Wednesday, November 21, 2007

GenMAPP and the Cytoscape Developer Retreat

The GenMAPP project enjoyed their first Summer of Code this year, and things went so well for them that they invited several of their students to the Cytoscape developer's retreat. Maital Ashkenazi joined the development team in Amsterdam for the retreat and she was kind enough to send us a report from the event. Maital writes:

The annual Cytoscape retreat and symposium was hosted by the Human Genetics Department of the Academic Medical Center in Amsterdam last week. Core developers, plug-in writers and Cytoscape users gathered for four days packed with tutorials, an application showcase, public symposium and development planning. This year, the GenMAPP project, along with Cytoscape, mentored four Summer of Code students. Three of us attended the conference and presented our work.

On the evening prior to the conference’s start, we went to a “meet and greet” event. It was great to finally meet two of my mentors in person. We have been working together for the past six months, and we've met in Second Life, but this is the first time we actually got to see each other in real life.

The first and last days were dedicated to software development and planning. Although I've been present in numerous software development discussions, usually during my work at high-tech firms, it was fascinating to learn how groups from around the world collaborate. The atmosphere was great; I loved watching these passionate and dedicated developers discuss priorities, envision architectures and set timelines. I especially enjoyed the decision process regarding the core redesign intended for version 3.0. We separated into two groups, each in a different room, and discussed aspects related to the new design. There were programmers with years of experience and familiarity with Cytoscape core and others less experienced, yet everyone's opinions were listened to and carefully examined. When we re-gathered we realized that one group studied this subject top-down, while the other went bottom-up. Discussions kept going and decisions were made.

The third day of the retreat was application showcase day. I had the opportunity to demo my plug-in, a search tool that enables searching biological networks on multiple attribute fields using logical operators and wildcards. It was exciting to talk in front of such big crowd. I demonstrated some aspects of the query syntax and showed how simple queries can be used in order to gain biological insight from a biological network. The first question after my demo was “Where can I download this plug-in?!?!” A big smile spread over my face, as I was just realizing that people were interested in my work. That smile kept growing as more and more people approached to congratulate me on a successful demo. Most satisfying of all, though, was to hear people suggest that I turn my plug-in into a core plug-in and have it distributed along with Cytoscape! Seeing what other plug-in developers have come up with brought up a few new ideas that I would love to incorporate into Cytoscape.

I want to thank Google for helping to sponsor my travel to the conference, but I want to thank Google even more for exposing me to the fascinating world of open source. Now that I have seen how open source development gets done I am even more excited to be a part of Cytoscape developers’ team than I was before I met them in person.

This journey would also not have been possible without the help of the conference organizers, who sponsored my accommodation. Thank you!

Many thanks to Maital for giving us a better view of the GenMAPP and Cytoscape developers' world. You know we always love to hear from Summer of Coders about the conferences they've attended - whether you're a kernel hacker or a bioinformatics geek - so post a comment and let us know what you've been up to lately.


Gary Bader said...

Excellent write up Maital!

Liorsion said...

Sounds very exciting and useful, the great open source meeting. Loved reading your description of it!