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	{{TutorialsTopNav}}		{{TutorialsTopNav}}
−	=Outline=	+	==Overview==
−	In this tutorial, you will learn how to:
−	*Create a new Project.
−	*Load microarray data.
−	*Merge data from several loaded microarray experiments.
−	*Download data from a remote instance of the caArray database (supported by NCI).
−	*Rename a project and/or project node.
−	*Remove a project and/or project node.
−	*Save project files that you have created.
−	*Load, add, and/or modify remote data.
		+	The Workspace is located in the upper-left-hand corner of the application. It is used to contain open data files and store analysis results during a geWorkbench session. When geWorkbench is launched, an empty Workspace folder is displayed.
−	=Overview=
−	This section covers three areas - (1) the logical organization of data within geWorkbench into projects and workspaces, (2)working with data files in this logical structure,  and (3) special handling of microarray data files, including obtaining data from local and remote sources, and merging multiple data files into one.  These topics are bundled into one because these various operations are all handled within the same '''Project Folders''' component.
−	=Workspaces and Projects=	+	[[Image:Workspace.png]]
−	In the '''Project Folders''' component there is a top-level object called a workspace.  The workspace can contain one or more separate projects, and each project can contain opened data files and analysis results. An analogy might be that a workspace is like a drawer in a filing cabinet, and projects are individual folders in that drawer. Projects allow data to be grouped, for example by experiment.  A project can contain many different types of data, for example microarray data, FASTA sequence files and graphical images.  The workspace as a whole, with all its projects and data nodes, can be saved and restored.  However, only one workspace can be open at one time.
−	=Microrray data and merging=
−	When working with microarray data, all data to be analyzed must be present within one data node in a project.  If the data exists as multiple files containing results from single arrays, the data must be merged into a single node before it can be used.  geWorkbench can perform this merging step either at the time data is read in, or later in a separate step.  Once merged, such a dataset can be saved to disk; it will be saved in the geWorkbench matrix file format.
		+	The workspace as a whole, with all its projects and data nodes, can be saved and restored.  However, only one workspace can be open at one time.  Creating a new workspace or loading a saved workspace will overwrite the current workspace.
−	=Supported data formats=
−	*Microarray
−	**Affymetrix MAS5/GCOS files - produced by the Affymetrix data analysis programs.
−	**Affymetrix File Matrix - a spreadsheet-type multi-experiment format; this is the native file type created by geWorkbench from merged datasets.
−	**Tab-delimited text (RMAExpress file) - A simple columnar file format, as produced by the program RMAExpress.
−	**Genepix .GPR files - Produced by a popular analysis program for two-color microarrays.
−	**Affymetrix CEL files - these files of probe level data can be viewed graphically in geWorkbench but not used directly for analysis.
−	*Other
−	**FASTA files. DNA or amino-acid sequence files in FASTA format.
−	**PDB files - protein 3-dimensional structure files can be viewed in the JMol Viewer in geWorkbench.
−	**NetBoost Edge List - used by a component still under development.
−	=Tutorial: Working with Projects=	+	* To view the next level down in the hierarchy, click on the “+” icon to expand the branch.
−	==Creating a new project==	+	* To collapse a branch, click on the “-” icon.
−	All data must belong to a project.  Right-click on the '''Workspace''' entry in the '''Project Folders''' window at upper left to create a new project.
