geWorkbench (genomics Workbench) is an
open-source software platform for integrated
genomic
Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...
data analysis. It is a desktop application written in the programming language
Java. geWorkbench uses a component architecture. , there are more than 70 plug-ins available, providing for the visualization and analysis of
gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. The ...
, sequence, and structure data.
geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8
National Centers for Biomedical Computing funded through the NIH Roadmap (
NIH Common Fund
The National Institutes of Health Common Fund is an initiative of the National Institutes of Health (NIH) aimed at supporting research collaboration between two or more NIH institutes and centers (ICs). The fund offers flexible support for cuttin ...
). Many systems and structure biology tools developed by MAGNet investigators are available as geWorkbench plugins.
Features
* Computational analysis tools such as t-test, hierarchical clustering, self-organizing maps, regulatory network reconstruction, BLAST searches, pattern-motif discovery, protein structure prediction, structure-based protein annotation, etc.
* Visualization of gene expression (heatmaps, volcano plot), molecular interaction networks (through
Cytoscape
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 f ...
), protein sequence and protein structure data (e.g., MarkUs).
* Integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
* Component integration through platform management of inputs and outputs. Among data that can be shared between components are expression datasets, interaction networks, sample and marker (gene) sets and sequences.
* Dataset history tracking - complete record of data sets used and input settings.
* Integration with 3rd party tools such as
Genepattern
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 genomi ...
,
Cytoscape
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 f ...
, and
Genomespace
GenomeSpace is an environment for genomics software tools and applications. It helps users manage their analysis workflows involving multiple diverse tools, including web applications and desktop tools and facilitates the transfer of data betwee ...
.
Demonstrations of each feature described can be found
GeWorkbench-web Tutorials
Versions
* geWorkbench is
open-source software that can be downloaded and installed locally. A zip file of the released version Java source is also available.
* Prepackaged installer versions also exist
for Windows, Macintosh, and Linux.
See also
*
Genome Compiler
Twist Bioscience is a public biotechnology company based in South San Francisco that manufactures synthetic DNA and DNA products for customers in a wide range of industries. Twist was founded in 2013 by Emily Leproust, Bill Banyai, and Bill Pec ...
References
External links
* {{Official website, www.geworkbench.org, includes installation, tutorials, FAQs, known issues
- geworkbench release downloads- geWorkbench plugins
Bioinformatics software
Software using the BSD license
Cluster analysis
Systems biology
Protein structure
Gene expression