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."

[WWW] Find out more

What is GenMAPP?

GenMAPP is a visualization and analysis tool for biological data. GenMAPP illustrates the relationships between various genes and proteins to help researchers understand their data in terms of connected, biological pathways. Over 15,000 people from >40 countries have registered to download the GenMAPP program. There are over 260 publications that reference GenMAPP or use GenMAPP to display data in the context of biological pathways. GenMAPP is 100% open source and all new development is in Java, MySQL, Derby, XML, and Web technologies such as wiki in collaboration with the [WWW] UCSF library, [WWW] BiGCaT Bioinformatics, and the [WWW] Cytoscape Consortium. Our development team is composed of individuals who are both biologists and programmers, providing a unique perspective on building and using open source tools. More...

Accepted GSoC Projects

  1. Enhanced search strategy in Cytoscape: by Maital Ashkenazi, mentored by David States, Allan Kuchinsky, and Gary Bader

  2. Visual history of pathway modification: by Martijn van Iersel, mentored by Alexander Pico, Kristina Hanspers, and Patrick Ahles

  3. GSoC Pathway Editor for WikiPathways: by Thomas Kelder, mentored by Kristina Hanspers, Alexander Pico, and Bruce Conklin

  4. Graph layout library for GenMapp: by Nikolic Aleksandar, mentored by Michael Smoot, Gary Bader, and Scooter Morris

Resources

Communication

For Students

For Mentors

Overview of Ideas

As we are prototyping new features and functions for GenMAPP 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 (do you think genes are cool?), then you should apply!

IDEA 1: WikiPathways: Content Management

Ever hear of Wikipedia? Well, we are doing the same thing for biological pathways. A major hurdle to scientific research involving pathways is collecting and maintaining the information from the scattered (and busy) experts in various fields of study around the world. In the same manner as wikipedia, we'd like to bring the power of editing pathways to the people. While complementary, this approach is in contrast to more traditional efforts involving specialized groups of curators. The success of a wiki relies on good content management, resolving changes, divergences, convergences and disputes in a way that is fair, impartial and effective. A good wiki also needs intuitive search and navigation strategies that evolve with the complexity of the site. Let's work on a body of code that controls content management and navigation for wiki projects. We can test the code immediately on our WikiPathways site. We already have content and eager contributors. If we build it, they will come.

IDEA 2: Innovative & Intuitive Interfaces

A major downfall of most informatics tools in the biological domain is their poorly designed, clunky GUIs. As biologists, we have a lot of ideas about how the interfaces should look, feel and work. As developers, we often think about what can be done instead of what should be done. Like most interfaces, our interfaces need to display available options and provide easy access to common functions. We can immediately implement it for the interfaces to be used in the next version of GenMAPP.

IDEA 3: Visualizing Multiple Data Points/Types

Biological networks are frequently associated with data that come from a diversity of sources -- e.g. gene expression via microarrays, protein abundance via mass spectrometry, chromosomal abberations via comparative genomic hybridization, genetic polymorphisms. A number of approaches have been developed for overlaying data from multiple sources on network nodes and edges, for example mapping multiple gene expression measurements onto a 'striped' node color overlay. We are seeking proposals that implement novel, alternative ways of visualizing multiple data measurements on network nodes and edges.

IDEA 4: Network Workspace Sharing/Publishing

Currently, users are able to save their session in a single file for later use or to pass to their colleagues. We are seeking proposals to create a novel system for saving an interactive project to the web. You could imagine that a biologist in Boston could share their new molecular interaction network on the web and their collaborator in Paris could immediately interact with it. This would support more sharing and collaboration in biology.

IDEA 5: New Network Visualizations

We have a core set of basic graph (network) layout algorithms, from both proprietary and open source libraries. Biologists clearly need more advanced layout algorithms that consider biological information when performing the layout. We seek proposals to write new layout algorithms that make use of biological attribute data. For instance, a layout could organize nodes with different attributes in concentric rings, with each ring representing one type of node, or nodes with different degree. Lots of cool ideas are showcased at [WWW] http://www.visualcomplexity.com/

IDEA 6: Advanced Editing Features and Tools

We have a simple editing tool with a limited set of features. This is sufficient to support most tasks. However, additional tools and features would be useful in supporting tasks like preparation of figures for publication or presentation. Examples of such features are

and other features/tools that one might expect in products like Adobe Illustrator and Microsoft PowerPoint. We seek proposals for enhancing our network editing environment with novel features and tools.

If you want to apply

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

For more background information see:

If you are selected

last edited 2007-06-08 19:28:26 by MartijnVanIersel