NEWS: Our paper describing the fuge toolkit has been accepted for publication in the journal of bioinformatics. An electronic version of the paper is available online on the web site of the journal.

Khalid Belhajjame, Andrew R. Jones and Norman W. Paton. A Toolkit for Capturing and Sharing FuGE Experiments. Bioinformatics, 2008.

The aim of the toolkit made available through this page is to ease the specification and sharing of FuGE experimental processes. Using the toolkit, users are able to capture experiments in any extension of FuGE. The toolkit also provides users with a Web interface for browsing collected experiments using pre-defined canned queries.

A demonstration that shows the web interface generated by the toolkit for browsing GelML experiments is available and can be accessed here

The toolkit architecture is illustrated in Figure 1. For data capture, we make use of PEDRo, a Java standalone application that, given an XML Schema document (specifying a FuGE extension in this case), generates a data entry tool for specifying experiments in that model.

Figure 1: Toolkit architecture

The data entry tool provides users with forms and assists them in their use. For example, sample values that can be accepted by a field in a form are displayed when they are available. Also, if a field represents a term from a controlled vocabulary, then the user is provided with a drop down list containing the legal terms that can be used as a value for the field in question. Once the experiment is specified, the user can export it as an XML document that validates against the XML Schema of the experiment model.

The experiments specified using the data entry tool can be stored within a database system to allow their dissemination. We use for this purpose eXist, a freely available open source and native XML database management system.

Users can browse stored experiments using the Data Access Web Application. This is a collection of Java Server Pages that interact with the eXist database system to answer users' requests. Specifically, users are provided with a set of canned queries. These are encoded in the form of pre-defined XQuery queries that are issued by the Data Access Web Application to the eXist database system for processing. The results of queries are XML documents that are rendered in a user readable format using XML style sheets. The toolkit comes with generic XSL style sheets for rendering XML documents in a tabular format.

As a proof of a concept, we used the toolkit to capture and browse GelML experiments. You can visit the You can visit the web page generated by the toolkit for browsing GelML experiments here.

Useful links

• A user guide that provides useful information for installing and using the toolkit.
• A web page generated by the toolkit for browsing GelML experiments.
• An evaluation that we conduct to assess how well the system scale in the presence of a large number of experiments.