As some of you may know, I participated in Google Summer of Code 2008.  And the project I worked on is called Cytoscape.  So if any of you are interested in this project, here are a few links:

Google Summer of Code 2010 — GenMAPP, Cytoscape, WikiPathways & Reactome

• Organization Profile
• Cytoscape-Discuss Google Group
• Project Ideas

For those of you who are interested in working on the project idea I worked on two years ago, it’s this one:

IDEA 16: Automatic (Smart) Node and Edge Label Layout

Cytoscape currently has a large number of layout algorithms that place nodes according to various criteria. However, a common problem with all of these layout algorithms is that node and edge labels are not accounted for in the aesthetic criteria of the algorithm. This means that labels frequently end up in awkward locations which are hard to read, overlap or obscure other labels, and otherwise don’t look quite right. As a consequence, users are frequently forced to adjust the position of labels s, which is a time consuming and tedious process. To fix this, we propose developing a layout algorithm for labels. Perhaps this algorithm could be integrated with a normal layout algorithm, or perhaps it could be a subsequent step that lays the labels out in an intelligent fashion once the nodes have been placed. Some work has been done on this, but more layouts are needed.

Language and Skills: Java, graph layout algorithms

Idea by: Mike Smoot

Potential Mentors: Ruth Isserlin, Gary Bader

My blog posts that are related to this project can be found here.

I just came across this WordPress blogpost congratulating their Google Summer of Code 2009 students.  And at the very bottom, Jane Wells, the author, asks: “Where are all the geek girls?” I’m sure this isn’t a surprise to anybody, but what is surprising is the fact that the number of GSoC applicants went down this year.  This is disappointing, since a lot of us are really trying to get the word out.  Just looking at the University of Toronto for example, we’ve held many info sessions for GSoC 2009.  We even had threads on our department bulletin board answering any questions students might have regarding GSoC.  And I’m sure we’re not the only ones promoting it, so I personally found this very surprising — at first at least.

But now that I stop and think about it, the GSoC application deadline was definitely during one of the busier weeks for post-secondary students.  Thinking back, I was extremely stressed out last year around this time as well, since there were so many assignments and other evaluations to take care of while I was trying to apply for GSoC 2008.  I eventually had to sacrifice my assembly programming assignment to complete my GSoC proposal.  But I’m really glad I did so, because my proposal got accepted, and I still managed to get a passing grade for that one assignment (barely!).

This year, many of my friends considered applying for GSoC.  However, on top of all the deadlines, many of my friends were still looking for PEY internship positions.  So they eventually had to give up this awesome opportunity.  I’m not sure if prolonging the application period would have helped my friends in particular, but I’m sure a lot of students would benefit from the extra few days, and maybe they could work around their busy schedules and submit at least one proposal. :D

For those of you who were unable to apply to GSoC this year, remember to do so next year!  It really was an awesome opportunity for me last year, and it has definitely helped me a lot in finding internship positions.  And for those of you who are wondering what I was working on last summer for GSoC 2008, click here!