Integrated Genome Browser (IGB) (pronounced Ig-Bee) is an

open-source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...

genome browser In bioinformatics, a genome browser is a graphical interface for display of information from a biological database for genomic data. Genome browsers enable researchers to visualize and browse entire genomes with annotated data including gene predic ...

, a

visualization Visualization or visualisation may refer to: * Visualization (graphics), the physical or imagining creation of images, diagrams, or animations to communicate a message * Data visualization, the graphic representation of data * Information visualiz ...

tool used to observe biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from

DNA microarrays A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to ...

History

Integrated Genome Browser was first developed at

Affymetrix Affymetrix is now Applied Biosystems, a brand of DNA microarray products sold by Thermo Fisher Scientific that originated with an American biotechnology research and development and manufacturing company of the same name. The Santa Clara, Califor ...

for their scientists and public sector collaborators to visualize data from genome-wide tiling arrays. The first iterations of IGB were developed using funding from

NIH The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late 1 ...

awarded to company scientists Gregg Helt and Tom Gingeras. In 2004, Affymetrix released IGB as open source software, along with the Genoviz SDK, a graphics library for building genome browser applications. The first release of the code base was done as a compressed file archive. Soon after, the code was imported into a new repository at SourceForge. Since then, all development has proceeded in public under an open source model. In early 2008, a group led by former Affymetrix employee Ann Loraine began developing and maintaining IGB, supported by funding from the National Science Foundation and new investigator funds from UNC Charlotte. Since then, Loraine, her students, and collaborators have added many new features and capabilities, notably support for visualizing high-throughput sequencing data from Illumina and other platforms. In 2014, they migrated the source code to a git repository at

Bitbucket Bitbucket is a Git-based source code repository hosting service owned by Atlassian. Bitbucket offers both commercial plans and free accounts with an unlimited number of private repositories. Services Bitbucket Cloud Bitbucket Cloud (previo ...

Description

IGB is built on top of the Genoviz SDK, a

Java Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mo ...

library that implements key visualization features such as dynamic, real-time zooming and scrolling through a genomic map, a feature of the IGB browser that sets it apart from many similar tools. IGB is also distinguished by the ease with which individual labs can set up data source servers to share data, notably, via

REST Rest or REST may refer to: Relief from activity * Sleep ** Bed rest * Kneeling * Lying (position) * Sitting * Squatting position Structural support * Structural support ** Rest (cue sports) ** Armrest ** Headrest ** Footrest Arts and ente ...

-style Web services ( Distributed Annotation System) and a simple file-system based approach called QuickLoad. Integrated Genome Browser 9

Supported formats

IGB reads data in dozens of formats, including BAM, BED,

CHP,

FASTA FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. History The original FASTA program ...

, GFF,

GTF GTF may stand for: Companies and organizations * Georgia Tech Foundation * German Taekwondo Federation * German Taxpayers Federation * German Tennis Federation * Global Tamil Forum * Global Thinkers Forum, in London, England * Graduate Theologica ...

, PSL, SGR, and WIG. The most up-to-date list is available at the BioViz Wiki. IGB can output visualized data in dozens of formats via the FreeHEP library. These include

EPS EPS, EPs or Eps may refer to: Commerce and finance * Earnings per share * Electronic Payment Services, in Hong Kong, Macau, and Shenzhen, China * Express Payment System, in the Philippines Education * Edmonton Public Schools, in Edmonton, ...

PostScript PostScript (PS) is a page description language in the electronic publishing and desktop publishing realm. It is a dynamically typed, concatenative programming language. It was created at Adobe Systems by John Warnock, Charles Geschke, ...

PDF Portable Document Format (PDF), standardized as ISO 32000, is a file format developed by Adobe in 1992 to present documents, including text formatting and images, in a manner independent of application software, hardware, and operating systems. ...

, EMF,

SVG Scalable Vector Graphics (SVG) is an XML-based vector image format for defining two-dimensional graphics, having support for interactivity and animation. The SVG specification is an open standard developed by the World Wide Web Consortium sinc ...

SWF SWF ( ) is an Adobe Flash file format used for multimedia, vector graphics and ActionScript.Open Screen Pr ...

, CGM,

GIF The Graphics Interchange Format (GIF; or , see pronunciation) is a bitmap image format that was developed by a team at the online services provider CompuServe led by American computer scientist Steve Wilhite and released on 15 June 1987. ...

, PNG, and PPM.

References

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External links

Genoviz SDK at Bitbucket

IGB installer download site
Free bioinformatics software