Creating CellML exposures¶
CellML models in the Auckland Physiome Repository are presented through exposures. An exposure is a view of a particular revision of a workspace, and is quite flexible in terms of what it can present. A workspace may contain one or more models, and any number of models may be presented in a single exposure. Exposures generally take the form of some documentation about the model(s), a range of ways of looking at the model(s) or their metadata, and links to download the model(s).
The example below shows the main exposure page for the Bondarenko et al. 2004 workspace. This workspace contains two models, which can be viewed via the Navigation pane on the right hand side of the page.
If you click on one of the model navigation links, it will take you to the page for that particular model. Exposures most often present a single model, although they can present any number of models, each with its own documentation and views.
Most of the CellML exposures in the repository are currently of this type, with a main documentation page containing navigation links to the model or models themselves.
The model pages have links that enable the user to do things like view the model equations, look at the citation information, or run the model as an interactive session using the OpenCell application. These links are found in the pane titled Views available on the right hand side of the page.
This tutorial contains instructions on how to create one of these standard CellML exposures, as well as information about how to create other alternative types of exposure.
Creating standard CellML exposures¶
In this example I will use a fork of the the Beeler Reuter 1977 workspace. Creating a fork of a workspace creates a clone of that workspace that you own, and can push changes to. You can fork any publicly available workspace in the Auckland Physiome Repository. For more information on this feature, refer to the information on features or collaboration, or see the relevant section of the tutorial.
At this point you are recommended to submit the workspace for publication, using the state: menu at the top right of the workspace view page. This is especially important if you decide to make an exposure public, as having a private workspace for a public exposure will impede access of linked data, such as images for the introduction to that particular exposure.
Choose the revision to expose¶
As an exposure is created to present a particular revision of a workspace, the first thing to do is to navigate to that revision. To do this, first find the workspace - if this is your own workspace, you can click on the My Workspaces button in the navigation bar of the repository and find the workspace of interest in the listing displayed. After navigating to your workspace, click on the history button in the menu bar.
Now you can select the revision of the workspace you wish to expose by clicking on the manifest of that revision. Usually you will want to expose the latest revision, which appears at the top of the list.
After selecting the revision you wish to expose, click on the workspace actions menu at the far right end of the menu bar and select create exposure.
Building the exposure¶
Selecting the create exposure option in the menu bar will bring you to the first page of the exposure wizard. This web interface allows you to select the model files, documentation files, and settings that will be used to create the exposure.
The initial page of the exposure creation wizard allows you to select the main documentation file and the first model file. Select the HTML annotator option and the HTML documentation file for the workspace in the Exposure main view section. For the New Exposure File Entry section, choose the CellML file you wish to expose, and select CellML as the file type.
Documentation should be written in HTML format. Some previous users of the CellML repository may be familiar with the tmpdoc style documentation, which has be deprecated. For an example of what a fairly standard HTML documentation file might look like, take a look at the documentation for the Beeler Reuter 1977 model.
Once you have selected the documentation and model files and their types, click on the Add button. This will take you to the next step of the wizard, where you can select various options for the model you have chosen to expose, and will allow you to add further model files to the exposure if desired.
The wizard shows a subgroup for each CellML file to be included in the exposure. For each CellML file, select the following options:
- Documentation file - select the HTML file created to document the model
- View generator - select HTML annotator option
- Basic Model Curation
- Curation flags - CellML model repository curators may select flags according to the status of the model
- License and Citation
- File/Citation format - select CellML RDF metadata to automatically generate a citation page using the model RDF
- License - select Creative Commons Attributions 3.0 Unported, in the cases where the above option is unsuitable.
- Source Viewer
- Language Type - select xml
- SedML file
- The SedML file associated with the given CellML file; if specified, the ‘Launch with OpenCOR’ link will open this file instead of the CellML file.
- Manifest path
- A COMBINE archive manifest file associated with the CellML file; if specified, a COMBINE Archive download link will be enabled for the exposure page for this CellML file.
After selecting the subgroup options, you need to select the Update button to apply the chosen options for the exposure builder, as this is an independent subform to the main form. The options you selected will be ignored if this Update button is not selected, and the options will be replaced by the default options when you click Build before this was done.
For exposures where you wish to expose multiple models, click on the Add file button at this stage to create another subgroup. You can then use this to set up all the same options listed above for the additional model file. Remember to click Update when you have completed selecting the options for each subgroup before adding another subgroup.
After setting all the options for the models you wish to expose, click on the Build button. The repository software will then create the exposure pages and display the main page of the exposure.
Making your work publicly accessible¶
In order to make the exposure visible and searchable, you will need to publish it. You can choose to submit your exposure for review, so that the repository administrators or curators will know to publish it for you. Naturally, if you have sufficient privileges you can publish it directly.
Other types of exposure¶
Because the exposure builder uses HTML documentation, it is possible to create customized types of exposure that differ from the standard type shown above. For example, you might want to create an exposure that simply documents and provides links to models in a workspace that are encoded in languages other than CellML. You can also use the HTML documentation to provide tutorials or other documents, with resources stored in the workspace and linked to from the HTML.
Examples of other exposure types:
Making an exposure using “rollover”¶
As explained earlier, an exposure aims to bring a particular revision to the attention of users who are browsing and searching the repository.
“Rolling over” an exposure is the method used when a workspace already has an existing exposure, and the updates to the workspace have not fundamentally changed the structure of the workspace. This means that all the information used in making the previous exposure is still valid for making a new exposure of a more recent revision of the workspace. Strictly speaking, an exposure can be rolled over to an older revision as well, but this is not the usual usage.
A forked workspace contains all of the revision history of the workspace it was created from, but has no linkages to any of the exposures that existed for the original workspace. However, you may navigate to the history of the original workspace and select any exposure, then select the wizard tab to the link to its exported structure, from which the exposure can be migrated over. Please see the section on migrating exposure for more details.
From the view page of your workspace, select “exposure rollover”.
The exposure rollover button takes you to a list of revisions of the workspace, with existing exposures on the right hand side, and revision ids on the left. Each revision id has a radio button, used to select the revision you wish to create a new rolled over exposure for. Each existing exposure also has a radio button, used to select the exposure you wish to base your new one on. The most common use case is to select the latest exposure and the latest revision, and then click the Migrate button at the bottom of the list.
The new exposure will be created and displayed. When a new exposure is created, it is initially put in the private state. This means that only the user who created it or other users with appropriate permissions can see it, and it will not appear in search results or model listings. In order to publish the exposure, you will need to select submit for publication from the state menu.
The state will change to “pending review”. The administrator or curators of the repository will then review and publish the exposure, as well as expiring the old exposure.