The genome browser is used to visualize data of various kinds plotted against the genome. Tiling microarrays and ChIP-chip are two possible use-cases. It was originally written by Chris Bare.
For more information see:
The current build process is a mix of SBT 0.12.x and ant. There will be an SBT-only setup in the future.
cd genomebrowser-core sbt clean package cd .. cp genomebrowser-core/target/scala-2.9.2/*.jar lib ant
log4j junit gaggle (see gaggle.systemsbiology.net) colorpicker.jar from https://colorchooser.dev.java.net/ and http://javagraphics.blogspot.com/2007/04/jcolorchooser-making-alternative.html sqlite
CaliforniaIconPack, Crystal project icons, Icons stolen from Eclipse.
Features that straddle the zero point on circular chromosomes aren't handled properly.
- NCBI interface:
- lproks.cgi and leuks.cgi were replaced by ftp://ftp.ncbi.nih.gov/genomes/GENOME_REPORTS/ need to be worked into NCBI API
- Data exchange (NCBI/UCSC) should be external dependency