Cytoscape Wiki|
← Revision 4 as of 2007-07-25 00:15:08
Size: 2231
Comment:
|
← Revision 5 as of 2007-07-25 00:33:27 →
Size: 2440
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 45: | Line 45: |
|
=== Software with Graph Analysis Functionalities === * [http://vlado.fmf.uni-lj.si/pub/networks/pajek/ Pajek] * [http://jung.sourceforge.net/ JUNG] * [http://cneurocvs.rmki.kfki.hu/igraph/ igraph] * |
RFC Name : Consolicated Graph Analysis Plugin |
Editor(s): Keiichiro Ono |
Status: Open for Comments |
Proposal
This document is for consolidated graph analysis plugin development plan.
Biological Questions / Use Cases
Some network visualization/analysis tools have built-in graph analysis features such as:
- Shortest path
- Cluster analysis
- Graph traverse
- Graph Statistics:
- Mean shortest path
- Degree distribution
- Average number of interaction partners
- Clustering coefficient
- Topological coefficient
Some of these are implemented as Cytoscape plugins, but there is no one simple plugin to provide all of these. The purpose of this project is creating a core plugin to provide all of these functionality.
General Notes
Requirements
Deferred Items
Open Issues
Functions needs to be implementd:
- (Please add functions we need to implement...)
Backward Compatibility
Expected growth and plan for growth
References
Software with Graph Analysis Functionalities
[http://jung.sourceforge.net/ JUNG]
Implementation Plan
Comments
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.