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

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I cannot believe that school starts on Wednesday… Summer break passed so fast and iGEM comp team will be kicked out from the office soon. Our classes will start, but we will continue working on our projects, alone… randomly meeting around the campus, and meeting weekly to see each other and to give updates…

Let me introduce myself. My name is Nina Revko. I am a senior in Bioengineering graduating in December. This is my last semester of college, which makes me sad and glad at the same time. I am a community college transfer student and two years at Berkeley passed so fast. I should admit that getting into iGEM this summer was one of my greatest experiences. It gave me clarity and understanding of what I thought Bioengineering had been like when I selected this field, it closed the gap by bridging chemistry and biology with engineering, it also showed me an ideal setting of perfectly selected working conditions when I was happy to come to work each day. And it is not over yet… I am happy!

Through the first part of summer I was working on the automation plugin for the assembly manager, then my project shifted to include workflows with Kepler, and for the last month, together with Thien, I have been collaborating with Joint BioEnergy Institute (JBEI). While other members of the team have been struggling with migrating and upgrading old Clotho to new Clotho, Thien and I have been working on coding and brainstorming of several new algorithms for oligodesign and assembly. In the coming months before Jamboree (if time permits) we also want to incorporate Clotho with Biostream-a protocol language, created by Microsoft in India.

So, the official iGEM time is over, but it does not mean that we will stop working on the projects…

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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

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Two months already passed, we are having the August code rush before school starts. We are making awesome process and stays on schedule, not only keeping our projects on track but also, as this is summer, having our daily lunch long chats and weekly movie nights. We also work with different groups thanks to the interdisciplinary of iGEM, from Berkeley Bioengineering and EECS professors to other research groups such as JBEI. Also with $tanFo®d.
Yesterday Doug tried to scare everyone at the meeting by drawing the timeline with a lot of red deadlines on the board. Indeed, we are finishing the new big-budget sequel to 2008 iGEM Best Software Tool Clotho, with new star duo Spectacles-Eugene and special appearance of Kepler. That means code to test, display case to make, speeches to practice, and obviously awards and glory to get.

In Cal team we trust.

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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.

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My name is Lesia Bilitchenko and I am one of the members of the 2009 Cal iGEM Computational Tools Team. It is my first summer research experience at Berkeley through the SUPERB program. Sadly next week the program is coming “officially”  to an end. Unbelievable how quick 8 weeks of hard work but also great fun can pass. I can definitely say my summer was not boring at all. From field trips to Stanford, Berkeley labs (the tour of the Advanced Light Source facility was very fascinating), the iGEM bowling experience to the research on developing a language for the Synthetic Biology community and not to forget our weekly group meetings, my summer was well divided.  Though this does not mean the end of the project which I am working on. There are so many capabilities that can be added to the language and after all November (the month of the iGEM jamboree!!) is still relatively far away.Â

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Instead of the normal grind and tedious pipetting that normally fills our days, the comp team and the wet team got together on Monday for a little bowling action. The outing was an unambiguous success!

Around noon we all met at the mining circle to discuss how we were going to fit 18 people into 3 cars… Somehow we all managed to end up at the Ranch 99 plaza at about the same time. There was a period of intense indecision about where we would eat, but finally Bing made an executive decision: Korean Food!

The poor waitress looked a little horrified when 18 hungry iGemmers walked through the doors. Someone mumbled “Table for 18 please,” and the waitress hurried away to play tetris with several tables in the corner. A short time later, we were all seated in relatively close proximity, laughing and discussing non-biological subjects.

I thought the food was outstanding. But then again, I’m not really picky and you would be hard pressed to find food I don’t like.

Bing led the caravan to Albany Bowl and we all stood in line to be outfitted in our super stylish bowling shoes. I had a particularly fly pair of neon kicks. The management dusted off the old disco vinyls and turned on the laser lights and smoke machines.

Patrick and I were desperately pursuing a turkey (three strikes in a row). After a single strike we would cry “33% turkey!! 33% turkey!!” Even though we got dangerously close to a whole turkey, with a whopping “66% turkey,” several times, neither of us were able to catch the elusive gobbler.

Reluctantly, we exchanged our chic footwear at the counter and began the journey back to campus to continue the grueling pipetting regiments.

Finally all of us would like to thank iGEM for sponsoring this social event. It was a blast and a welcome break from the lab =]

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