Abstract

WebGimm is a Java Web Start based tool for performing gene and sample clustering analysis of microarray data and enrichment analysis on the results of clustering. WebGimm operates on the client-server paradigm and offloads the burden of computation from the user's machine to our servers. The client is based on the Java platform and hence is available for Windows, MacOS X as well as various flavours of Linux and UNIX systems. Further, being based on Java Web Start, it can be launched very easily from a JNLP link as well as from the user's desktop and updated with new features seamlessly. Users use the client to upload their data for analysis, upon which the client displays a small preview of the data for user's convenience. The tool also provides options for pre-processing the input if desired. Users can specify the clustering algorithms to be used as well as appropriate parameters for the same. Once all options for analysis are selected, the client submits a computation request and the data to the servers hosted by the Laboratory for Statistical Genomics. Users are provided with updates about the progress of computation. On completion of clustering, users can proceed to perform enrichment analysis on the results of clustering analysis. WebGimm includes an integrated Functional Treeview which can be used for viewing the results of clustering analysis and the associated functional annotations. Users can also download the results of their analysis from the server. Availability of options for data pre-processing, a range of clustering algorithms, enrichment analysis and a very well integrated display of the results of analysis makes WebGimm a unique tool of its kind.

Availability

WebGimm can be launched as a Java Web Start application from this link, or by cliking on the logo above.

Help about using the client is available from this link.

Example input data for clustering analysis can be found here.

Source code for the client as well as the server is available here. Instructions about installing the client and the server are available here.

Java Web Start needed to launch this application is a standard component of the Java runtime available from Sun Microsystems.

Contact

mario.medvedovic@uc.edu