Difference between revisions of "Component Configuration Manager"

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{{TutorialsTopNav}}
 
{{TutorialsTopNav}}
  
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==Overview==
  
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==Overview==
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geWorkbench supports the dynamic loading and unloading of individual components for analysis and visualization.  The Component Configuartion Manager (CCM) lists each available component, provides descriptive and license information, and controls loading and unloading.  The ability to customize the loaded components may be useful to those who intend only to use particular types of analysis.  It may in some cases also increase the responsiveness of the application, as potentially fewer viewer components may need to respond to particular data events (new data set, marker set activation etc.).
  
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With release 1.7.0, geWorkbench now supports the dynamic loading and unloading of individual components for analysis and visualization.  The Component Configuartion Manager (CCM) lists each available component, provides descriptive and license information, and controls loading and unloading.  The ability to customize the loaded components may be useful to those who intend only to use particular types of analysis.  It may in some cases also increase the responsiveness of the application, as potentially fewer viewers may need to respond to particular data events (new data set, marker set activation etc.).
 
  
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In brief, components can be loaded by checking the box adjacent to their entry in the list, and hitting Apply.  Components can be unloaded in the same way, by unchecking their box and applying the change.
  
 
As shipped, the CCM may appear as in the figure below, with only basic components configured.  Individual components can be added by clicking on their check boxes.
 
As shipped, the CCM may appear as in the figure below, with only basic components configured.  Individual components can be added by clicking on their check boxes.
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[[Image:CCM_Main.png|{{ImageMaxWidth}}]]
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'''Note on Workspace saving''' - The state of the CCM as to which components are loaded is not saved when the [[Workspace]] is saved.  It is stored separately.
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==Available Component List==
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The list of components includes the following column headings:
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* '''On/Off''' - checking will select the component for loading.  Unchecking the box will lead to the component being unloaded.
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* '''Name''': Component name
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* '''Author''' - Component author or source of primary calculation code.
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* '''Version''' - Component version
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* '''Tutorial''' - Link to web-based tutorial/manual if available.
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* '''Tool URL''' - Link to tool home page if available.
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==Component Dependencies==
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geWorkbench tracks component dependencies, for example between an analysis component and its viewer.  These dependencies are all handled in the CCM.
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There are two types of dependency:
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* '''Required''' - If component A requires component B, then if A is selected for loading in the CCM, B will also be selected.  The relationship is reciprocal - if A requires B, then B requires A.
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* '''Recommended''' - If component B is recommended for use with component A, then if A is selected, the user will be notified that B is recommended. However, component B will not be automatically selected for addition when component A is loaded.  The user must select B manually.
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An example of a required relationship is shown in the following figure, where adding the MRA-FET component also requires adding the MRE-FET Results Viewer component.
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[[Image:CCM_adding_MRA_dependency_check.png]]
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After clicking "Proceed", both components are selected to be added.
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[[Image:CCM_MRA_added.png]]
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If a component requires agreeing to a license, the license will also be displayed at this time, with the option to accept or reject it.
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An example of a recommended relationship, between ARACNe and Cytoscape, is illustrated below.
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[[Image:CCM_Recommended_relationship.png]]
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===Technical Note===
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Although the "Continue" button may appear to have focus, hitting Enter may not activate it.  However, using the space-bar may work.  This is due to cross-platform differences.
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==Framework Component Dependencies==
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The Filtering and Normalization framework components have been made dependent on all filter and normalization method components, respectively.  Thus these framework components can only be removed if first all filters or normalizers are removed in the CCM.
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==Controlling display of components==
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===Display===
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Displayed components can be limited by the following menu choices:
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* '''All'''
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* '''Only Loaded'''
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* '''Only Unloaded'''
  
  
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[[Image:T_CCM_defaults.png]]
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===Show by type===
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In addition, a pulldown menu allows only particular categories of components to be viewed.  The categories are not exclusive, a component can belong to multiple relevant categories.
  
  
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As each component is added, additional components may also be required, e.g. adding an analysis may require a particular viewer.  These dependencies are all handled in the CCM.  An example is shown in the following figure.
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[[Image:CCM_by_type.png]]
  
  
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[[Image:T_CCM_ARACNE.png]]
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Categories for components include:
  
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* '''Analysis''' - data analysis of any kind.
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* '''Filter''' - microarray data filtering.
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* '''Microarray''' - microarray data analysis or visualization (does not include filters or normalizers).
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* '''Network''' - creates, uses or visualizes networks.
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* '''Normalizer''' - microarray data normalization.
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* '''Others''' - any components that fall in none of the above categories.
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* '''Remote access''' - retrieves information from a remote source, e.g. BLAST, sequence retriever etc.
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* '''Sequence''' - operates on biological sequences.
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* '''Structure''' - operates on molecular structures (PDB files).
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* '''Visualizer''' - can visualize data or analysis results.
  
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==Individual controls==
 
  
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* Display : All, Only Loaded, Only Unloaded - selects which components to display.
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(Technical Note - The categories are defined dynamically by entries in each component's .cwb file. This file can be edited to add new categories).
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* Show by type: All, Parsers, Analysis plugins, Visualizers - filters displayed components by their category of action.
 
  
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===Keyword Search===
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The names of listed components can be searched by typing in a word here.  Displayed choices will be progressively narrowed as typing occurs.
  
