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Smith: /* How to Cite geWorkbench */

2015-01-27T20:57:21Z

‎How to Cite geWorkbench

Smith: /* geworkbench.org */

2015-01-27T20:56:41Z

‎geworkbench.org

Smith: /* geWorkbench Tutorials */

2015-01-27T20:56:21Z

‎geWorkbench Tutorials

Smith: /* geworkbench.org */

2015-01-27T20:55:21Z

‎geworkbench.org

Smith: /* Help */

2015-01-27T20:49:14Z

‎Help

Smith: /* Choose OBO Source */

2015-01-27T20:24:46Z

‎Choose OBO Source

Smith at 19:46, 22 April 2014

2014-04-22T19:46:31Z

Smith: /* Remove */

2014-01-10T21:58:20Z

‎Remove

Smith: /* Links to external sites */

2013-11-08T22:25:43Z

‎Links to external sites

Smith: /* Merge Datasets */

2013-11-08T22:18:07Z

‎Merge Datasets

@@ Line 196: / Line 196: @@
 ===How to Cite geWorkbench===
-[http://wiki.c2b2.columbia.edu/workbench/index.php/Cite How to Cite geWorkbench] - Instructions for citing geWorkbench in publications.
+[http://wiki.c2b2.columbia.edu/workbench/index.php/Cite Instructions] for citing geWorkbench in publications.
 ===Show Splash Screen===

@@ Line 188: / Line 188: @@
 ===geworkbench.org===
-The [http://www.geworkbench.org '''geWorkbench project'''] home page.
+The [http://www.geworkbench.org geWorkbench project] home page.
 ===geWorkbench Tutorials===

@@ Line 192: / Line 192: @@
 ===geWorkbench Tutorials===
-[http://wiki.c2b2.columbia.edu/workbench/index.php/Tutorials geWorkbench Tutorials] - Full documentation and examples for each component of geWorkbench.
+Full [http://wiki.c2b2.columbia.edu/workbench/index.php/Tutorials documentation and examples] for each component of geWorkbench.
 ===How to Cite geWorkbench===

@@ Line 188: / Line 188: @@
 ===geworkbench.org===
-[http://www.geworkbench.org '''geWorkbench.org'''] - This is the URL of the geWorkbench project home page.  It contains full information about geWorkbench.
+The [http://www.geworkbench.org '''geWorkbench project'''] home page.
 ===geWorkbench Tutorials===

@@ Line 186: / Line 186: @@
-===Links to external sites===
+===geworkbench.org===
 [http://www.geworkbench.org '''geWorkbench.org'''] - This is the URL of the geWorkbench project home page.  It contains full information about geWorkbench.
-===About===
+===geWorkbench Tutorials===
 Displays the geWorkbench startup splash screen with developer credits.
+===Show Welcome Screen===
 The Wecome Screen is displayed the first time a new version of geWorkbench is run on a computer.  It displays introductory information about how to learn about using geWorkbench.  It may also provide version-specific notices.
 * The Welcome Screen is dismissed by pushing its "Hide" button.
-* The Welcome Screen can be recalled at any time by selecting "Welcome Screen" under the main menu bar Help entry.
+* The Welcome Screen can be recalled at any time by selecting "Show Welcome Screen" under the main menu bar Help entry.
 * The Welcome screen remembers whether is was being displayed or not last time geWorkbench was closed, and will be in the same state when geWorkbench is next run.

@@ Line 137: / Line 137: @@
 ===Choose OBO Source===
-By default, each time geWorkbench starts, it downloads the latest Gene Ontology OBO file from the geneontology.org website, and then loads this file for use by its components (e.g. GO Viewer, GO Analysis, CNKB).  However, the "Choose OBO Source" entry in the Tools menu allows a local file to be chosen instead.
+By default, each time geWorkbench starts, it downloads the latest Gene Ontology OBO file from the [http://geneontology.org/page/download-ontology geneontology.org download site], and then loads this file for use by its components (e.g. GO Viewer, GO Analysis, CNKB).  However, the "Choose OBO Source" entry in the Tools menu allows a local file to be chosen instead.
 If the OBO Source setting is changed in either direction between remote and local, geWorkbench must be restarted before the change will take effect.

