RFC Name : Pathway Walking Plugin

Editor(s): Steve Surrette, Ellen Tsai, Frankie Ng, Nancy Zhou, Sam Fernald

Date: 12-05-07

Status: being coded

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Currently there are methods of obtaining gene and protein interactions from online database mergers; however, those sources are outdated and do not allow for step-by-step creation of a network. Our senior design group proposes to create a plugin that allows users to download the neighbors of a selected node by accessing multiple online databases at the same time and have the data merged together, while still showing where the data came from.

Use Cases

General Notes

Five bioengineering students at UCSD are enrolled in a senior deign class and have decided to work on a plugin for Cytoscape. After reviewing the Future Cytoscape Features page on the Wiki, we have decided to work on a plugin that implements “pathway walking”. We hope to complete the plugin by the end of next March.


We have designed the plugin on a software flowchart that can be viewed in the Implementation Plan and plan to perform most of the coding starting in January and optimize the code until March.

Implementation Plan





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Pathway_walking_plugin (last edited 2009-02-12 01:04:00 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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