Cytoscape Retreat 2008
July 16-19, 2008
This year’s Cytoscape Retreat was hosted by Gary Bader’s lab at the University of Toronto. I thoroughly enjoyed the the city (my first visit), the campus, and the retreat. The timing couldn’t have been better, dovetailing with the ISMB meeting later in the week. The retreat is a great opportunity to meet face-to-face with all the developers that I otherwise know only through email. The Cytoscape Retreat also highlighted for me a few important developments:
Cytoscape Momentum
The first presentation highlighted recent stats on Cytoscape usage that I found really impressive in terms of growth:
- 35,000 visits per month
- 2,500 downloads per month
- 1000 on mailing lists
- 40 plugins
- BiNGO plugin downloaded 5000 times!
The second day of the retreat was focused on plugins and usage. From year to year, this section continues to grow in sophistication and breadth. See the full list of presentations.
The tone in general at the retreat was excitement about being involved in such a strong project. This impression was then multiplied when we witnessed a strong Cytoscape presence and interest at the behemoth ISMB meeting!
Growing Concensus on 3.0
The first day included a series of presentations on OSGi, Spring and code architecture. These set a healthy tone for discussion and decisions that lead to a huge step forward for 3.0 development from where we were at last Fall by the end of the prior retreat. In the final analysis, there was concensus on the path forward and a committment to developing enough documentation along the way to keep everyone afloat.
Developing Community
Overlapping with this year’s Google Summer of Code allowed us to meet a number of the students before the end of the program. This was a tremendous opportunity to interact and build a repoire with the GSoC students. Also this year, we had a record number of participants from outside the core group. This allowed us to interact with plugin developers and users in a uniquely productive way. This really helped to grow the community of developers around Cytoscape, both in breadth and depth. In my experience, the Cytoscape community really excels at cohesion and communication, providing a built-in reward system for participation. This is how a good open source software development community should run.
There was also a lot of discussion this year about developing teaching materials. This includes presentations, tutorials, workshops, handouts, etc. There seems to be a critical mass, finally, of both the materials and the demand for materials. I don’t normally teach, but I’ve given 4 workshops on Cytoscape in the past month! I am going to work with others in the group to collect and organize these Cytoscape materials to promote their distribution to new users, use in future talks or courses, and maintenance by developers. If you have any ideas on how best to organize this type of information for these purposes, please comment.
