Integrated Genome Browser (IGB) is an open source

Open source

The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...

 genome browser

Genome browser

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 prediction and structure, proteins, expression, regulation, variation,...

, a visualization

Visualization (graphic)

Visualization is any technique for creating images, diagrams, or animations to communicate a message. Visualization through visual imagery has been an effective way to communicate both abstract and concrete ideas since the dawn of man...

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

Sequence alignment

In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...

, and data from DNA microarrays.

History

Integrated Genome Browser was originally developed at Affymetrix

Affymetrix

Affymetrix is a company that manufactures DNA microarrays; it is based in Santa Clara, California, United States. The company was founded by Dr. Stephen Fodor in 1992. It began as a unit in Affymax N.V...

 to support visualization of data from the company's tiling array platform and was also partly supported via NIH

National Institutes of Health

The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...

 funding. It was released as open source in 2004. The National Science Foundation

National Science Foundation

The National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health...

 later funded further development of the tool as the front end for a companion data repository for plant genomic data sets.

Description

IGB is built on top of the Genoviz SDK, a Java

Java (programming language)

Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...

 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

Representational State Transfer

Representational state transfer is a style of software architecture for distributed hypermedia systems such as the World Wide Web. The term representational state transfer was introduced and defined in 2000 by Roy Fielding in his doctoral dissertation...

-style Web services (Distributed Annotation System

Distributed Annotation System

The Distributed Annotation System is used in bioinformatics to share and collate genomic annotation information. It is an open source project.From the web site:...

) and a simple file-system based approach called QuickLoad.

Supported formats

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

Affymetrix

Affymetrix is a company that manufactures DNA microarrays; it is based in Santa Clara, California, United States. The company was founded by Dr. Stephen Fodor in 1992. It began as a unit in Affymax N.V...

 CHP, FASTA

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 :...

, GFF, GTF

Gene transfer format

The Gene transfer format is a file format used to hold information about gene structure. It is a tab-delimited text format based on the general feature format , but contains some additional conventions specific to gene information. A significant feature of the GTF is that it is validatable:...

, 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

FreeHEP

FreeHEP is an open source Java library designed to make programming high energy physics applications easier. While the name and main focus of the project is high energy physics, many self-contained APIs in the library are generic and suitable for non-physics applications.FreeHEP is distributed...

 library. These include EPS

Encapsulated PostScript

Encapsulated PostScript, or EPS, is a DSC-conforming PostScript document with additional restrictions which is intended to be usable as a graphics file format...

, PostScript

PostScript

PostScript is a dynamically typed concatenative programming language created by John Warnock and Charles Geschke in 1982. It is best known for its use as a page description language in the electronic and desktop publishing areas. Adobe PostScript 3 is also the worldwide printing and imaging...

, PDF, EMF

Windows Metafile

Windows Metafile is a graphics file format on Microsoft Windows systems, originally designed in the 1990s. Windows Metafiles are intended to be portable between applications and may contain both vector graphics and bitmap components....

, SVG, SWF

SWF

SWF is an Adobe Flash file format used for multimedia, vector graphics and ActionScript. Originating with FutureWave Software, then transferred to Macromedia, and then coming under the control of Adobe, SWF files can contain animations or applets of varying degrees of interactivity and function.,...

, CGM

Computer Graphics Metafile

Computer Graphics Metafile is a free and open international standard file format for 2D vector graphics, raster graphics, and text, and is defined by ISO/IEC 8632.-Overview:...

, GIF, PNG, and PPM

Portable pixmap

The phrase Netpbm format commonly refers to any or all of the members of a set of closely related graphics formats used and defined by the Netpbm project....

.

External links

• Genoviz SDK at SourceForge
• IGB Bioviz site at the University of North Carolina at Charlotte
  University of North Carolina at Charlotte
  The University of North Carolina at Charlotte , also known as UNC Charlotte or simply Charlotte, is a public research university located in Charlotte, North Carolina, United States...
  
  
• Affymetrix IGB site
• IGB page at the Huntsman Cancer Institute
  Huntsman Cancer Institute
  Huntsman Cancer Institute is an NCI-designated cancer research facility and hospital located on the campus of the University of Utah in Salt Lake City, Utah. It is the only National Cancer Institute-designated Cancer Center in the Intermountain West. This title ensures patients benefit from the...