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Petri Klemelä, Aleksi Kallio, Taavi Hupponen, Massimiliano Gentile , Rimvydas Naktinis, Eija Korpelainen (CSC - IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland)The Chipster genome browser is a Java based interactive tool for navigating and visualizing data with genomic coordinates. Our primary goal has been to enable users to view their data and analysis results already during the analysis and not just in the end of the workflow. In practice this is achieved by direct support for commonly used file types, integration into Chipster analysis environment (http://chipster.csc.fi/), and efficient memory management. BAM and BED files are sorted and indexed automatically and coverage is calculated in real time. Users can use BED files for rapid navigation, highlight SNPs, and zoom all the way from chromosome into nucleotide level. Genome browser has a three tier architecture for better extensibility and performance, with the presentation layer implemented using the standard Java Graphics2D library. We have also initiated a new collaborative project to develop innovative genomic visualizations using OpenGL rendering and welcome interested collaborators.