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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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==Overview==
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[[Image:geworkbench_banner.png]]
  
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Welcome to '''geWorkbench'''.  The current version is 2.2.1, released July 29th, 2011.'''
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See the [[Media:GeWorkbench_2.2.1_Changes.txt| list of the most important fixes, changes and enhancements]]. This release was entirely devoted to improvements of existing components.  More than 90 issues were addressed.
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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=4239 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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| style="width: 50%; background-color: #F2F8C7;"|
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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 2.2.1==
 
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geWorkbench 2.2.1 provides a number of improvements, especially as related
 
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to network import, display and export, sequence retrieval, and pattern
 
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discovery. If a network is generated or loaded that may be to large to
 
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view in Cytocape, it can now instead by viewed as a text file. The
 
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new "Fold Change" analysis component is included, which was to be released
 
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in version 2.2.0 but was omitted. A new feature to overlay a t-test result
 
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onto a Cytoscape network, which was inadvertantly disabled in release
 
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2.2.0, now works again.  The Gene Ontology analysis component now supports
 
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uses of  alternate ontology files (e.g. from the GO website).  Sequence
 
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retrieval for DNA sequences is now done using the UCSC refGene table, and
 
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is available for all organisms with genomes supported by UCSC.
 
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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/.

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