@@ Line 11: / Line 11: @@
-The first two items in the menu, "File" and "Edit", apply to the Workspace, described in the next section.
+The first two items in the menu, "File" and "Edit", apply to the [[Workspace]], described in the next section.
 ==Background on the Workspace==
-The Workspace is used for data organization and management.  It arranges data nodes and the results of analysis on the data in a hierarchical fashion.
+The [[Workspace]] is used for data organization and management.  It arranges data nodes and the results of analysis on the data in a hierarchical fashion.
-* '''Workspace''' - A workspace contains all the data for a geWorkbench session.  Only one workspace can be present at a time.  A workspace can be saved and reloaded.
+* '''Workspace''' - A [[Workspace]] contains all the data for a geWorkbench session.  Only one [[Workspace]] can be present at a time.  A [[Workspace]] can be saved and reloaded.
 * '''Data nodes''' - These contain data either loaded from files on disk or retrieved from the network.
 * '''Result nodes''' - After an analysis is done in geWorkbench, a result node is created as a child of the data node from which it was created.
-The following diagram shows the Workspace with a single data node and its child t-test analysis result node.
+The following diagram shows the [[Workspace]] with a single data node and its child t-test analysis result node.
@@ Line 28: / Line 28: @@
 ==File==
@@ Line 40: / Line 39: @@
 * '''File''' - Open a specific data file from disk.   A standard file browser will appear, and the user can select from any of the [[Local_Data_Files#Supported_data_formats | file types]] that geWorkbench can directly load.
-** '''Note''' - The Open File action is also available by right-clicking on the Workspace node.
+** '''Note''' - The Open File action is also available by right-clicking on the [[Workspace]] node.
-* '''Workspace''' - Open a previously saved geWorkbench workspace.  A standard file browser will appear with which to locate the desired workspace file.   As shown in the figure below, a dialog will appear warning the user that the current workspace will be overwritten.  The user is offered the option to save the current workspace before proceeding.
+* '''Workspace''' - Open a previously saved geWorkbench [[Workspace]].  A standard file browser will appear with which to locate the desired [[Workspace]] file.   As shown in the figure below, a dialog will appear warning the user that the current [[Workspace]] will be overwritten.  The user is offered the option to save the current [[Workspace]] before proceeding.
@@ Line 48: / Line 47: @@
 ===Save===
-* '''Workspace''' - Save the current geWorkbench workspace to a file on disk.  All projects, data and result nodes will be saved.
+* '''Workspace''' - Save the current geWorkbench [[Workspace]] to a file on disk.  All data and result nodes will be saved.
 * '''Dataset''' - Save the currently selected data node.  This is implemented for the following data types:
 ** Microarray gene expression -  data is saved using the geWorkbench ".exp" format, regardless of the original format. This allows saving e.g. a merged dataset, and/or any array and marker sets that may have been created.
@@ Line 62: / Line 61: @@
 ===New===
-* '''Workspace''' - Create a new workspace.  Doing so will destroy the existing workspace, so the user will be prompted as to whether to save the current workspace.  This is shown in the diagram below.
+* '''Workspace''' - Create a new [[Workspace]].  Doing so will destroy the existing [[Workspace]], so the user will be prompted as to whether to save the current [[Workspace]].  This is shown in the diagram below.
@@ Line 68: / Line 67: @@
 ===Merge Datasets===
-If more than one microarray expression data file or data set originating from the same platform has been loaded into the Workspace, they [[Local_Data_Files#Microrray_data_and_merging_datasets | can be merged]] into one for analysis.  Highlight the microarrays/datasets to be merged, then select "Merge Datasets".  The microarray data nodes to be merged must all be from the same platform (chip type).
+If more than one microarray expression data file or data set originating from the same platform has been loaded into the [[Workspace]], they [[Local_Data_Files#Microrray_data_and_merging_datasets | can be merged]] into one for analysis.  Highlight the microarrays/datasets to be merged, then select "Merge Datasets".  The microarray data nodes to be merged must all be from the same platform (chip type).
 Requirements for merging microarray data files or data sets:
@@ Line 79: / Line 78: @@
 ====Example: Merging microarray data nodes====
-'''1.''' In the Workspace, select the microarray data nodes that you want to merge.
+'''1.''' In the [[Workspace]], select the microarray data nodes that you want to merge.
 [[Image:Menu_Bar_Merge_Select_Files.png]]
@@ Line 95: / Line 94: @@
 ===Remove===
-This option will remove one or more selected data nodes from the Workspace. (Multiple selection is supported). It will not remove the Workspace node itself.
+This option will remove one or more selected data nodes from the [[Workspace]]. (Multiple selection is supported). It will not remove the [[Workspace]] node itself.
 ===Exit===
-Close geWorkbench.  The user will be prompted as to whether to save the workspace before closing.
+Close geWorkbench.  The user will be prompted as to whether to save the [[Workspace]] before closing.
 [[Image:Menu_Bar_Exit.png]]
@@ Line 114: / Line 113: @@
-The first three entries, "Analysis", "Filtering", and "Normalization" are context sensitive.  They will display the components of each type available for the data node type currently selected in the Workspace.  Only components which have been loaded in the [[Component Configuration Manager]] will be displayed.
+The first three entries, "Analysis", "Filtering", and "Normalization" are context sensitive.  They will display the components of each type available for the data node type currently selected in the [[Workspace]].  Only components which have been loaded in the [[Component Configuration Manager]] will be displayed.
 The following choices are available under the "Commands" menu:

← Older revision		Revision as of 22:25, 8 November 2013
Line 188:		Line 188:

	[http://www.geworkbench.org '''geWorkbench.org'''] - This is the URL of the geWorkbench project home page. It contains full information about geWorkbench.		[http://www.geworkbench.org '''geWorkbench.org'''] - This is the URL of the geWorkbench project home page. It contains full information about geWorkbench.
−
−	[https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/GeWorkbench '''Knowledge Center'''] - The National Cancer Institute's Molecular Analysis Tools Knowledge Center provides user support for geWorkbench. (Note - This site is no longer being maintained).

	===About===		===About===

← Older revision		Revision as of 22:18, 8 November 2013
Line 68:		Line 68:

	===Merge Datasets===		===Merge Datasets===
−	'''NOTICE''' - ''Merging expression datasets already loaded into the Workspace is not working in geWorkbench 2.5.0. However, if you load two or more expression datafiles of the same format together (by selecting more than one file) they will be automatically merged''.
−
	If more than one microarray expression data file or data set originating from the same platform has been loaded into the Workspace, they [[Local_Data_Files#Microrray_data_and_merging_datasets \| can be merged]] into one for analysis. Highlight the microarrays/datasets to be merged, then select "Merge Datasets". The microarray data nodes to be merged must all be from the same platform (chip type).		If more than one microarray expression data file or data set originating from the same platform has been loaded into the Workspace, they [[Local_Data_Files#Microrray_data_and_merging_datasets \| can be merged]] into one for analysis. Highlight the microarrays/datasets to be merged, then select "Merge Datasets". The microarray data nodes to be merged must all be from the same platform (chip type).