 Version 9.1.0 home screen | |
| Operating system | UNIX, Linux, Mac, MS-Windows |
|---|---|
| Type | Bioinformatics tool |
| License | CPL 1.0 |
| Website | bioviz |
Integrated Genome Browser (IGB) (pronounced Ig-Bee) [1] is an open-source genome browser, a visualization tool used to observe biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.
Integrated Genome Browser was first developed at Affymetrix 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 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.
In 2020, Oracle's Java Magazine named the Integrated Genome Browser as one of the 25 greatest Java apps ever written.
IGB is built on top of the Genoviz SDK, [2] a Java 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-style Web services (Distributed Annotation System) and a simple file-system based approach called QuickLoad.
IGB reads data in dozens of formats, including BAM, BED, Affymetrix CHP, FASTA, GFF, GTF, 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, PostScript, PDF, EMF, SVG, SWF, CGM, GIF, PNG, and PPM.
BioJava is an open-source software project dedicated to provide Java tools to process biological data. BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a huge range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid application development and analysis.
BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project.
IntelliJ IDEA is an integrated development environment (IDE) written in Java for developing computer software written in Java, Kotlin, Groovy, and other JVM-based languages. It is developed by JetBrains and is available as an Apache 2 Licensed community edition, and in a proprietary commercial edition. Both can be used for commercial development.
jMonkeyEngine is an open-source and cross-platform game engine for developing 3D games written in Java. It uses shader technology extensively and can be used to write games for Windows, Linux, macOS, Raspberry Pi, Android, and iOS. It uses Lightweight Java Game Library as its default renderer and another renderer based on Java OpenGL. it also supports OpenGL 2 to OpenGL 4.
Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.
The completion of the human genome sequencing in the early 2000s was a turning point in genomics research. Scientists have conducted series of research into the activities of genes and the genome as a whole. The human genome contains around 3 billion base pairs nucleotide, and the huge quantity of data created necessitates the development of an accessible tool to explore and interpret this information in order to investigate the genetic basis of disease, evolution, and biological processes. The field of genomics has continued to grow, with new sequencing technologies and computational tool making it easier to study the genome.
GenePattern is a freely available computational biology open-source software package originally created and developed at the Broad Institute for the analysis of genomic data. Designed to enable researchers to develop, capture, and reproduce genomic analysis methodologies, GenePattern was first released in 2004. GenePattern is currently developed at the University of California, San Diego.
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases and searching in large networks. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged. Cytoscape also has a JavaScript-centric sister project named Cytoscape.js that can be used to analyse and visualise graphs in JavaScript environments, like a browser.
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.
The Android SDK is a software development kit that includes a comprehensive set of development tools. These include a debugger, libraries, a handset emulator based on QEMU, documentation, sample code, and tutorials. Currently supported development platforms include computers running Linux, Mac OS X 10.5.8 or later, and Windows 7 or later. As of March 2015, the SDK is not available on Android itself, but software development is possible by using specialized Android applications.
Biology data visualization is a branch of bioinformatics concerned with the application of computer graphics, scientific visualization, and information visualization to different areas of the life sciences. This includes visualization of sequences, genomes, alignments, phylogenies, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging data. Software tools used for visualizing biological data range from simple, standalone programs to complex, integrated systems.
The UCSC Genome Browser is an online and downloadable genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels. The Genome Browser Database, browsing tools, downloadable data files, and documentation can all be found on the UCSC Genome Bioinformatics website.
IGB may refer to:
GeneNetwork is a combined database and open-source bioinformatics data analysis software resource for systems genetics. This resource is used to study gene regulatory networks that link DNA sequence differences to corresponding differences in gene and protein expression and to variation in traits such as health and disease risk. Data sets in GeneNetwork are typically made up of large collections of genotypes and phenotypes from groups of individuals, including humans, strains of mice and rats, and organisms as diverse as Drosophila melanogaster, Arabidopsis thaliana, and barley. The inclusion of genotypes makes it practical to carry out web-based gene mapping to discover those regions of genomes that contribute to differences among individuals in mRNA, protein, and metabolite levels, as well as differences in cell function, anatomy, physiology, and behavior.
The Chromium Embedded Framework (CEF) is an open-source software framework for embedding a Chromium web browser within another application. This enables developers to add web browsing functionality to their application, as well as the ability to use HTML, CSS, and JavaScript to create the application's user interface.
geWorkbench is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java. geWorkbench uses a component architecture. As of 2016, there are more than 70 plug-ins available, providing for the visualization and analysis of gene expression, sequence, and structure data.
CGView is a freely available downloadable Java software program, applet and API for generating colorful, zoomable, hyperlinked, richly annotated images of circular genomes such as bacterial chromosomes, mitochondrial DNA and plasmids. It is commonly used in bacterial sequence annotation pipelines to generate visual output suitable for the web. It has also been used in a variety of popular web servers and databases (BacMap).
The High-performance Integrated Virtual Environment (HIVE) is a distributed computing environment used for healthcare-IT and biological research, including analysis of Next Generation Sequencing (NGS) data, preclinical, clinical and post market data, adverse events, metagenomic data, etc. Currently it is supported and continuously developed by US Food and Drug Administration, George Washington University, and by DNA-HIVE, WHISE-Global and Embleema. HIVE currently operates fully functionally within the US FDA supporting wide variety (+60) of regulatory research and regulatory review projects as well as for supporting MDEpiNet medical device postmarket registries. Academic deployments of HIVE are used for research activities and publications in NGS analytics, cancer research, microbiome research and in educational programs for students at GWU. Commercial enterprises use HIVE for oncology, microbiology, vaccine manufacturing, gene editing, healthcare-IT, harmonization of real-world data, in preclinical research and clinical studies.
Echinobase is a Model Organism Database (MOD). It supports the international research community by providing a centralized, integrated web based resource to access the diverse and rich, functional genomics data of echinoderm evolution, development and gene regulatory networks.