There are several ways of obtaining and using models from the Auckland Physiome Repository, and which you choose will depend on the way you intend to use the models. If you are simply interested in running a particular model and viewing the output, you can use links found on model exposure pages to get hold of the model files. There links available for a large number of models that will load the model directly into the OpenCell application, allowing you to explore simulation results with the help of a model diagram.
If you intend to use the model for further work, for example saving changes to the model or creating a new model based on an existing model or parts of an existing model, you should use Git to obtain the files. In this way you also obtain the complete revision history of the files, and can add to this history as you make your own changes.
The Auckland Physiome Repository has a basic search function that can be accessed by typing search terms into the box at the top right hand side of the page. You can use keywords such as cardiac or insulin, author names, or any other terms relevant to the models you want to find.
If your search is yielding too many results, you may either try to narrow it down by choosing more or different keywords (eg. goldbeter 1991 instead of just goldbeter), or you can click the Advanced Search link just under the search box on the results page. This will take you to a search page where you can select specific item types (eg. exposures or workspaces).
Once you have found the model you are interested in, there are several ways you can view or download it.
The most common use of the Auckland Physiome Repository web interface is probably to view information about models found on exposure pages, and to then download the models from these pages for simulation in a CellML supporting application.
Below is an example of a CellML exposure page. It contains documentation about the model(s), a diagram of the what the model(s) represent, and a navigation pane that allows the user to select between available versions of the model. Many models only have one version, but in this case there are two variants.
If you click on one of the model variant navigation links, you will be taken to a sub-page of the exposure which will allow you to view the actual CellML model in a number of ways.
On this page there are a number of options under a Views available panel at the right hand side.
The OpenCell session that is loaded when clicking on the Simulate using OpenCell link looks something like this:
All data in the Auckland Physiome Repository are stored in workspaces and each workspace is a Git repository. The most comprehensive method of downloading content from Auckland Physiome Repository is to clone the workspace containing the desired data. In this manner you will have a local copy of the entire history of that data, including all provenance data, and the ability to step back through the history of the workspace to a state that may not be available via the download links in the exposure pages discussed above. If you would like to modify the contents of workspace, making use of Git will ensure accurate provenance records are maintained as well as all the other benefits of using a version control system.
As software tools like OpenCOR and MAP Client evolve, they will be able to hide a lot of the Git details and present the user with a user interface suitable for their specific application areas. Directly using Git is, however, currently the most powerful way to leverage the full capabilities of Auckland Physiome Repository.
If you are using the command line Git client, you can easily clone the underlying repository for an exposure simply by selecting the text box inside the Collaboration portlet and paste that command into a terminal, or right click on the name of the workspace under the Source portlet and copy that URL and then paste that into your Git client.
Detailed instructions for working with Git can be found in the CellML repository tutorial.