−	[[Image:T_NewProject.png]]	+	The Workspace may contain several heterologous datasets. These datasets can include input (source) data and derived data (results) associated with an experiment as well as image files. Source data can be loaded from the user’s local storage or from remote servers.  Loading datasets into the geWorkbench Workspace does not change their physical storage locations.
		+	'''Note''' - The top menu-bar items [[Menu_Bar#File|File]] and [[Menu_Bar#Edit|Edit]] also apply to items in the Workspace.  They offer many of the same options shown below, except e.g. Microarray merging is only available from the top level [[Menu_Bar#File|File]] menu.
−	==Renaming a project==	+	==Workspace Menu Options==
−	'''1.''' Right-click on '''Project''' folder.	+	Right-clicking on the Workspace node gives a menu with the following options
−	'''2.''' Select '''Rename'''.
		+	[[Image:Workspace_right_click_menu.png]]
−	[[Image:T_ProjectFolder_RenameProject.png]]
		+	===Open Files===
		+	* Loading data from local files is covered in the chapter [[Local_Data_Files | Local Data Files]]
		+	* Retrieving data from remote sources (caArray) is covered in [[Remote_Data_Sources | Remote Data Sources]]
−	'''3.''' In the pop-up screen rename your project.
−	'''4.''' Click on the '''OK''' button	+	===Open PDB File from RCSB Protein Data Bank===
		+	If '''Open PDB File from RCSB Protein Data Bank''' is chosen, a dialog box appears.
		+	[[Image:Project_Folders_Project_Open_RCSB_PDB.png]]
−	==Renaming a project data node==	+	Type in the name of a PDB structure entry and it will be retrieved from the RCSB Protein Data Bank and loaded into geWorkbench.
−	'''1.''' Right-click on a Project Folder data node.	+	==Workspace Data Node Menu Options==
−	'''2.''' Select '''Rename'''.	+	Right-clicking on a data node will produce a popup menu with the following options:
−	[[Image:T_RenameNode.png]]
		+	[[Image:Workspace_data_node_right_click.png]]
−	'''3.''' In the pop-up screen rename your data node.	+	===Save===
−	[[Image:T_ProjectFolder_RenameDataset2.png]]	+	Save the currently selected data node.  This is implemented for at least the below data types.  If saving of a particular type has not been implemented, the "Save" option will be disabled (grayed-out).
		+	* '''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.
		+	* '''FASTA''' - saved in FASTA format (.fasta).
		+	* '''PDB''' - saved in PDB format (.pdb).
		+	* '''Network''' - saved using the Adjacency Matrix "ADJ" format (.adj).
		+	* '''t-test result''' - saved as comma separated value (.csv) file.
		+	* '''Image''' - saved as PNG file (.png).
−	'''4.''' Click on the '''OK''' button.	+	For each file type, a file browser with a filter for the target file type extension (e.g. .fasta) will be opened.
		+	===Export to tab-delim===
		+	This option will only appear for microarray gene expression datasets.  It allows the microarray dataset to be exported in a spreadsheet format, as a tab-delimited text file.  The first row contains array names and the first column contains the marker names.
−	==Removing a project==	+	This export format does not preserve array or marker sets that may have been defined in geWorkbench for the dataset.  However, it can be used to save a copy of e.g. merged, filtered, and/or normalized data in a format easily used by other programs.
−	'''1.''' Right-click on '''Project''' folder.	+	When exporting, the file save dialog will display the name of the dataset, minus any recognized file-type suffixes that may be present (e.g. .soft).
−	'''2.''' Select '''Remove'''.	+	===Rename===
		+	A dialog box will appear in which a new name can be entered.
−	==Removing a project data node==	+	[[Image:Workspace_Rename_Node.png]]
−	'''1.''' Right-click on the data node.	+	===Remove===
−	'''2.''' Select '''Remove'''.	+	The selected data nodes and any child data nodes will be removed. Multiple selections can be made.
		+	==Data Node Hover-text Information==
−	==Saving a data node to a file==	+	For microarray datasets, adjacency matrices (network nodes), sequence and pattern nodes, moving the mouse cursor over the data nodes will display additional details about a dataset.
