Google Summer of Code 2007

"Google Summer of Code is a program that offers student developers stipends to write code for various open source projects. Google works with a several open source, free software and technology-related groups to identify and fund several projects over a three month-period. Historically, the program has brought together over 1,000 students with over 100 open source projects to create hundreds of thousands of lines of code."

• get more open source code created and released for the benefit of all

• inspire young developers to begin participating in open source development

• help open source projects identify and bring in new developers/committers

• provide students in Computer Science and related fields the opportunity to do work related to their academic pursuits during the summer (think 'flip bits, not burgers')

• give students more exposure to real-world software development scenarios (e.g., distributed development, software licensing questions, mailing list etiquette

[http://code.google.com/summerofcode.html Find out more]

What is Cytoscape?

Cytoscape is an open-source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other data. Cytoscape's software core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features.

Overview of Ideas

As we are prototyping new features and functions for Cytoscape, we are exploring a number of more general areas ideal for Google Summer of Code students. If you have solid CS skills and have interests in the biological domain, then you should apply.

IDEA: Cytoscape in a Browser

• you will develop a Javascript library and thin-client application that use built-in Web browser capabilities to provide a subset of Cytoscape functionality for viewing, editing, and analyzing networks.

IDEA: Non-biological Networks

• social
• environmental
• publications: degrees of separation

IDEA: Cellular-level Visualization

• zooming from cell to molecular!

IDEA: Animating the Temporal Dimension

IDEA: Export Clickable HTML Pages

• Save project to Web Report

IDEA: Model Timecourse Data

• w.r.t. Transcriptional networks

IDEA: Mapping multiple data points/types per node

IDEA: Matrix view of networks

IDEA: Scripting language to facilitate layout or editing

• e.g., A transports B

IDEA: Illustrator, AutoLISP, powerpoint features/tools

IDEA: Layout Ideas

IDEA: General scripting

IDEA: Data cleaning

If you want to apply

We would like to know who you are and how you think. Incorporate the following into your application:

• Your interests w.r.t. programming
• The background behind your interests
• Your ideas for a project (or expand from one above)
• Refer to and link to other projects or products that illustrate your ideas
• What can you bring to the team?

For more background information see:

• [http://cytoscape.org Cytoscape Website]: Our open source network visualization tool.

If you are selected

You will be working with an active team of software developers that also speak biology. You will work on intellectually stimulating and challenging tasks as part of a very collegial and supportive community of software developers.

You will be gaining experience in a rapidly evolving field on the intersection of computer and biological sciences. You will learn a lot about information visualization, user interface programming, and human-computer interaction techniques. You will gain experience in the emerging and dynamic field of network visualization and analysis.

You will work on applications that help to improve the practice of medicine and the quality of life. You will make a difference.