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Description: Cytoscape is able to visualize very large network with thousands of nodes and edges. Cytoscape provides three ways to select a subset of a network, Select, QuickFind and Filter. Filter, a Cytoscape plugin, is a powerful selection tool, which is able to do selection based on complex criterion. However, the feedback from Biologist is that “it is useful, but hard to use”. For example, (1) filters are saved globally only, not in session; (2) Filter names are generated automatically, which is not meaningful to human; (3) the text field does not have Google suggestion/ not dynamic, as QuickFind does. Therefore, it is necessary to redesign the UI of the filter and make it more user friendly. '''Description''': Cytoscape is able to visualize very large network with thousands of nodes and edges. Filter, a Cytoscape plugin, is a powerful selection tool, which is able to do selection based on complex criterion. However, the feedback from Biologist is that “it is useful, but hard to use”. For example, (1) filters are saved globally only, not in session; (2) Filter names are generated automatically, which is not meaningful to human; (3) the text field does not have Google suggestion/ not dynamic, as QuickFind does. Therefore, it is necessary to redesign the UI of the filter and make it more user friendly.
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The goal of this RFC is to provide a new design of filter UI, which use familiar GUI components to represent each filter. The new design should have the following characteristic, The goal of this RFC is to provide a new design of filter UI, which use familiar GUI components to represent each filter. The new design should have the following characteristics,
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4. Single Filter type will be determined automatically by the data type of attribute, string type- -> text field, numeric type (including Boolean type) --> RangeSlider bar. 4. Single Filter type will be determined automatically by the data type of the attribute, string type- -> text field, numeric type (including Boolean type) --> RangeSlider bar.
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5. Composite filter will be consist of a list of single filter with “AND” relationship 5. Composite filter will be consist of a list of single filters with logical “AND” relationship
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6. Suggestions will be added for each text field 6. Suggestions will be added for each text field as in QuickFind
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== Backward Compatibility ==

RFC Name : ...

Editor(s): ...

TableOfContents([2])

About this document

This is an official Request for Comment (RFC) for Filters UI Redesign.

Description: Cytoscape is able to visualize very large network with thousands of nodes and edges. Filter, a Cytoscape plugin, is a powerful selection tool, which is able to do selection based on complex criterion. However, the feedback from Biologist is that “it is useful, but hard to use”. For example, (1) filters are saved globally only, not in session; (2) Filter names are generated automatically, which is not meaningful to human; (3) the text field does not have Google suggestion/ not dynamic, as QuickFind does. Therefore, it is necessary to redesign the UI of the filter and make it more user friendly.

For details on RFCs in general, check out the [http://www.answers.com/main/ntquery?method=4&dsid=2222&dekey=Request+for+Comments&gwp=8&curtab=2222_1&linktext=Request%20for%20Comments Wikipedia Entry: Request for Comments (RFCs)]

Status

Open for public comment

How to Comment

To view/add comments, click on any of 'Comment' links below. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Here is an example to get things started: ["/Comment"].

Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.

Proposal

The goal of this RFC is to provide a new design of filter UI, which use familiar GUI components to represent each filter. The new design should have the following characteristics,

1. filter panel will be placed in CytoPanel_3

2. filter name will be given by user

3. user has the option to save the filter in session or globally

4. Single Filter type will be determined automatically by the data type of the attribute, string type- -> text field, numeric type (including Boolean type) --> RangeSlider bar.

5. Composite filter will be consist of a list of single filters with logical “AND” relationship

6. Suggestions will be added for each text field as in QuickFind

Biological Questions / Use Cases

Scenario: A user already imported network and attributes into Cytoscape, he/she want to select a set of nodes whose attribute “Unique identifier” has pattern “YL*” and its attribute “gal1RGexp” < 0.05.

1. Click the filter icon on the tool bar

2. CytoPanel_3 shows up on the left side of the Cytoscape window. TabbedPane “Advanced selection” is selected.

3. Click the option icon, a pulldown menu shows “create, delete, rename, copy”. select “create”

4. Filter creation dialog show up. Type in “My first filter” and click OK button.

5. A combobox for attribute selection show up, choose “Unique Identifier” and click add button

6. A text field with label “Unique identifier” show up.

7. Choose “gal1RGexp” at the attribute combobox and click the “Add” button

8. A rangeSliderBar shows up. Define the range of the value by move the bars.

9. When user type in the text on the textfield and move the slider bar, the selection on the canvas is changing accordingly.

Design

1. The initial state

  • attachment:filterInitialScreen.JPG

2. The composite filter

  • attachment:filtercomposite.JPG

Note:

(1) The Advanced panel holds the default settings, it is collapsed by default.

(2) Suggestion will be added to the textfield as QuickFind does

(3) The JSliderBar will be replaced by JRangeSliderBar.

(4). Boolean meta – multiple sliders, logical “and” only

(5). The “Apply” button will show up for large network only (>1000 nodes)

3. String filter/Numeric filer/ Interaction filter

They are all special cases of the composite filter, i.e. only one attribute is selected.

4. Alternative design

attachment:AlternativeDesign.JPG

Deferred Items

• Topology filter -- will use local attribute (network specific), normal attribute filter, and technically it is feature of network, not index

• Complex Boolean operation (how to handle?)

Open Issues

Expected growth and plan for growth

combine Filter and QuickFind

Filter API redesign

References

Implementation Plan

Filters/select/QuickFind should work together, try not to duplicate the code

1. front-end (GUI) --- 1~2 weeks

2. back-end --- ???? weeks

Comments

Filters_UI_Redesign (last edited 2009-02-12 01:04:01 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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