RFC Name : Consolicated Graph Analysis Plugin

Editor(s): Keiichiro Ono

Status: Open for Comments

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This document is for consolidated graph analysis plugin development plan. The purpose of this project is collecting general graph analysis algorithms in one place and provide users a common interface to access the functions.

Biological Questions / Use Cases

Some network visualization/analysis tools have built-in graph analysis features such as:

These functions are useful for most of users (both biology/non-biology) to see the general characteristics of the graph. 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 easy access to these functionality.

General Notes

We will use the incremental approach for this project.

  1. Collect analysis plugins already available for Cytoscape.
  2. Implement a common UI for them.
  3. Design a expandable backend system which accepts additional analysis algorithms without changing the core.
  4. Implement individual algorithms. These can be added later.


The following functions will be implemented. Some of them will be ported from other libraries (such as JUNG).




Graph Generators (Optional)

Note: We do not have to implement all of them at once. We will implement small group of functions first.

Deferred Items

Open Issues

Functions needs to be implementd:

Backward Compatibility

Expected growth and plan for growth


Software with Graph Analysis Functionalities

Implementation Plan


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Consolidated_graph_analysis_plugin (last edited 2009-02-12 01:03:00 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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