geWorkbench workbench http://wiki.c2b2.columbia.edu/workbench/index.php/Home MediaWiki 1.27.7 first-letter Media Special Talk User User talk geWorkbench geWorkbench talk File File talk MediaWiki MediaWiki talk Template Template talk Help Help talk Category Category talk 0 1 13233 13231 2022-03-02T21:47:24Z Floratos 4 wikitext text/x-wiki __NOTOC__ <!-- <sgallery width="700" showinfopane="false" timed="true" delay="4000" showcarousel="false"> ARACNe_with_t-test_home_gallery.PNG MarkUs_home_gallery.PNG Dendrogram_home_gallery.PNG Volcano_plot_home_gallery.PNG JMol_viewer_home_gallery.PNG Skybase_home_gallery.PNG TF_binding_site_prediction_home_gallery.PNG Motif_discovery_home_gallery.PNG BLAST_home_gallery.PNG CCM_home_gallery.PNG Gene_Ontology_home_gallery.PNG </sgallery> --> [[Image:geworkbench_banner.png]] {| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10" width="700px" |colspan="2"| <h2>Overview</h2> '''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"> * 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. * providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc. * validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. <br/> 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]). <!-- In the past, geWorkbench has received support from [https://cabig.nci.nih.gov/ caBIG^&reg;, NCI's cancer Biomedical Informatics Grid initiative]. <br/> End-user and developer support for geWorkbench is provided through the caBIG^&reg; [https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page Molecular Analysis Tools Knowledge Center], a component of the caBIG^&reg; [https://cabig.nci.nih.gov/esn/ Enterprise Support Network]. --> </toggledisplay> |- | style="width: 50%; background-color: #F2F8C7;"| <h2>Quick Start</h2> Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away. | style="width: 50%; background-color: #C7F8CB;"| <h2>Current Release</h2> The latest production version of geWorkbench (v2.6.0.3) was released on December 21, 2016. * [[Release_Descriptions#Brief_overview_of_changes_in_geWorkbench_release_2.6.0|See changes included in latest release]]. * [[Release_Descriptions|See history of past releases]]. * [[Download_and_Installation|Download geWorkbench]]. |- |style="background-color: #D8FAFA;" colspan="2"| <h2>Web-enabled Version</h2> [[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/. |} finydngmb10j6rny073teizzqzhlz02