−	It is here that, among other things, you can create the matrix multi-experiment file format used by geWorkbench from a merged dataset.	+	Microarray datasets: hover text displays number of markers and arrays.
−	'''1.''' Right-click on data node that you want to save.
−	'''2.''' Click '''Save'''.	+	[[Image:Dataset_hover_microarray.png]]
−	[[Image:T_NodeOptionsMenu.png]]
		+	Adjacency Matrix: hover text displays number of nodes and edges in the network.
−	A standard file '''Save''' screen will come up.
−	'''3.''' Choose a location.	+	[[Image:Workspace_Dataset_hover_network.png]]
−	'''4.''' Enter a name.
−	'''5.''' Click on the '''Save''' button.	+	Sequence node:
		+	[[Image:Workspace_hover_sequences.png]]
−	=Tutorial: Loading microarray data files - local=
−	In this example, we will load 10 individual Affymetrix MAS5 format files, and merge them into a single dataset.  The origin of these file is described in the section [[Tutorial_-_Data]]	+	Pattern node:
−	Next, right-click on the '''New Project''' entry and select '''Open Files'''.	+	[[Image:Workspace_Pattern_Hover.png]]
−	[[Image:T_OpenFiles.png]]	+	==Workspaces==
		+	===Saving the Workspace===
		+	Saving the workspace saves all its data to a file on disk.  The workspace can later be reloaded to resume work.
−	A file browser will appear with which you can select the files you wish to open.  The default is to browse for local files, that is on your own computer.  geWorkbench can also access data from caArray databases.	+	====Special considerations on saving and restoring workspaces====
		+	* '''Versions''' - Workspaces in general may not be compatible across different versions of geWorkbench.
		+	* '''Loaded components''' - The configuration in the [[Component_Configuration_Manager| CCM]] of which components are loaded and which are not is not saved when the workspace is saved; it is maintained separately.
		+	* '''Changes to loaded components''' - If a workspace is saved, and then changes are made to which components are loaded in the [[Component_Configuration_Manager| CCM]], then in rare cases problems may occur when one attempts to reload the saved workspace.
−	[[Image:T_OpenFile_MAS5.png]]
		+	[[Image:File_Save_Workspace.png]]
−	Here, we will select file type '''Affymetrix GCOS/MAS5''' as shown.	+	===Opening a Saved Workspace===
−	Make sure to check the '''Merge files''' checkbox.  This will create the merged data node as the files are read in.	+	File->Open-Workspace.
−	We will select 10 MAS5 format text files from the directory cardiogenomics.med.harvard.edu, which is included in the geWorkbench tutorial download.	+	Only one workspace at a time can be loaded in geWorkbench.  Opening a saved workspace will destroy the existing workspace. For this reason, if you opt to open a workspace, you will be prompted as to whether to save the existing workspace first.
−	Click '''Open'''.
		+	[[Image:File_Open_Workspace.png]]
−	A message will appear giving information about associating an annotation file with the dataset.	+	A dialog box will appear in which the location and file name to which to save the workspace can be chosen.
−	[[Image:T_Annotation-selection1.png]]
−	A file browser will then open with which you can, if you wish, select an annotation file matching your dataset.  This is needed if you intend to use features of geWorkbench such as the Sequence Retriever or  GO Terms component (Gene Ontology).	+	[[Image:File_Save_Workspace_Dialog.png]]
		+	===Creating a New Workspace===
−	[[Image:T_Annotation-selection2.png]]	+	Only one workspace at a time can be loaded in geWorkbench.  Creating a new workspace will destroy the existing workspace.  For this reason, if you opt to create a new workspace, you will be prompted as to whether to save the existing workspace first.
		+	A new workspace can only be created from the top level menu bar.
−	A status bar will display as the data is loaded:	+	[[Image:File_New_Workspace.png]]
−	[[Image:T_File-loading-status-bar.png]]
−		+	Select '''File->New->Workspace'''.
−
