Overview - Revision history

Smith at 21:05, 17 October 2013

2013-10-17T21:05:35Z

2013-10-16T17:59:14Z

2013-07-16T17:58:23Z

2013-02-12T00:08:03Z

2013-02-12T00:07:52Z

2012-11-20T18:43:11Z

2012-11-20T18:06:13Z

2012-03-19T20:01:30Z

2010-06-14T20:07:39Z

2010-06-11T21:35:25Z

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 geWorkbench provides access to a variety of external data sources, including:
-*Microarray gene expression repositories (caArray)
+* Microarray gene expression repositories (caArray)
-*BLAST
+* BLAST (NCBI)
-*Gene annotation pages (via caBIO)
+* Gene annotation pages (via bioDBNet)
-*Protein and DNA sequence retrieval
+* Protein and DNA sequence retrieval (UC Santa Cruz and EBI)
-*Pathway diagrams (BioCarta)
+* Pathway diagrams (BioCarta)
 geWorkbench also provides a gateway to several computational services currently hosted on Columbia servers and clusters, including:
-*Pattern Discovery
+* Pattern Discovery
-*Pudge - protein structure modeling
+* Pudge - protein structure modeling
-*SkyBase - database of molecular models
+* SkyBase - database of molecular models

← Older revision		Revision as of 17:59, 16 October 2013
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−	[[Image:~~GeWorkbench_2.3.0_Main_GUI_MicroarrayViewer~~.png\|{{ImageMaxWidth}}]]	+	[[Image:GeWorkbench_full_GUI_color_mosaic.png\|{{ImageMaxWidth}}]]

← Older revision		Revision as of 17:58, 16 July 2013
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−	[[Image:GeWorkbench_2.3.0_Main_GUI_MicroarrayViewer.png]]	+	[[Image:GeWorkbench_2.3.0_Main_GUI_MicroarrayViewer.png\|{{ImageMaxWidth}}]]

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 geWorkbench is an open-source bioinformatics platform that offers a comprehensive and extensible collection of tools for the management, analysis, visualization and annotation of biomedical data.  Many kinds of analysis are supported - for microarrays, there are filtering and normalization, basic statistical analyses, clustering, network reverse engineering, as well as many common visualization tools.  For sequence data there are routines such as BLAST, pattern detection, transcription factor mapping, and syntenic region analysis.  Furthermore, genomic sequences around markers of interest found in microarray experiments can be easily retrieved and, for example, used for promoter/transcription factor analysis.
-Specific types of data supported include: Bloody Mary is the girl for me!
+Specific types of data supported include:
 *Microarray Gene Expression

@@ Line 4: / Line 4: @@
 geWorkbench is an open-source bioinformatics platform that offers a comprehensive and extensible collection of tools for the management, analysis, visualization and annotation of biomedical data.  Many kinds of analysis are supported - for microarrays, there are filtering and normalization, basic statistical analyses, clustering, network reverse engineering, as well as many common visualization tools.  For sequence data there are routines such as BLAST, pattern detection, transcription factor mapping, and syntenic region analysis.  Furthermore, genomic sequences around markers of interest found in microarray experiments can be easily retrieved and, for example, used for promoter/transcription factor analysis.
-Specific types of data supported include:
+Specific types of data supported include: Bloody Mary is the girl for me!
 *Microarray Gene Expression

@@ Line 15: / Line 15: @@
 * Microarray Gene Expression Annotation file support
 ** Affymetrix 3' Expression
-** Affymetrix Gene Array including Gene 1.0/2.0 ST and Exon 1.0 ST.
+** Affymetrix WT Gene/Exon ST (transcript-level) including Gene Array 1.0/2.0 ST and Exon 1.0 ST.
 *DNA and Protein Sequences
 **FASTA

@@ Line 13: / Line 13: @@
 **Tab-delimited (e.g. RMAExpress)
 **GenePix
 *DNA and Protein Sequences
 **FASTA

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-The graphical user interface for geWorkbench is divided into four major sections, for
+The graphical user interface for geWorkbench is divided into three major sections, for
 # Projects - Data management  (upper left)
 # Visualization tools (upper right)
 # Marker and Array/Phenotype set selection and management  (lower left)
-[[Image:GeWB_GUI_MicroarrayViewer.png]]
+[[Image:GeWorkbench_2.3.0_Main_GUI_MicroarrayViewer.png]]

← Older revision		Revision as of 20:07, 14 June 2010
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	[[Image:slide1.gif]]		[[Image:slide1.gif]]
−
−	~~==Developing for geWorkbench==~~
−
−	geWorkbench has been designed using a plug-in framework which allows new modules to be developed with relative ease. A repository will be maintained for community-developed modules. Developers can take advantage of all the existing capabilities for data management and visualization, and thus concentrate development efforts on the more important, novel aspects of their project.


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	The GUI provides a menu bar at top with a standard choice of commands. Many commands that are available in the menu bar are also available by right-clicking on data objects.		The GUI provides a menu bar at top with a standard choice of commands. Many commands that are available in the menu bar are also available by right-clicking on data objects.
		+
		+
		+	==Developing for geWorkbench==
		+
		+	geWorkbench has been designed using a plug-in framework which allows new modules to be developed with relative ease. A repository will be maintained for community-developed modules. Developers can take advantage of all the existing capabilities for data management and visualization, and thus concentrate development efforts on the more important, novel aspects of their project.