GenMAPP’s Summer Harvest

Friday, September 24, 2010

The GenMAPP organization’s efforts focus on building software tools to analyze and visualize biological data. We joined forces with Cytoscape, WikiPathways, PathVisio and Reactome for this year's Google Summer of Code to offer students a unique opportunity to work at the intersection of biology and computing.

This was our 4th year participating in the program and we reached some new milestones. We mentored 10 excellent students (more than any prior year) with a 100% success rate. We integrated and released more code from this summer’s harvest than in prior years. And most importantly, we continued to expand our development community, as many of this year’s students are enthusiastic about continuing to work with us beyond the summer.

Our projects this year covered a broad range of topics:

Alternative Splicing Analysis Plugin for Cytoscape, by Anurag Sharma
CyAnnotator and CyAnimator Plugins, by Avinash Thummala
User Interface Development in PathVisio, by Bing Liu
Tools for Exploring Pathway Relations in WikiPathways, by Chetan Bansal
Expression Data Reader plugin for Cytoscape, by Dazhi Jiao
Improving Cytoscape’s Labels Experience, by Gerardo Huck
KEGG Global Map Browser, by Kozo Nishida
Semantic Network Summary for Cytoscape, by Layla Oesper
Reactome-WikiPathways Converter, by Leontius Pradhana
Edge-Weighted Layout for Cytoweb, by Tomithy Too

As part of the open source experience, we invite our Google Summer of Code students to our annual Cytoscape Retreat. This is a great way to engage students in both our development and user communities. One student pointed out a truism that is rediscovered from time to time in our digital age, “face-to-face meetings turn out to be very efficient.” Here are some other gems of reflection and advice from our students this year:

“The most rewarding part was when I was told that I should merge my changes back from my branch into the trunk"

“It has been the chance to meet and interact with wonderful people from various parts of the world, be it virtual or physical. I had a chance to physically meet another graduate student from my university and a professor from USA due to Google Summer of Code.”

“They opened up my perspective about a lot of things — how the industry looks like, where people with similar skill domain as me put themselves in the society, how important the projects I am involved in are, and other subjects unimaginable if I were to not join Google Summer of Code.”

“Got a taste of open-source development which is just amazing and I would like to keep attached with this project even after this GSOC ends.”

“This program is a great initiative, I loved the amount of exposure the participating students get and it definitely is one of the most exciting summers someone can ever get.”

“The most rewarding part is to be able to go to the cytoscape retreat. It is absolutely helpful to the project, and helpful to get to know the mentors and others.”

“Be the best user of the software. If you are the best user, you write and participate [in] the software project spontaneously.”

“At the beginning of the summer, I really had my doubts on whether or not I had gotten in too far over my head. So I very much enjoy being able to look back at what I was able to accomplish and realize that I was able to supersede my original expectations for myself.”

“Don’t be afraid to ask questions. Your mentors are an amazing source of information, and they are really interested in helping you in any way possible.”

“Be cool.”
This post is cross posted from my Next Nucleus blog, where you can read more about our previous years with Google Summer of Code.

By Alexander Pico, Google Summer of Code Mentor for GenMAPP