Basics - Revision history

Smith: /* Data representation */

2014-04-22T19:42:10Z

‎Data representation

Smith: /* Layout of the Graphical User Interface */

2014-04-22T19:39:23Z

‎Layout of the Graphical User Interface

Smith: /* Visualization and Analysis tools */

2014-04-22T19:38:30Z

‎Visualization and Analysis tools

Smith at 19:36, 22 April 2014

2014-04-22T19:36:47Z

Smith: /* Prior to releases 2.3.0 */

2013-10-15T20:11:55Z

‎Prior to releases 2.3.0

Smith: /* As of release 2.3.0 */

2013-10-15T20:11:30Z

‎As of release 2.3.0

Smith: /* As of release 2.3.0 */

2013-10-15T20:09:16Z

‎As of release 2.3.0

Ut2102: /* Prior to releases 2.3.0 */

2013-07-16T16:16:43Z

‎Prior to releases 2.3.0

Ut2102: /* As of release 2.3.0 */

2013-07-16T16:16:20Z

‎As of release 2.3.0

Smith: /* As of release 2.3.0 */

2013-02-26T19:15:11Z

‎As of release 2.3.0

@@ Line 82: / Line 82: @@
 ==Data representation==
-geWorkbench works on a single dataset at one time, as selected in the [[Workspace]].  For working with data from multiple microarrays simultaneously, for example for statistical analysis or clustering, all of the data must be represented as a single two-dimensional array of experiments and markers.   Such a representation can be created externally, for example in Excel, or geWorkbench can read in expression results from single arrays and merge them into a combined dataset.  The merging process is described in detail in [[Local_Data_Files#Merging_Microarray_Files|Local Data Files]].
+geWorkbench works on a single dataset at one time, as selected in the [[Workspace]].  For working with data from multiple microarrays simultaneously, for example for statistical analysis or clustering, all of the data must be represented as a single two-dimensional array of experiments and markers.   Such a representation can be created externally, for example in Excel, or geWorkbench can read in expression results from single arrays and merge them into a combined dataset.  The merging process is described in detail in [[Local_Data_Files#Merging_Microarray_Files|Local Data Files]] and also in [[Menu_Bar#Merge_Datasets|Menu Bar]].
 An option at the time of file read-in allows multiple files to be opened and merged simultaneously, either from disk or from remote data sources such as caArray.  Alternatively, single datasets that have already been read-in can also be merged at a later time.  Either route creates a single data object in the [[Workspace]] representing all of the arrays.  This object can be viewed, for example, using the color mosaic component.  The merged representation can be saved to the geWorkbench *.exp file type.

@@ Line 20: / Line 20: @@
 The graphical user interface for geWorkbench is divided into three major sections, for
-# Data management - [[Workspace]] (upper left)
+# (1) Data management - [[Workspace]] (upper left)
-# Visualization tools (right)
+# (2) Visualization tools (right)
-# Marker and Array/Phenotype set selection and management  (lower left)
+# (3) Marker and Array/Phenotype set selection and management  (lower left)

@@ Line 73: / Line 73: @@
 ==Visualization  and Analysis tools==
-geWorkbench works such that only the visualization and analysis components relevant to the type of dataset currently selected in the [[Workspace]] area (1) are displayed through tabs in their respective areas (2 and 4).  Thus choosing a microarray dataset will result in a different set of tabs being displayed as compared with those seen when a nucleotide sequence file is selected.   When a new data file is loaded, or an analysis produces a new data set, not only is it added to the [[Workspace]] (1), but an appropriate viewer in the Visualization area (2) is automatically selected.
+geWorkbench works such that only the visualization and analysis components relevant to the type of dataset currently selected in the [[Workspace]] area (1) are displayed in the Visualization Area (2) or in the command menus.  Thus choosing a microarray dataset will result in a different set of visualizers being displayed as compared with those seen when a nucleotide sequence file is selected.   When a new data file is loaded, or an analysis produces a new data set, not only is it added to the [[Workspace]] (1), but an appropriate viewer in the Visualization area (2) is automatically selected.
 ==Component Interoperability==

