University Home
Manchester Centre for Integrative Systems Biology

Plugins


Since version 1.5, the Taverna workflow system has a plugin mechanism which enables the software to be tailored to specific scientific domains. The following Taverna plugins have been developed here at the MCISB for use in systems biology and informatics in general:

  • PDFRenderer - enables Taverna to display PDF files
  • CSVRenderer - allows Taverna to display files in comma separated values format as a table
  • Excel2CSVReader - a local java processor which outputs a comma separated values String from a worksheet in an Excel file



PDFRenderer

This plugin is a renderer which can be used for viewing PDF documents from the Taverna workbench. The following steps are required to install this plugin:

  • Click on Tools > Plugin Manager
  • Click on the 'Find New Plugins' button and add a New Plugin Site by entering "MCISB" as site name and "http://dbk-ed.mib.man.ac.uk/taverna/1.7/plugins/" as the site URL then click OK
  • Click on PDF Renderer followed by install. This plugin will now be downloaded and installed
  • To enable the display of PDF documents in Taverna, the data must be tagged with a MIME type of 'application/pdf'.


CSVRenderer

This plugin is a renderer which can be used for viewing CSV documents which have been generated from Taverna workflows. To install this plugin:

  • Click on Tools > Plugin Manager
  • Click on the 'Find New Plugins' button and add a New Plugin Site by entering "MCISB" as site name and "http://dbk-ed.mib.man.ac.uk/taverna/1.7/plugins/" as the site URL then click OK
  • Click on CSVRenderer followed by install. This plugin will now be downloaded and installed
  • To enable the display of CSV files as tables in Taverna, the data must be tagged with a MIME type of 'text/csv'.
  • The tabular display can then be selected by pressing shift and left clicking the results CSV object and selecting view as comma separated values.



Excel2CSVReader

This plugin is a local Java processor which can be used for reading specfic worksheets from Excel files into a CSV document as part of a workflow. The following steps are required to install this plugin:

  • Click on Tools > Plugin Manager
  • Click on the 'Find New Plugins' button and add a New Plugin Site by entering "MCISB" as site name and "http://dbk-ed.mib.man.ac.uk/taverna/1.7/plugins/" as the site URL then click OK
  • Click on Excel2CSVReader followed by install. This plugin will now be downloaded and installed
  • Once Taverna has been re-started, this processor will be available in the service palette under the local services > local java widgets > io directory.

This processor requires 2 inputs, the path to an Excel file on your local file system and the worksheet number in the Excel file that you want outputted as a CSV document: