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Installing and using plugins video on youtube (featuring the BioCatalogue plugin)

Using the Taverna Workbench Plugin Manager, you are able to add to the functionality of Taverna by installing additional components depending on your requirements. This guide will illustrate how to use the Taverna Plugin Manager, and how to install a plugin for browsing the BioCatalogue from within Taverna, adding REST service support and an enhanced XPath functionality to the list of available services.

To use the Taverna Plugin Manager, navigate to the top menu bar of the Taverna Workbench, and select the Advanced tab, and subsequently the Updates and Plugins option. Alternatively, you may access this menu option by directly pressing F12 (function key 12). The resulting pop-up window will allow you to view the plug-ins currently installed in your version of Taverna (including any that require an update), find new plugins, and also disable/uninstall any plugins you no longer require the use of.

By clicking on the Find Updates button in the pop-up window, any pre-installed plugins will be updated to the current specification available on the remote servers.

The Find New Plugins button, however, will direct you to a secondary window, allowing you to browse the currently available plugins that are not pre-installed, and even include a third-party Web site where you can browse for additional plugins. By scrolling to the Prototype Plugins section of this window, a number of experimental plugins should be visible, including: BioCatalogue; REST Activity; and an XPath Activity plugins. Select these plug-ins to install and click on the Install button at the bottom of the window. This will now show a series of progress dialog boxes as each plugin is installed in turn. This process may take a while to complete (depending on the Internet connection). Once you have installed all the various plug-ins, you must restart the Taverna Workbench in order to use their capabilities.

On re-starting the Taverna Workbench, the first apparent difference to the Taverna Workbench is a new Service Catalogue Perspective below in the toolbar. Clicking on this tab allows you to access the vast content of the BioCatalogue Web service repository. By simply typing in a search term into the search box, we can instantly access the results and view the associated service and service provider data. An example of this search could include the word "KEGG". This would result in a number of results being returned. Clicking on the "Kegg" service, in the services tab pops up a window that contains detailed information about the service, including: the service submitter; the status of the service (whether it is down or not); and any example data or descriptions that would help a researcher use the service in one of their workflows. Similarly, a clicking on the DDBJ tag in the tag cloud also brings up a detailed information window.

We can also add a service directly into the Taverna Workbench by simply clicking on the small window button with a " + " in the top left of the icon (located on the far right of the bottom right panel of the pop-up window - above the star icon). If you navigate back to the design perspective, you should now see the added service in the Workflow Diagram and Workflow Explorer]. You can now freely integrate this service into the remainder of your workflow as you would a normal service.

A direct advantage of using the BioCatalogue Perspective within the Taverna Workbench is the ability to access content of existing services included in workflows. If you click on the DDBJ_Ensembl service that has been added, and then the Details tab in the Workflow Explorer, you will be able to see a new tab that has appeared at the bottom of the panel, called: "BioCatalogue Information". Clicking on this will return you to the BioCatalogue pop-up window and list all the detailed information with regards to service in question - all gathered dynamically straight from the BioCatalogue Web repository.

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