists maximise their ability to reuse existing knowledge and enable others to make use of their achievements in novel work. Annotations ensure scientists are able to find existing data and are also able to correctly interpret and apply their own data. These tutorials are designed to help demonstrate and promote practices which will aid attendees in their own work. Attendees are encouraged to raise issues specifically related to their needs with the tutors.

Documentation for the software used in this tutorial is available online, including the most recent version of this tutorial itself. This tutorial guides the particpant through three common computational modelling scenarios faced by scientists working toward the virtual physiologial human. We use these scenarios to achieve scientific outputs using the covered tools tools and demonstrating practices we believe will help ensure reproducible and reusable science. Each of the scenarios listed below should be worked through in order and in each scenario we provide examples using either OpenCOR or the MAP workflow tool.

When interacting directly with Mercurial, this tutorial demonstrates how to work with the Physiome Model Repository using TortoiseHg, which provides a Windows explorer integrated system for working with Mercurial repositories.

Brief mention of the equivalent command line versions of the TortoiseHg
actions will also be mentioned, so that these ideas can also be used without
a graphical client, and on Linux or OS X and similar systems. These will be denoted
by boxes like this.

This tutorial requires you to have:

• A Mercurial client such as TortoiseHg or Mercurial installed;
• The OpenCOR CellML modelling environment and/or the MAP workflow tool installed; and
• A text editor such as Notepad++ or gedit.

• Creating a new piece of work
  • Working with the repository using Mercurial
    • Registering an account and logging in
    • Mercurial username configuration
  • A new CellML-based piece of work
    • Create a new workspace
    • Populate with content
    • Push back to the repository
  • A new image segmentation study

• Reproducing published data
  • Reproducing model behavior in OpenCOR
    • Cloning an existing workspace
    • Check the model
    • Revert to an earlier version of the model
  • Recreating a published image segmentation study
    • Import workflow

• Find an existing piece of work and extend it
  • Extending an existing CellML model
    • Forking an existing workspace
    • Cloning your forked workspace
    • Quietening the self excitation
    • Adding an electrical stimulation protocol
  • Wrapping your favorite tool as a MAP client plugin