Cytoscape Wiki
About this document
This is an official Request for Comment (RFC) for a Cytoscape Quick Find Feature.
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, please scroll down to the bottom of the page. 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.
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
This RFC proposes a new Cytoscape Quick Find feature. The goal of the feature is to enable Cytoscape users to quickly find nodes, and select them in the network view.
The feature will be based loosely on [http://www.google.com/webhp?complete=1&hl=en Google Suggest]. In Google Suggest, a user types a few characters, and Google automatically provides matching search terms which begin with these characters. Along the same lines, a Cytoscape users will type a few characters into a text box, and Cytoscape will automatically provide matching nodes which begin with these characters. The user can then select one of these matching terms, and the nodes will be automatically selected in the network view.
Here is a screenshot of my current prototype in action:
attachment:quick_find.png
By default, Quick Find will automatically index nodes based on Semantics.CANONICAL_NAME, and matching nodes will automatically be selected in the network view.
For more advanced users, the Quick Find feature will also support the following:
- Users can configure Quick Find to index nodes based on any attribute. Only those attributes on type: String or Simple List of Strings will be available for indexing.
- Users can configure the action for selecting nodes:
- Select Matching Nodes Only (default)
- Select Node Neighborhood (and keep all other nodes visible).
- Select Node Neighborhood (and hide all other nodes).
For the last two action options, the user will also be able to select a radius size for the neighborhood.
Quick Find will work with all Cytoscape plugins, so long as those plugins use CyAttributes to store attribute values.
Biological Questions / Use Cases
Quick Find addresses numerous biological use cases:
- Quickly find a single node, even if you do not know its exact name. For example, a user may wish to find the node named: "TGF-Beta". Using the current Cytoscape find feature, you must know the exact name of the node or enter a regular expression. With Quick Find, you simply start typing: "TGF", and Cytoscape will present all possible matches.
- Quickly find a neighborhood of nodes, and hide the rest of the network. This is particularly useful for exploring very large networks. For example, a user may wish to view the immediate neighborhood of TGF-Beta, and hide the rest of the network.
- Quickly find all nodes which match a specific attribute value. For example, a user may load a BioPAX network, and wish to view only those nodes which are located in the nucleus.
Deferred Items
None defined yet.
Required Changes to the Core
- In order for the Quick Find feature to always fit within the main Cytoscape tool bar, we will need to shrink the tool bar icons.
Open Issues
None defined yet.
Backward Compatibility
As this is a new feature, there are no backward compatibility issues.
Comments
EthanCerami, 07/05/2006 - This is a sample comment to get things started. Blah, blah, blah...