Berkeley Engineering Blogs

…on and on… or at least until we finish the dang project!

School started this Wednesday, so we’ve been traipsing the campus, picking our way through the hordes of incoming freshmen wandering around with their copies of the campus map. And yet I’ve already been asked for directions by three different freshmen!

Oops, forgot to introduce myself. I’m Richard Mar, a senior L&S Computer Science major on the Berkeley iGEM computational team. I work with Joanna on Spectacles, a visual design tool for synthetic biological parts. It’s a bit hard to believe that just two months ago Spectacles didn’t exist, and now we have an application that’s close to completion!

Here’s what we started with: we were to build a visual piece with drag ‘n’ drop functionality so the user could take part symbols, arrange the symbols in some way, and then get something useful out of it. I would like to mention something before I go on- drag ‘n’ drop in Java is PAINFUL if anything other than text is being dragged and dropped. As such, we spent a week and a half trying out different possible solutions, from the AWT drag ‘n’ drop facilities, to the fancy new JavaFX platform. We were very close to picking JavaFX, but it is stupidly difficult to integrate into a Swing application (this took up nearly a full week of failed attempts to make it work).  Finally, I wound up taking the NetBeans Visual Library and hacked it into a Swing app. Now, I say ‘hacked’ because the Visual Library is intended for use with NetBeans modules, and not vanilla Swing apps. As such, some things are broken (keyboard focus, anyone?), but so far no major problems have cropped up.

Anyhow, Joanna and I still have a sizable chunk of work to do on Spectacles before November, so we’ll be quite busy for the time being. And before I forget- there’s an Easter egg in any build of Spectacles with a version number ending in ‘KC’. But you didn’t hear it from me, m’kay? ;D

For many, this week marked the end of summer session classes, and perhaps the beginning of a week-and-a-half-long break before the fall semester begins. But for Berkeley’s iGEM computational team, it’s still full steam ahead.

I suppose I should introduce myself before going any further. My name is Joanna Chen, and I am on the Berkeley iGEM computational team. I will be a senior in Bioengineering once the semester starts. My subproject for iGEM is Spectacles, a visual design tool for synthetic biology parts. It’s been quite a full but overall enjoyable summer for me with iGEM, and I can’t believe it’s already halfway through August. The two-and-a-half months I’ve spent at iGEM have passed rather quickly. School is starting in 10 days!

That means 7 more weekdays for the team to finish up some key parts of the new and improved Clotho. Well, not really, since we do expect to still be doing things for iGEM after school starts. But, only 7 more weekdays during which we will all be in the office together, spending a good portion of our day coding for or discussing new parts of Clotho. Only 7 more days to get the various key parts of Clotho tied together before our schedules change and we might no longer see each other every day.

This week, we have also finally received access to our pictures from the iGEM photoshoot a few weeks ago.  Here are some pictures of the team:

2009 Computational team - (left to right) Richard, Bing, Lesia, Doug, Adam, Thien, Nina, Joanna

Adam and Lesia - the Eugene language subteam

Doug and Bing discussing databases

Nina and Thien thinking about automation

Richard and Joanna - the Spectacles subteam

Every year, the iGEM barbecue is great opportunity to mingle with folks from other schools. This year’s was close to home, a picnic area up in Tilden Park. We met the teams from Stanford, UCSF, and JBEI’s high school biotech group, for an afternoon of food and fun. During lunch, we casually inquired the other teams about their projects, trying not to seem like spies. Afterwords, there was a large soccer match. Berkeley wet lab and dry lab split up on opposite teams. When the wet lab scored, Patrick cheered, “We just instantiated a new scoring object!” Doug resigned to being player-coach goalkeeper after his back injuries resurfaced. Eventually, our lack of coordination became too much to stomach, and he went out and single-handedly scored for us. In addition to soccer, there were kites being flown, volleyball being played, and frisbees being thrown. The Stanford folks got restless, and started climbing trees. Overall, the barbecue was enjoyable, despite the overcast day. I still somehow managed to get sunburned.