1. Software Tools

Here we introduce the tools used in this module and provide instructions for getting them set up to perform the tasks in this module.

1.1. MAP Client

The Musculoskeletal Atlas Project Client (MAP Client) is an open-source cross-platform framework for managing workflows. A workflow, as far as MAP Client is concerned, consists of a number of connected workflow steps. The MAP Client framework is a plugin-based application where the plugins are workflow steps. MAP Client is a Python based application which makes use of the Qt widget library.

Documentation for the project can be found at MAP Client documentation.

MAP Client is available to download from MAP Client download

To get the best out of the MAP Client you will need to get some plugins, by default the MAP Client comes with five basic plugins. A collection of available plugins can be found at MAP Client plugins.

1.2. OpenCOR

OpenCOR is a very flexible model management, editing, and simulation tool with many features. The full Tutorial on CellML, OpenCOR & the Physiome Model Repository tutorial covers a lot of material that is relevant to this tutorial, but before continuing here it is useful to quickly run through the section Create and run a simple CellML model: editing and simulation to get a bit of familiarity with the tool.

Instructions for obtaining and using OpenCOR are covered in the Install and Launch OpenCOR. If you are using one of the DTP computers, then the correct version of OpenCOR will already be installed, but for the purposes of this module you need to install the 17 March 2018 snapshot, or newer, verison of OpenCOR.

1.2.1. Connecting OpenCOR to your PMR account

Once you have OpenCOR installed, we want to connect it to PMR to enable you to archive and share your work. If you follow the instructions over at Using PMR with OpenCOR to create an account on the teaching instance of the Physiome Model Repository (PMR) and then set up OpenCOR to use that account. You can use this CellML model as the test model for that part of the tutorial.

Here is a video tutorial explaining how to connect the PMR with OpenCOR.


The teaching instance of the repository is a mirror of the main repository site found at http://teaching.physiomeproject.org/, running the latest development version of PMR2. User accounts are periodicly synchronised from the main repository, but if you recently created an account on the main site you might need to also create a new account on the teaching instance.

Any changes you make to the contents of the teaching instance are not permanent, and will be overwritten with the contents of the main repository whenever the teaching instance is upgraded to a new release of PMR2. For this reason, you can feel free to experiment and make mistakes when pushing to the teaching instance. Please subscribe to the cellml-discussion mailing list to receive notifications of when the teaching instance will be refreshed.

See the section Migrating content to the main repository for instructions on how to migrate any content from the teaching instance to the main (permanent) Auckland Physiome Repository.