Google Summer of Code + Cytoscape Retreat
This year we had the unique opportunity to meet the majority of our GenMAPP Google Summer of Code students in the middle of the program during our Cytoscape Retreat in Toronto.
Here’s what Stephen had to say:
“This years Cytoscape retreat was hosted at the University of Toronto in the beautiful and new Terrence Donnelly Center for Cellular and Biomolecular research. It was a four day affair consisting of intensive development discussions coupled with user and plugin tutorials. Throughout the four days I was able to meet and talk extensively with a number of the core developers, other Google summer of code students, and members of the dedicated user base.The first day tackled how to proceed on refactoring the code base to come out with a cleaner release… The second day focused on user and plugin demonstrations. Getting to see all of the excellent tools developed as plugins for Cytoscape expanded my awareness of the scope and quality of research being done. In addition along with the other summer of Code students I presented my project to the group… Overall the second day opened my eyes to all of the excellent tools developed with Cytoscape and gave me a sense of where my project fit in.
The third day was definitely the highlight for me as there was an extremely useful and helpful developers tutorial in the morning. This session certainly saved me hours of headaches as it clarified a number of otherwise blurry pieces of the API. I then was able to sit in on a very interesting discussion started by one of Cytoscape’s founders Trey Ideker, about what Cytoscape 10.0 would look like (the current release is 2.6)… It was this effort to look at the big picture and see what place a tool like Cytoscape might have in the future which got me really excited.
Overall the retreat was an excellent opportunity to meet with members of the Cytoscape community and hear about all of the exciting work being done. It allowed me to fill the gap between what I could glean from the mailing lists and what the community was really like. I always really enjoy meeting and talking with people in person and so the retreat was a major delight for me. Finally I would just like to extend my utmost thanks to Google for making this extremely rewarding experience possible.”
Pekka was one of the high quality applicants that we simply did not have the mentoring capacity (nor slots) to accommodate. We were so enthusiastic about involving Pekka in our work we invited him to our retreat to meet and interact with the developers and GSoC students.
“When I found myself standing at the Lester B Pearson Airport in Toronto, I was still a bit amazed how I had ended up there. About two months ago I had applied for Google Summer of Code project and my hopes were high. Unfortunately it was not my time to become chosen. However my disappointment soon vanished as I found out that I was still invited to participate Cytoscape Developer Retreat 2008 in Toronto. Yay!…Next morning the actual conference started. The agenda for the morning contained some very interesting discussions about developement of Cytoscape. During the afternoon topics a bit more technical and harder to understand for a person not directly involved in Cytoscape development, but I still tried to learn what I could.
Next day it was time for my own speech about a layout plug-in I had written. Although I was bit nervous and had some technical problems during my presentation, the speech went well and I was happy I had had an opportunity to talk about our work. I also talked about it with many people and received some interesting ideas for future development…
Friday was scheduled for tutorials and brainstorming. This was the most useful day for me, and it was very interesting to discuss about the future of Cytoscape and the possibilities Cytoscape API offers for the plug-in dvelopers… I’m very happy I was invited to come to Toronto and that I was to able to go there. I’d like to thank Google making my trip possible, Alexander Pico for helping me with the arrangements and Gary Bader and all the other organizer for making it a week to remember! Hope to see you all again!”
We were really impressed when some of our students made youtube videos demonstrating their GSoC projects. Check them out!
Gang’s two-part screencast of GLay:
Patrick’s demo of the Random Network generator:
Victoria’s Automatic Label Layout video on blip.tv
As you can see, it was a great Summer!
