GeWorkbench
{{Short description|Genomic data analysis software}}
{{lowercase title}}
{{Infobox software
| name = geWorkbench
| logo = GeworkbenchLogo.png
| logo size = 250px
| screenshot =
| caption =
| developer = Columbia University,
First Genetic Trust
National Cancer Institute
| released = {{Start date and age|2004}}
| latest release version = 2.6.0.3
| latest release date = {{Start date and age|2016|12|21}}
| programming language =
| operating system = Windows, Linux, Mac OS X
| platform = x86
| language = English
| genre = Genome data analysis
| license = BSD-like[http://wiki.c2b2.columbia.edu/workbench/index.php/GeWorkbench_License geWorkbench license]
| website = {{URL|www.geworkbench.org}}
}}
geWorkbench{{Cite journal
| last1= Floratos |first1= A.
| last2= Smith |first2= K.
| last3= Ji |first3= Z.
| last4= Watkinson |first4= J.
| last5= Califano |first5= A.
| title= GeWorkbench: An open source platform for integrative genomics
| doi= 10.1093/bioinformatics/btq282
| journal= Bioinformatics
| volume= 26
| issue= 14
| pages= 1779–1780
| year= 2010
| pmid= 20511363
| pmc =2894520
}} (genomics Workbench) 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{{Cite web|url=http://wiki.c2b2.columbia.edu/workbench/index.php/Plugins|title=Plugins - Workbench}} available, providing for the visualization and analysis of gene expression, sequence, and structure data.
geWorkbench is the Bioinformatics platform of MAGNet,[http://magnet.c2b2.columbia.edu/ MAGNet] the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing{{cite web |url=http://www.ncbcs.org/ |title=Home |website=ncbcs.org}} funded through the NIH Roadmap (NIH Common Fund{{Cite web |url=http://commonfund.nih.gov/researchteams |title=NIH Roadmap - Research Teams of the Future |access-date=2013-07-16 |archive-url=https://web.archive.org/web/20130621191343/https://commonfund.nih.gov/researchteams/ |archive-date=2013-06-21 |url-status=dead }}). 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), 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, Cytoscape, and Genomespace.
Demonstrations of each feature described can be found at GeWorkbench-web Tutorials.[http://wiki.c2b2.columbia.edu/workbench/index.php/Tutorials 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{{Cite web|url=http://wiki.c2b2.columbia.edu/workbench/index.php/Download_and_Installation|title=Download and Installation - Workbench}} for Windows, Macintosh, and Linux.
References
{{Reflist}}
External links
- {{Official website|www.geworkbench.org}}, includes installation, tutorials, FAQs, known issues
- [http://wiki.c2b2.columbia.edu/workbench/index.php/Download_and_Installation - geworkbench release downloads]
- [http://wiki.c2b2.columbia.edu/workbench/index.php/Plugins - geWorkbench plugins]
Category:Bioinformatics software