IGB Developer's Guide
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Version control

The main repository address is: https://bitbucket.org/lorainelab/integrated-genome-browser.

The IGB project uses git. 

 

 

IGB versioning - major and minor releases

IGB uses semantic versioning, described in Semantic Versioning 2.0.

IGB releases have version names like 8.3.0 or 8.4.2, following the naming convention [M].[N].[P], where M, N, and P are integers.

In IGB, N is the major release number, M is the minor release number, and P is the micro or "bug fix" release number. 

All new minor and bug fix releases of IGB support all API methods supported in earlier versions with the same major release number. New releases that increment the minor or micro numbers may contain changes to the API, but these will maintain backwards-compatibility with all prior versions from the same major release. This means that new minor or bug fix releases can run any IGB App built against earlier versions from the same major release.

New major releases of IGB will contain so-called "contract breaking" changes to the IGB API. This means that a new release that increments the major number (e.g., releasing IGB N.0.0) may include changes to the API methods that affect IGB Apps built using the previous major release.

For App Developers

To ensure that users can run your App when a new major version is released, you should re-build your App using the latest IGB platform and release it in the usual way. However, if you are unable to release an update to your App, users will always be able to run it using older versions of IGB, which they can get from our files download page at Sourceforge.

Genoviz SDK

IGB depends on the Genoviz Software Development Kit (Genoviz SDK) which is version-controlled in a separate repository at https://bitbucket.org/lorainelab/genoviz-sdk. When you build IGB, the compilation tool we use (mvn) will obtain the latest copy of the genoviz compiled code (a "jar" file) and install it locally.

 

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 "BioView" - 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. 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. 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.

In 2004, Affymetrix released IGB and NGSDK as open source software. This first release was done as a "tarball" on their Web site. In Jan. 2005, Affymetrix developers imported the tarball contents into a new CVS repository at Sourceforge and began using that for further development, discarding the internal repository at Affymetrix. In addition, they changed the name of the graphics library from "Neomorphic Genome Software Development Kit" to "Genoviz Software Development Kit". However, many of the graphics library's class names retain the prefix "Neo" - e.g., NeoWidget, NeoMap, etc.

In 2004, Ann Loraine joined the University of Alabama at Birmingham as an Assistant Professor, where she wrote funding proposals requesting further support for IGB and the Genoviz SDK. In 2008, she joined the College of Computing and Informatics at UNC Charlotte. Later that year, NSF awarded her a new grant to develop IGB and its companion data distribution site IGB Quickload. Developers at Affymetrix continued contributing to the code for several years after that. You can see their work by searching for commits from developers "chyekk" (Ed Erwin) and "gregghelt." 

After joining UNC Charlotte, Loraine and colleagues migrated the code to a subversion repository, also hosted at Sourceforge.  We continued to use this repository for many years. In 2014, we migrated the source code for IGB and the Genoviz SDK to a new git repository hosted at Atlassian's Bitbucket. 

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 released, 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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