Pathway_walking_plugin

<<TableOfContents: execution failed [Argument "maxdepth" must be an integer value, not "[2]"] (see also the log)>>

Proposal

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there are methods of obtaining gene and protein interactions from online database mergers; however, those sources are outdated and do not allow for step-by-step creation of a network.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

• Database queries can take a long time
• Duplicates will only be displayed once, but the plugin will indicate how many and which databases the node came from.
• Inform the user about the number of Nodes that will be obtained if the network is expanded from the selected Node

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.

Requirements

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

Timeline

Comments

• Add comment here…

How to Comment

Edit the page and add your comments under the provided header. 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.