Cytoscape GPU Assisted Graph Layout Plugin

Student Name: Gerardo Huck
Mentor Name: Daniel Abel
Organization: GenMAPP

Abstract

The aim of this project is to create a Cytoscape plugin capable of performing fast and accurate graph representations using the GPU.

While traditional implementations of layout algorithms perform a very good work with relatively small graphs, their high computational cost becomes a limiting factor when working with large graphs. Moreover, there are certain domains in which large graphs are part of the everyday work. That makes drawing pleasant representations of large graphs still a very challenging problem for Computer Science.

Here an implementation of a force directed graph layput algorithm for Cytoscape is proposed. This implementation would produce state-of-the-art graph drawings, while taking only a fraction of the time that the traditional implementat

Full project proposal:  http://socrates2.cgl.ucsf.edu/GenMAPP/wiki/Google_Summer_of_Code_2009/Gerardo/Proposal

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Reference material

 http://socrates2.cgl.ucsf.edu/GenMAPP/wiki/Google_Summer_of_Code_2009/Gerardo/ReferenceMaterial

SVN Repository

 svn+ssh://grenache.ucsd.edu/cellar/common/svn/csplugins/trunk/soc/ghuck

Milestones

May 28 - Apeksha Godiyal has released under GPLv3 the code used in the paper "Rapid Multipole Graph Drawing on the GPU".

June 15 - The code provided by Apeksha has been modified for using the latest CUDPP library release (1.0a). Also, it now runs fine in linux as a command line program. (See attachment: Screenshot-uk.graph.png)

August 3 - Linux version of the plugin working! (See attachment: PluginScreenshot-uk.graph.jpg)

August 18 -'Pencils down' date, Google Summer of Code 2009 is over. Several improvements have been made to the plugin.

What I'm working on right now

Right now it is impossible for me to spend time in this project. GSoC has finished and I got a new full time job... Anyway, I hope that I can resume soon!

To Do List

Build different versions of the plugin (Win 32 bits, Win 64 bits, Linux 32 bits, Mac).
Start Porting this plugin to Cytoscape 3.0 (when the new API is already stable).

View Results of benchmarks

Here are some of the results of benchmarking the latest release of this plugin against Cytospace's "Force Directed" layout:
 http://socrates2.cgl.ucsf.edu/GenMAPP/wiki/Google_Summer_of_Code_2009/Gerardo/Benchmarks

Get the current release of this plugin

Follow the link below to get the latest release of the plugin and intructions for install it.
 http://socrates2.cgl.ucsf.edu/GenMAPP/wiki/Google_Summer_of_Code_2009/Gerardo/Get