92. Data Visualization for Distributed Bioinformatics 

Gregg Helt, Suzanna Lewis, Nomi Harris, and Gerald M. Rubin 
Berkeley Drosophila Genome Project, University of California, Berkeley, California 
gregg@fruitfly.berkeley.edu 

A significant challenge for genome centers is to make the data being generated available to biologists in a succinct and meaningful way. We are addressing this problem by creating extensible, reusable graphical components specifically designed for developing genome visualization applications. With careful planning and design this toolkit enhances the ability for others and ourselves to rapidly develop genome visualization applications for the Internet and as editing applications. 

The visualization toolkit is written in the Java programming language. Our applications are being designed to read XML files. We will describe our component based approach and demonstrate a variety of visually distinct applications that are all based upon the same underlying components. These range from whole genome views of chromosomes to multiple alignment views of sequence data. The different views of the data are interconnected via shared, common data models that underlie the various displays. The views are also linked to external databases to retrieve and display textual data on selected features. Different types of analysis can be dynamically performed on the data and the results displayed on the maps. This analysis code is dynamically loaded when requested, to minimize the initial loading time. 

Other groups can reuse this work in various ways: genome centers can reuse large parts of the genome browser with minor modifications, bioinformatics groups working on sequence analysis can reuse components to build front ends for analysis programs, and biology labs can reuse components to publish results as dynamic Web documents. 

The BDGP has established a collaborative agreement with a small startup, Neomorphic, to develop improved versions of the widgets initially begun at the BDGP. This will provide the additional resources necessary to allow us to provide commercial-grade, thoroughly documented products. Under the terms of this collaboration, all the products of the collaboration will be made available to academic and government institutions for a nominal fee.