Berkeley Engineering Blogs

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

Thursday night found us sitting around in the Oakland Airport, playing sudoku and utilizing precious free wifi before setting off for a night flight to Boston.  We have spent the week finalizing our presentation and our poster, so everyone is a bit exhausted at the beginning of the journey.

Action shot of Bing in the airport.  Bam!

Dramatic cell phone shot.

No action or drama here.  Just sudoku.  The adventure begins!

Our presentations (those of the Wet Lab and the Computational Team) are both on Saturday, and we have all of Friday to practice the presentations over and over, to make sure that they are informative, but captivating, and most of all that we keep them within the 20 minute time limit…  There will be a question and answer session after the presentation, and this is a new concept to many of us, so Terry and Chris will be coaching us on how to reach into the resources of the work we have been doing to answer questions effectively and interestingly. 

We came into the predawn world of drizzly Boston at 5:30 am, surprisingly not too grumpy and even a bit cheery. We were, however, in great need of some shut-eye to get rid of that red-eye to face the rest of the day full of practice presentations.    

You can feel how extreme the predawn Boston was with the blurriness of this picture.

Jamboree, here we come!  

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 :).

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