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.

After Clotho’s Alpha release things have been quite slow here. Matt went off to Bakersfield to resolve his ACL injury and Anne had to leave back to Washington since her engineering program had finished. I went off to Cabo with my family and then started prepping kind of all out for my GRE’s.

August flew by and not too much was completed. I hope Doug’s not too angry with me for the unproductiveness! In either case, speed’s definitely picking up now. Matt and I are now in charge of new parts to Clotho. Matt is in charge of two new main parts: drag and drop handling, and custom code plug-in capabilities. My part’s all slightly technical (it’s called the PoBoL Parts Manager) and we haven’t yet provided any documentation to show the techies, but we’ll definitely provide snapshots soon!

All the power to Wet Lab for going at their project in such tenacious efforts! And to Marlee for her HR work.

Hey all,

Testing sessions were a mix between fun and some kind of crazy. I stayed up til about 5AM to prepare for the 1st testing session! Though I must admit, I’m normally up til about 3AM. Anyway, enjoy the visuals. I’ll be introducing my teammates along the way, and of course the software testers!

Left: Anne Van Devender, teammate. Right: Doug Densmore, advisor. We’re waiting for the testers, and it looks like we’re pretty excited to begin.

Left: Matthew L.E. Johnson, teammate. Middle: Anne. Right: Doug. I believe Matt’s starting up Clotho, and we’re all watching quietly.

Left: Matt. Right: Dirk VandePol, wetlab teammate. Dirk was the third tester of Clotho, and is a high school teacher, to my knowledge. Matt’s currently assisting him with the Clotho SequenceView.

Left: Doug, Right: Cici. Cici is one of the wetlab members as well. She’s a high school student, one of the only two on the wet team.

A bunch of people. Right now we’re gathering everyone’s final remarks from the very first testing session. Dr. Chris Anderson (leftmost) is explaining what he sees as the greatest asset behind Clotho, which is its eventual connectivity and seamlessness between different pre-existing tools.

The one and only picture I have so far posted of our second testing session. I was mostly busy this testing session, so I had less pictures to choose from. You can see we moved up to a conference room, as opposed to our student offices :).