−	The merged dataset is listed in the Project folder. The data is displayed, in single array format, in the '''Microarray Viewer'''.  Note we have increased the intensity slider to maximum here.  You can scroll through the arrays from first to last using the slider.  The display in the '''Microarray Viewer''' is by marker in the linear order the markers appear in the data file.  It does not correspond in any way to a physical picture or representation of the actual 2-D microarray.
−
−	[[Image:T_Merged_MAS5_files.png]]
−
−
−	=Tutorial: Merging microarray data files after they have already been loaded.=
−
−	If data files are not merged at the time they are read in, they can also be merged later, as long as they are from the same chip type.
−
−
−	'''1.''' Select the read-in data files that you want to merge.
−
−	'''2.''' Click on '''File''' in the menu bar, and choose '''Merge Datasets'''.
−
−	The picture shows the resulting merged dataset created from several individual data files.
−
−	[[Image:T_MergeIndividual.png]]
−
−
−	The result is a new data node containing the merged data.  The original data nodes are still present.
−
−	[[Image:T_ProjectFolder_IndividMerged.png]]
−
−
−
−
−	=Tutorial: Working with remote data sources=
−
−	==The remote Open File dialog==
−	geWorkbench can retrieve data from certain remote data sources; currently only instances of the NCICB's caArray database are supported.  The Open File dialog allows remote sources to be added to the list of those available either manually or through discovery using grid services.  Entries (locations, parameters) for non-grid services can be edited.
−
−	As before, right-click on '''Project''' which will bring up the '''Open File''' dialog.  Click the '''Remote''' radio button.  The '''Open File''' dialog window will be expanded to include remote sources.
−
−	Note the distinction between the "Open File" button, which opens a local or remote file, and the "Go" button, described below, which connects to a chosen remote resource to allow browsing.
−
−	[[Image:T_OpenFile_Remote.png]]
−
−
−	They buttons at the bottom of the remote file dialog are:
−
−	'''Source''' button - lists remote resources.
−
−	'''Go''' button - downloads a list of all available experiments from the remote source.
−
−	'''Filtering''' - Allows one to see a list of particular types of experiements, such as by organism or chip type, on the remote source.
−
−	'''Add A New Resource''' button - Opens the Data Source Definition Page used to add a remote data source.
−
−	'''Edit''' button - Edits remote source parameters.
−
−	==Loading data from a remote instance of caArray==
−
−	geWorkbench can download data from instances of caArray.  In the File->Open dialog, click the '''Remote''' setting.
−
−	You can '''Add a New Resource''' or '''Edit''' existing connection settings to set up a connection to an instance of caArray.  The configuration for connecting to the production instance of caArray at the NCI is shown here:
−
−	[[Image:T_caArray_EditConnection.png]]
−
−
−	If you click on the red '''Go''' button next to the caArray data source at the bottom of the dialog, all available caArray experiments at that location will be displayed.
−
−	Instead, you can select only particular kinds of experiments by pushing the '''Filter''' button.  Here we show experiments of type "Human" being selected.
−
−
−	[[Image:T_caArray_Filter.png]]
−
−
−
−	And here are the resulting entries in the database:
−
−	[[Image:T_caArray_Human_Expts.png]]
−
−
−
−	Select an experiment and push the '''Show Arrays''' button to see the individual array datasets available for download for this experiment.
−
−	[[Image:T_caArray_ShowArrays.png]]
−
−
−	Now we will select four of the arrays and push the '''Open''' button to begin the download.  Dont' forget to click the '''Merge''' button first if desired to merge the data into a single dataset.
−
−	[[Image:T_caArray_Open4Arrays.png]]
−
−
−
−	You will be prompted to select the quantitation type from those available for the experiment.  Here we select CHP Signal:
−
−	[[Image:T_caArray_QuantType.png]]
−
−
−
−	The resulting data set will appear in the Project Folders component as shown previously