@@ Line 20: / Line 20: @@
 The graphical user interface for geWorkbench is divided into three major sections, for
-# Data management - Workspace and Projects (upper left)
+# Data management - [[Workspace]] (upper left)
 # Visualization tools (right)
 # Marker and Array/Phenotype set selection and management  (lower left)
@@ Line 63: / Line 63: @@
 ==Data management area==
+The [[Workspace]] is a top-level geWorkbench component that holds data, analysis results, images, sequences, networks and other types of input and output.  A [[Workspace]] and all the data within it can be saved and later reloaded.  Only one [[Workspace]] at a time can be open.  These operations will be described in detail in further sections of the tutorials.
 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.
@@ Line 74: / Line 73: @@
 ==Visualization  and Analysis tools==
-geWorkbench works such that only the visualization and analysis components relevant to the type of dataset currently selected in the Project Folders area (1) are displayed through tabs in their respective areas (2 and 4).  Thus choosing a microarray dataset will result in a different set of tabs being displayed as compared with those seen when a nucleotide sequence file is selected.   When a new data file is loaded, or an analysis produces a new data set, not only is it added to the Project area (1), but an appropriate viewer in the Visualization area (2) is automatically selected.
+geWorkbench works such that only the visualization and analysis components relevant to the type of dataset currently selected in the [[Workspace]] area (1) are displayed through tabs in their respective areas (2 and 4).  Thus choosing a microarray dataset will result in a different set of tabs being displayed as compared with those seen when a nucleotide sequence file is selected.   When a new data file is loaded, or an analysis produces a new data set, not only is it added to the [[Workspace]] (1), but an appropriate viewer in the Visualization area (2) is automatically selected.
 ==Component Interoperability==
-The features described above underly the most important design goal of geWorkbench, which is to allow the different components to interoperate easily.  The user is freed of the need to write programs to convert data from one format to another for different programs.  Both the Project component (1) and the Set Selection component(3) can hold shared data.  Typically each run of an analysis places either a new dataset into the active project, or a new set of markers or arrays into the Set Selection component.  These are then available to any other appropriate component for reuse.
+The features described above underly the most important design goal of geWorkbench, which is to allow the different components to interoperate easily.  The user is freed of the need to write programs to convert data from one format to another for different programs.  Both the [[Workspace]] (1) and the Set Selection component(3) can hold shared data.  Typically each run of an analysis places either a new dataset into the [[Workspace]], or a new set of markers or arrays into the Set Selection component.  These are then available to any other appropriate component for reuse.
 ==Data representation==
-geWorkbench works on a single dataset at one time, as selected in the Project Folders.  For working with data from multiple microarrays simultaneously, for example for statistical analysis or clustering, all of the data must be represented as a single two-dimensional array of experiments and markers.   Such a representation can be created externally, for example in Excel, or geWorkbench can read in expression results from single arrays and merge them into a combined dataset.  The merging process is described in detail in the section [[Tutorial_-_Projects_and_Data_Files|Projects and Data Files]].
+geWorkbench works on a single dataset at one time, as selected in the [[Workspace]].  For working with data from multiple microarrays simultaneously, for example for statistical analysis or clustering, all of the data must be represented as a single two-dimensional array of experiments and markers.   Such a representation can be created externally, for example in Excel, or geWorkbench can read in expression results from single arrays and merge them into a combined dataset.  The merging process is described in detail in [[Local_Data_Files#Merging_Microarray_Files|Local Data Files]].
-An option at the time of file read-in allows multiple files to be opened and merged simultaneously, either from disk or from remote data sources such as caArray.  Alternatively, single datasets that have already been read-in can also be merged at a later time.  Either route creates a single data object in the project folder representing all of the arrays.  This object can be viewed, for example, using the color mosaic component.  The merged representation can be saved to the geWorkbench *.exp file type.
+An option at the time of file read-in allows multiple files to be opened and merged simultaneously, either from disk or from remote data sources such as caArray.  Alternatively, single datasets that have already been read-in can also be merged at a later time.  Either route creates a single data object in the [[Workspace]] representing all of the arrays.  This object can be viewed, for example, using the color mosaic component.  The merged representation can be saved to the geWorkbench *.exp file type.
-The results of any data analysis are stored in the Project Folders as a child of the dataset from which they were created.
+The results of any data analysis are stored in the [[Workspace]] as a child of the dataset from which they were created.
 ==Limitations==
 As currently implemented, operations such as filtering and normalization directly alter the loaded dataset.  However, the original data file is not changed.

← Older revision		Revision as of 20:11, 15 October 2013
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	[[Image:Basics_Analysis_t-test.png]]		[[Image:Basics_Analysis_t-test.png]]
−
−	~~===Prior to releases 2.3.0===~~
−
−
−	~~The graphical user interface for geWorkbench is divided into four major sections, for~~
−
−	~~# Data management - Workspace and Projects (upper left)~~
−	~~# Visualization tools (upper right)~~
−	~~# Marker and Array/Phenotype set selection and management (lower left)~~
−	~~# Analytical tools (lower right)~~
−
−	~~[[Image:GeWB_GUI_MicroarrayViewer.png\|{{ImageMaxWidth}}]]~~
−
−
−	~~Areas 2, 3 and 4 are defined for convenience. The actual placement of a given component into any of these three areas is controlled by a configuration file and can be customized as desired.~~

	==Window Decorations==		==Window Decorations==

@@ Line 16: / Line 16: @@
 ==Layout of the Graphical User Interface==
-===As of release 2.3.0===
 The graphical user interface for geWorkbench is divided into three major sections, for

← Older revision		Revision as of 20:09, 15 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 16:16, 16 July 2013
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	# Analytical tools (lower right)		# Analytical tools (lower right)

−	[[Image:GeWB_GUI_MicroarrayViewer.png]]	+	[[Image:GeWB_GUI_MicroarrayViewer.png\|{{ImageMaxWidth}}]]

@@ Line 23: / Line 23: @@
 # Visualization tools (right)
 # Marker and Array/Phenotype set selection and management  (lower left)
 Commands for analysis, filtering and normalization are now available in a menu activated by right-clicking on any loaded data node.  They can also be found in the top level menu-bar under "Commands".  They will act on the currently selected data node.
-[[Image:GeWorkbench_2.3.0_Main_GUI_MicroarrayViewer.png]]
+[[Image:Basics_Analysis_t-test.png]]
 ===Prior to releases 2.3.0===