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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 Wikipedia Entry: Request for Comments (RFCs)


{*} This RFC is now officially closed to public comment, as Quick Find is now part of Cytoscape 2.4. I am, however taking feature requests for the next version of Quick Find, to be included in Cytoscape 2.5 (see below).

Cytoscape 2.5 Feature Requests (add your ideas below)


This RFC proposes a new Cytoscape Quick Find feature for Cytoscape 2.4. 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 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:


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:

Quick Find will work with all Cytoscape plugins, so long as those plugins use CyAttributes to store attribute values.

Implementation Plan

A prototype, available as a Cytoscape Plugin is available at: http://cbio.mskcc.org/~cerami/quick_find/

The working prototype supports the following features:

Items to be added soon:

Biological Use Cases Addressed

Quick Find addresses numerous biological use cases:

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.

The following changes are not required, but would be very nice to have:

Open Issues

None defined yet.

Backward Compatibility

As this is a new feature, there are no backward compatibility issues.

Peformance Stats

The following section will contain details regarding the performance of Quick Find.

All experiments below were conducted on a Dual 1.42 GHz Power PC G4, with 2GB of RAM and Mac OS X 10.4.6.

Time to index various networks

(Note that indexing occurs in a background daemon thread, and is not directly observable by the user).

BINDhuman.sif: 19,462 nodes, 30,779 edges. Time to index by CANONICAL_NAME. Conducted three trials.

BINDyeast.sif: 23,505 nodes, 60,457 edges. Time to index by CANONICAL_NAME. Conducted three trials.

Random.sif: 63,141 nodes, 50,000 edges. Time to index by CANONICAL_NAME. Conducted three trials.

Time to query various networks

BINDhuman.sif: 19,462 nodes, 30,779 edges.

Random.sif: 63,141 nodes, 50,000 edges.


EthanCerami, 07/05/2006 - This is a sample comment to get things started. Blah, blah, blah...

MikeSmoot, 7/5/06 - This is a very cool idea. Some thoughts:

GaryBader 7/5/6 - Also agree on the coolness of this plugin :) - do we need the find button? It seems that you could do without it to save some space. I guess it would be required if new users can't figure out what it does. In that case, maybe the background of the text input box (or default text) could say "Find...". Also, if we decide we need the button, a finesse feature would be to have the choice to hide the find button for advanced users - most web browsers and office apps have a feature similar to that to help manage the space taken up by toolbar buttons.

QuickFindRFC (last edited 2009-02-12 01:03:12 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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