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==Quick Start==
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__NOTOC__
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Please see the [[QuickStart| '''Quick Start''']] guide to geWorkbench to see how to get started using geWorkbench right away. We are continuing to develop new material for this guide.
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ARACNe_with_t-test_home_gallery.PNG
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Dendrogram_home_gallery.PNG
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==Overview==
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[[Image:geworkbench_banner.png]]
  
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Welcome to '''geWorkbench'''. The current version is 2.2.2, released August 19th, 2011.'''
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This release was a bug fix release, fixing several problems with the Gene Ontology Viewer and Analysis components.  It also improves the caArray download graphical interface by sorting arrays by name.    The [[Home#Brief Overview of Changes in geWorkbench 2.2.2|changes]] are also summarized below.
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<h2>Overview</h2>
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'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics.  Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
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The latest [https://gforge.nci.nih.gov/frs/shownotes.php?release_id=4240 Release Notes] and downloads can be obtained from https://gforge.nci.nih.gov/frs/?group_id=78.  Installation instructions can be found on the [http://wiki.c2b2.columbia.edu/workbench/index.php/Download  Download and Installation] page of this Wiki.
 
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'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics.  Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include:
 
 
* loading data from local or remote data sources.
 
* loading data from local or remote data sources.
 
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
 
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
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* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
 
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
 
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geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Roadmap]). Additionally, geWorkbench is supported by [https://cabig.nci.nih.gov/ caBIG<sup>&reg;</sup>, NCI's cancer Biomedical Informatics Grid initiative].
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geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Common Fund]).  
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In the past, geWorkbench has received support from [https://cabig.nci.nih.gov/ caBIG<sup>&reg;</sup>, NCI's cancer Biomedical Informatics Grid initiative].
  
 
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End-user and developer support for geWorkbench is provided through the caBIG<sup>&reg;</sup> [https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page Molecular Analysis Tools Knowledge Center], a component of the caBIG<sup>&reg;</sup> [https://cabig.nci.nih.gov/esn/ Enterprise Support Network].
 
End-user and developer support for geWorkbench is provided through the caBIG<sup>&reg;</sup> [https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page Molecular Analysis Tools Knowledge Center], a component of the caBIG<sup>&reg;</sup> [https://cabig.nci.nih.gov/esn/ Enterprise Support Network].
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<h2>Quick Start</h2>
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Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
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| style="width: 50%; background-color: #C7F8CB;"|
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<h2>Current Release</h2>
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The latest production version of geWorkbench (v2.6.0.3) was released on December 21, 2016.
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* [[Release_Descriptions#Brief_overview_of_changes_in_geWorkbench_release_2.6.0|See changes included in latest release]].
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* [[Release_Descriptions|See history of past releases]].
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* [[Download_and_Installation|Download geWorkbench]].
  
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==Graphical User Interface==
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<h2>Web-enabled Version</h2>
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[[Image:GeWorkbench_2.2.0_CNKB_Cytoscape.png|1024px]]
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[[GeWorkbench-web/Overview|'''geWorkbench-web''']] provides installation-free access to the geWorkbench plug-ins through a pure browser interface. You can create and account and access the application at: http://geworkbench.c2b2.columbia.edu/geworkbench/.  
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The figure above shows the full geWorkbench graphical user interface.  The Cellular Network Knowledge Base B-cell interactome was queried for interactions of two master regulator genes, and the result displayed in Cytoscape.
 
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==Brief Overview of Changes in geWorkbench 2.2.2==
 
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Release Date: 8/19/2011
 
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* In the caArray download dialog, arrays are now sorted by name.
 
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* The following problems in using the Gene Ontology components were fixed:
 
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** Marker sets returned from the Tree Browser was not properly appearing in marker selection pulldown menus (e.g. ARACNe hub marker selection).
 
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** After restoring a saved workspace, the reference gene list in the GO analysis component was not populated.
 
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** In some cases, the GO Tree Browser returned markers having no EntrezID along with the expected markers.
 
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==Brief Overview of Changes in geWorkbench 2.2.1==
 
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Release Date: 7/29/2011
 
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This release augments the recently released version 2.2.0,  and includes more than 90 additional enhancements and bug fixes, with many focused on network import, display and export, sequence retrieval, and pattern discovery.  It also corrects two omissions from release 2.2.0. 
 
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* Alternate file viewer for large networks that may be too large to view in Cytoscape.
 
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* Improvements to display of probeset-level networks.
 
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* Networks can now be imported either from ARACNe adjacency matrix files or from SIF files. Networks can be represented by gene symbols, Entrez IDs, probeset names, or other identifiers.
 
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* Adds support for use of alternate ontology files (e.g. from the GO website) for gene ontology analysis.
 
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* Sequence retrieval for DNA sequences is now based on refSeq records from the UCSC refGene table, and is available for all organisms with genomes supported by UCSC.
 
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* The new "Fold Change" analysis component, omitted from release 2.2.0, is included.
 
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* A feature to overlay a t-test result onto a Cytoscape network, not functional as released in version 2.2.0, now works correctly.
 
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* Bonferroni correction added to the ARACNe GUI.
 
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For a full list of changes, see  [[Media:GeWorkbench_2.2.1_Changes.txt| Changes]].
 
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geWorkbench v2.2.1 can be downloaded from https://gforge.nci.nih.gov/frs/?group_id=78. Full installation instructions are available there in the Release Notes, and also on the geWorkbench website at http://www.geworkbench.org. In-depth documentation is also available in the geWorkbench [[Tutorials|Tutorials]].
 
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==Previous Releases==
 
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See the [[PreviousReleases | Previous Releases]] page for full details.
 

Latest revision as of 16:47, 2 March 2022


Geworkbench banner.png

Overview

geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data. Example use cases include: [show details]

Quick Start

Please see the Quick Start guide to geWorkbench to see how to get started using geWorkbench right away.

Current Release

The latest production version of geWorkbench (v2.6.0.3) was released on December 21, 2016.

Web-enabled Version

geWorkbench-web provides installation-free access to the geWorkbench plug-ins through a pure browser interface. You can create and account and access the application at: http://geworkbench.c2b2.columbia.edu/geworkbench/.

Retrieved from "http://wiki.c2b2.columbia.edu/workbench/index.php?title=Home&oldid=13233"