Version 3 (modified by kostas.karasavvas@…, 2 years ago)

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Goal

Enacting Taverna workflows via a web browser


Introduction

The Taverna Web Interface Generator is a web application that allows a user to run arbitrary Taverna workflows through a web page. The bioinformatician finds the required Taverna workflow in the myExperiment repository and makes a note of that workflow’s identifier. Appending that identifier to our web application’s URL constucts the URL that can be shared with the end user. The latter visits the URL and is presented with that workflow’s web form interface, where he can configure and execute it. Behind the scenes, the web application acquires the workflow details from myExperiment and constructs the appropriate user interface using templates. The user interface acts as an intermediary between the user and the Taverna server (using the REST API). The actual workflow results reside in the server and the web application fetches them on request.

The generator takes advantage of all available information in myExperiment to create an easy to understand interface for the user. For example, the workflow’s description is displayed together with tooltips for inputs’ descriptions as well as examples inputs. The users will have all the information they need, i.e. they need not be familiar with the workflow. Of course, that means that the generated interface is only as good as the available information that the workflow submitter provided. If information is missing in the repository it will also be missing from the interface. A link of the original workflow submission from myExperiment is provided if further information is required.

References

  1. Taverna: a tool for building and running workflows of services. Duncan Hull, Katy Wolstencroft, Robert Stevens, Carole Goble, Mathew R. Pocock, Peter Li, Tom Oinn. Nucleic acids research, Vol. 34, Web Server issue, pp. W729-W732, 2006
  2.  http://www.taverna.org.uk/documentation/taverna-2-x/server
  3. myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic acids research, Vol. 38 (suppl 2): W677-W682, 2010.
  4.  http://www.myexperiment.org

Installation and Requirements

The web application is implemented in Ruby, so a Ruby development environment needs to be available. Native packages of libxml, libopenssl and zlib may be required. Please use your favorite package manager to install them (an apt-get example is given). Note that some of the following native packages might already be installed in your system. For Debian-based systems, use this command:

$ sudo apt-get install ruby rubygems gcc build-essential libxml-ruby libopenssl-ruby libxml2-dev

To install the taverna web interface generator you only need the following command:

$ sudo gem install t2-web

Testing

Start the web application by typing:

$ t2_webapp.rb

Note that in some systems the executable will not be automatically in the path. Run:

$ gem environment

and add the value of EXECUTABLE DIRECTORY to your PATH.

Contact

  • Kostas Karasavvas -- kostas (dot) karasavvas (at) nbic (dot) nl
  • Marco Roos -- m (dot) roos1 (at) uva (dot) nl

Back to parent project elabfactory.