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* Name: Component name
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==Controls==
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* Version: Component version
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Once the desired changes to the list of components has been made, the changes are put into effect by pushing the '''Apply''' button.
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* Author: Component author or source of primary calculation code.
 
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* Author URL: some components have a URL to the author's website configured.
 
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* Tool URL: some components have a URL to their own website configured.
 
  
  
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* View license - If a license is required for a component, it can be displayed by highlighting the component in the list and pressing this button.
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* '''Apply''' - if any changes have been made to the check-boxes indicating which components are to be loaded, pushing "Apply" causes the changes to actually be be made.  
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* View documentation - Provided for displaying extra documentation about the component if available.
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* '''Reset''' - If changes have been made but "Apply" has not been pushed, set all checkboxes  back to their previous state.
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* View external site - same as the Tool URL link.
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* '''Close''' - Close the CCM window.
  
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* Apply - if any changes have been made to the check-boxes indicating which components are to be loaded, pushing "Apply" causes the changes to actually be be made.
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* '''View license''' - If a license is required for a component, it can be displayed by highlighting the component in the list and pressing this button.
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* Reset - If changes have been made but "Apply" has not been pushed, set all checkboxes  back to their previous state.
 
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Close - Close the CCM window.
 

Latest revision as of 14:50, 22 April 2014

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Overview

geWorkbench supports the dynamic loading and unloading of individual components for analysis and visualization. The Component Configuartion Manager (CCM) lists each available component, provides descriptive and license information, and controls loading and unloading. The ability to customize the loaded components may be useful to those who intend only to use particular types of analysis. It may in some cases also increase the responsiveness of the application, as potentially fewer viewer components may need to respond to particular data events (new data set, marker set activation etc.).


In brief, components can be loaded by checking the box adjacent to their entry in the list, and hitting Apply. Components can be unloaded in the same way, by unchecking their box and applying the change.

As shipped, the CCM may appear as in the figure below, with only basic components configured. Individual components can be added by clicking on their check boxes.

CCM Main.png


Note on Workspace saving - The state of the CCM as to which components are loaded is not saved when the Workspace is saved. It is stored separately.

Available Component List

The list of components includes the following column headings:

  • On/Off - checking will select the component for loading. Unchecking the box will lead to the component being unloaded.
  • Name: Component name
  • Author - Component author or source of primary calculation code.
  • Version - Component version
  • Tutorial - Link to web-based tutorial/manual if available.
  • Tool URL - Link to tool home page if available.


Component Dependencies

geWorkbench tracks component dependencies, for example between an analysis component and its viewer. These dependencies are all handled in the CCM.

There are two types of dependency:

  • Required - If component A requires component B, then if A is selected for loading in the CCM, B will also be selected. The relationship is reciprocal - if A requires B, then B requires A.
  • Recommended - If component B is recommended for use with component A, then if A is selected, the user will be notified that B is recommended. However, component B will not be automatically selected for addition when component A is loaded. The user must select B manually.

An example of a required relationship is shown in the following figure, where adding the MRA-FET component also requires adding the MRE-FET Results Viewer component.

CCM adding MRA dependency check.png


After clicking "Proceed", both components are selected to be added.


CCM MRA added.png


If a component requires agreeing to a license, the license will also be displayed at this time, with the option to accept or reject it.

An example of a recommended relationship, between ARACNe and Cytoscape, is illustrated below.


CCM Recommended relationship.png

Technical Note

Although the "Continue" button may appear to have focus, hitting Enter may not activate it. However, using the space-bar may work. This is due to cross-platform differences.

Framework Component Dependencies

The Filtering and Normalization framework components have been made dependent on all filter and normalization method components, respectively. Thus these framework components can only be removed if first all filters or normalizers are removed in the CCM.

Controlling display of components

Display

Displayed components can be limited by the following menu choices:

  • All
  • Only Loaded
  • Only Unloaded


Show by type

In addition, a pulldown menu allows only particular categories of components to be viewed. The categories are not exclusive, a component can belong to multiple relevant categories.


CCM by type.png


Categories for components include:

  • Analysis - data analysis of any kind.
  • Filter - microarray data filtering.
  • Microarray - microarray data analysis or visualization (does not include filters or normalizers).
  • Network - creates, uses or visualizes networks.
  • Normalizer - microarray data normalization.
  • Others - any components that fall in none of the above categories.
  • Remote access - retrieves information from a remote source, e.g. BLAST, sequence retriever etc.
  • Sequence - operates on biological sequences.
  • Structure - operates on molecular structures (PDB files).
  • Visualizer - can visualize data or analysis results.


(Technical Note - The categories are defined dynamically by entries in each component's .cwb file. This file can be edited to add new categories).

Keyword Search

The names of listed components can be searched by typing in a word here. Displayed choices will be progressively narrowed as typing occurs.

Controls

Once the desired changes to the list of components has been made, the changes are put into effect by pushing the Apply button.


  • Apply - if any changes have been made to the check-boxes indicating which components are to be loaded, pushing "Apply" causes the changes to actually be be made.
  • Reset - If changes have been made but "Apply" has not been pushed, set all checkboxes back to their previous state.
  • Close - Close the CCM window.
  • View license - If a license is required for a component, it can be displayed by highlighting the component in the list and pressing this button.
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