FISH Oracle 2

FISH Oracle 2 is a web-based software tool for the integrative analysis of cancer genomics data. It stores different kinds of downstream processed data from multiple samples in a single database. A powerful search interface allows to dynamically filter the data to be displayed with respect to different criteria. The combination of AJAX technology and a fast visualization engine facilitates a highly dynamic visualization for large amounts of data. FISH Oracle 2 is able to simultaneously display different data sets, thus simplifying their comparison. Filter and display options can be changed on the fly. High quality image export enables the life scientist to easily communicate the results, e.g. in presentations or publications. A comprehensive data administration assures to keep track of the data stored in the database.

Availability

Built on Java, the Google Web Toolkit and the AnnotationSketch component from GenomeTools (and Java bindings), The latest version of FISH Oracle is freely available as source code from github.com/mader/fishoracle. Installation and configuration of the application is documented in the user manual. Also, an automatic installation script is available for Ubuntu 12.04. A virtual machine offering a running instance of FISH Oracle is also available (3 GB).

All FISH Oracle related sources including the FISH Oracle application are available at github.com/mader or can be downloaded directly at this page:

We also offer a demo installation of FISH Oracle on our servers. Use the username guest and the password demo to log in.

Screencast

The video below illustrates the use of FISH Oracle 2 for searching and visualizing different kinds of genomic data in the context of genomic annotations. Use the navigation bar on the bottom of the video window to navigate the video. The button on the right-hand edge of the video window maximizes the video to fullscreen.

Publications

M. Mader, R. Simon and S. Kurtz:
FISH Oracle 2: A web server for integrative visualization of genomic data in cancer research
Journal of Clinical Bioinformatics, submitted

 

M. Mader, R. Simon, S. Steinbiss and S. Kurtz:
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.
Journal of Clinical Bioinformatics, 1:20 (2011)

Contact

Stefan Kurtz
Center for Bioinformatics, University of Hamburg
Bundesstr. 43, 20146 Hamburg, Germany
Phone +49 40 42838 7311, Fax. +49 40 42838 7312