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

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 =]

Well who wouldn’t?!?

You may think that if you don’t have access to a University Laboratory and fancy, enigmatic equipment (not to mention expen$ive), then practicing synthetic biology is out of reach.

Well, I found a website dedicated to
“makeing biology a worthwhile pursuit for citizen scientists, amateur biologists, and DIY biological engineers who value openness and safety.” DIYbio.org is a really interesting site with blog entries and information on local events and conferences. While clicking around the site I found an interesting entry concerning amateur participation in the iGEM 2009 competition. It seems that amateur participation won’t be allowed this year due to safety and bureaucratic concerns…

So, I’d like to pose this question to the other iGEMers: What would you imagine a safety framework for amateur of DIYbio might look like? How would it be enforced?

Hello All,

My name is Nade Sritanyaratana and I’m one of the members of the 2008 Cal iGEM Computational Tools Team! Mouthful, I know. I’m a 3rd year undergraduate at Berkeley in Bioengineering, and (to those wondering about Cal life) it’s been an amazing three years. I’ve been holding back on posting on the blog, because during the time we gained access to the blog our team was mad crazy programming to prepare for our testing sessions (which have just passed).

A little bit about our project. For those techies that want to know about the infrastructure as well, you can go here: http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development

For everyone else, here’s the quick description :). Synthetic biology is getting large. Very large. There are now so many biological DNA parts in various databases that it’s getting very difficult to organize them all. And there are a growing number of computer programs out there that edit DNA sequences, provide different ways of looking at DNA (other than your standard ACTG), etc. Our project hopes to consolidate all these tools into one nice working environment, kind of the same way Adobe Photoshop brings together many tools for a consolidated imaging program.

What can you expect from my posts? Lots of pictures. And if coding doesn’t keep me busy (as it already does), then hopefully a balanced amount of writing. I won’t write as much as the two under me, and I’ve got to admit they’re more amazing with this blog than I. Keep tuned for my next post (which will probably come up in the next few minutes) for pictures of my team, and pictures of our first two testing sessions.

Signing out,

Nade Sritanyaratana