---

Latest revision as of 17:07, 10 January 2014

Home | Quick Start | Basics | Menu Bar | Preferences | Component Configuration Manager | Workspace | Information Panel | Local Data Files | File Formats | caArray | Array Sets | Marker Sets | Microarray Dataset Viewers | Filtering | Normalization | Tutorial Data | geWorkbench-web Tutorials

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Overview

The Workspace is located in the upper-left-hand corner of the application. It is used to contain open data files and store analysis results during a geWorkbench session. When geWorkbench is launched, an empty Workspace folder is displayed.

The workspace as a whole, with all its projects and data nodes, can be saved and restored. However, only one workspace can be open at one time. Creating a new workspace or loading a saved workspace will overwrite the current workspace.

• To view the next level down in the hierarchy, click on the “+” icon to expand the branch.

• To collapse a branch, click on the “-” icon.

The Workspace may contain several heterologous datasets. These datasets can include input (source) data and derived data (results) associated with an experiment as well as image files. Source data can be loaded from the user’s local storage or from remote servers. Loading datasets into the geWorkbench Workspace does not change their physical storage locations.

Note - The top menu-bar items File and Edit also apply to items in the Workspace. They offer many of the same options shown below, except e.g. Microarray merging is only available from the top level File menu.

Workspace Menu Options

Right-clicking on the Workspace node gives a menu with the following options

Open Files

• Loading data from local files is covered in the chapter Local Data Files
• Retrieving data from remote sources (caArray) is covered in Remote Data Sources

Open PDB File from RCSB Protein Data Bank

If Open PDB File from RCSB Protein Data Bank is chosen, a dialog box appears.

Type in the name of a PDB structure entry and it will be retrieved from the RCSB Protein Data Bank and loaded into geWorkbench.

Workspace Data Node Menu Options

Right-clicking on a data node will produce a popup menu with the following options:

Save

Save the currently selected data node. This is implemented for at least the below data types. If saving of a particular type has not been implemented, the "Save" option will be disabled (grayed-out).

• 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.
• FASTA - saved in FASTA format (.fasta).
• PDB - saved in PDB format (.pdb).
• Network - saved using the Adjacency Matrix "ADJ" format (.adj).
• t-test result - saved as comma separated value (.csv) file.
• Image - saved as PNG file (.png).

For each file type, a file browser with a filter for the target file type extension (e.g. .fasta) will be opened.

Export to tab-delim

This option will only appear for microarray gene expression datasets. It allows the microarray dataset to be exported in a spreadsheet format, as a tab-delimited text file. The first row contains array names and the first column contains the marker names.

This export format does not preserve array or marker sets that may have been defined in geWorkbench for the dataset. However, it can be used to save a copy of e.g. merged, filtered, and/or normalized data in a format easily used by other programs.

When exporting, the file save dialog will display the name of the dataset, minus any recognized file-type suffixes that may be present (e.g. .soft).

Rename

A dialog box will appear in which a new name can be entered.

Remove

The selected data nodes and any child data nodes will be removed. Multiple selections can be made.

Data Node Hover-text Information

For microarray datasets, adjacency matrices (network nodes), sequence and pattern nodes, moving the mouse cursor over the data nodes will display additional details about a dataset.

Microarray datasets: hover text displays number of markers and arrays.

Adjacency Matrix: hover text displays number of nodes and edges in the network.

Sequence node:

Pattern node:

Workspaces

Saving the Workspace

Saving the workspace saves all its data to a file on disk. The workspace can later be reloaded to resume work.

Special considerations on saving and restoring workspaces

• Versions - Workspaces in general may not be compatible across different versions of geWorkbench.
• Loaded components - The configuration in the CCM of which components are loaded and which are not is not saved when the workspace is saved; it is maintained separately.
• Changes to loaded components - If a workspace is saved, and then changes are made to which components are loaded in the CCM, then in rare cases problems may occur when one attempts to reload the saved workspace.

Opening a Saved Workspace

File->Open-Workspace.

Only one workspace at a time can be loaded in geWorkbench. Opening a saved workspace will destroy the existing workspace. For this reason, if you opt to open a workspace, you will be prompted as to whether to save the existing workspace first.

A dialog box will appear in which the location and file name to which to save the workspace can be chosen.

Creating a New Workspace

Only one workspace at a time can be loaded in geWorkbench. Creating a new workspace will destroy the existing workspace. For this reason, if you opt to create a new workspace, you will be prompted as to whether to save the existing workspace first.

A new workspace can only be created from the top level menu bar.

Select File->New->Workspace.