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To include these in your project, see the top-level POM.xml file in the Integrated Genome Browser project code base.
Background
From the late 1990s until around 2005, IGB and its graphics library (now called the Genoviz SDK) were closed-source software.
The original GenoViz library - called "BioViewBioViews" - was first developed by Gregg Helt at UC Berkeley as part of his PhD research. Around then, Helt and two colleagues (Martin Reese and Cyrus Harmon) formed a bioinformatics software company called Neomorphic to commercialize the BioView library, licensed the software from the University. With funding and development support from the Bioinformatics Department at Smith Kline Beecham, they continued to improve the library, renaming it the Neomorphic Genome Software Development Kit. During this period, several companies purchased licenses, including Exelixis and Smith Kline Beecham. Also during this period, Celera Genomics and the Institute for Genomic Research (TIGR) hired Neomorphic to build genome browser and annotation software. Ann Loraine joined the company in 1999 and helped build the Neomorphic Annotation Station for TIGR.
In October 2000, Affymetrix purchased Neomorphic and re-focused software effort on supporting and developing Affymetrix DNA microarray products. In 2001, Gregg Helt and colleagues began developing Integrated Genome Browser to visualize and analyze data from genome tiling arrays, which contained probes selected from (mostly) regular intervals along the genome. Visualization of probe intensity data alongside gene models was essential to developing algorithms to normalize and analyze the data, and the team at Affymetrix developed some of the first visual analytics algorithms in bioinformatics. Also, they developed some of the first indexed, random access file formats to enable partial loading of data sets that were too large to fit into computer memory. Support from Affymetrix along with federal grants to PIs Tom Gingeras and Gregg Helt funded early IGB development during this period. Affymetrix released IGB as part of their NetAffx Web site in the early 2000s.
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Unfortunately, over the years the early development history pre-dating the 2004 open source release has been lost. In addition, early products built using Genoviz SDK are also lost. When the developers at Affymetrix prepared the first open source releasedrelease, it seemed simpler and less risky to simply migrate the code directly into a new CVS repository and go from there. Now, of course, we are using tools that are more sophisticated than before, and we can easily trace how the code has changed dating from Jan 2005 until the present day. If you have questions about what you see, feel free to get in touch.
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