The Densmore Manifesto v2.0

After more than a year and a half, 30+ applications, 10 interviews, countless “elevator talks”,  and thousands of miles of travel, I finally accepted an assistant professor, tenure track position in the Department of Electrical and Computer Engineering at Boston University. This was not an easy process or decision. The keys were my close collaborators at MIT and Harvard, Boston’s synthetic biology community, the plethora of opportunities for my wife, and an increased proximity to our families. While I am not looking forward to the Winters (I lost my Michigan layer of blubber), at least Santa will have a nice snowy landing for his sleigh. Thanks to everyone that helped me during this process and thanks to all the schools that took time out to interview me.

After a very successful IWBDA 2009, myself and a revamped executive committee are again organizing this workshop this year. It will be held in Anaheim California and will be a two day affair (June 14th-15th) at the Design Automation Conference (DAC). This year we have expanded the program while providing more networking and social activities. In addition, we have expanded the publication opportunities by partnering with PLoS One. For more information see: www.biodesignautomation.org

At iGEM 2009 we (Berkeley Software) won “Best Software Tool” again for the second year in a row! This is for our work on a new Clotho infrastructure, Eugene programming language, Spectacles visual editor, and Kepler workflow extensions. This year we shared the award with Illinois Tools as well.  Naturally we won a gold medal as well but more interesting to me was that out of more than 110 teams, only 3 US teams won major awards (us, Illinois, and Stanford). My team and I had a blast and I am looking forward to next year’s jamboree (perhaps in a more relaxing role next year). For the the complete results, check out this link.

At the beginning of September I started a new post doctoral appointment. I am now in the Bioengineering Department (no longer EECS) at UC Berkeley and am affiliated with the Synthetic Biology Engineering Research Center (SynBERC) and the Joint BioEnergy Institute (JBEI). My focus is to continue to develop Clotho with Prof. J.Christopher Anderson. In particular I will make the parts management and automated assembly pieces I have begun more robust, along with making sure Clotho works with JBEI’s registry of biological parts and data. I am also exploring the alternate assembly methods that are used at JBEI. This position is an excellent opportunity for me to continue working on biodesign automation while expanding my biological network. It also allows me to pursue faculty positions. Both JBEI and SynBERC have been very supportive of my work and I thank them for this opportunity.

Well, after much resistance (actually none I just caved in), I have gotten back into radio controlled cars again with a vengeance.  The latest craze in the hobby seems to be “short course” trucks and rock climbers. Therefore, I bought two Associated SC10s and a Losi 1/10 Comp Crawler. Both SC10s were in the kit form (building them is half the fun). One is “mine” and one is Erika’s. The idea would be to slowly re-introduce myself to the local racing scene with the SC10 and just use the Losi for fun/picnics/bashing, etc.  We’ll seen how that goes. Anyway here are the specs (I probably spent way too much money on this):

Mine (red, yellow, and blue SC10):

• Tekin RS electronic speed control
• Tekin Redline 13.5 turn brushless motor
• HiTec HS-5625MG Servo
• Ko Propo KR-407S Receiver
• Ko Propo EX5-UR transmitter
• Team Associated CVDs
• Team Associated ball bearing steering upgrade
• Team Associated titanium turnbuckles

Erika’s (metallic blue):

• LRP A.I. Brushless Reverse Digital speed controller
• LRP Eraser 15.5 turn motor
• HiTec HS-635HB servo
• Tactic TR-324 receiver
  
• Tactic TTX240 transmitter

Losi 1/10 Comp Crawler

• Novak GOAT 3s speed control
• Novak 21.5 turn brushless crawler motor
• Hobbico CS-170 servo
• Ko Propo KR-407S Receiver
• Losi MSX12 digial mini servo (for the dig unit)

This year myself and Marc Riedel, Soha Hassoun, and Ion Mandoiu are organizing the 1st International Workshop on Bio-Design Automation (IWBDA). This will be a workshop co-located with the Design Automation Conference (DAC) in San Francisco on July 27th. For more information, see www.biodesignautomation.org. In addition there is a write up by Melanie Swan here.

At the 2008 iGEM jamboree, UC Berkeley’s Tools team (which I led) won the award “Best Software Tool” for Clotho. In addition to winning this honor, we also won a gold medal overall (only 16 of the 84 teams received this distinction). There were a lot of great tools there and I am excited about the possibility of collaborating with many of these teams in the future. UC Berkeley’s wet team, Clonebots, also did great winning both a gold medal and being one of 6 finalists for the grand prize.

On June 20th, 2008 Erika and I got married. It was a super hot day but the ceremony was great and we had a blast. My brother Luke was my best man and Erika’s sister Monica was her maid of honor. My nephew Zach was the ring bearer and my cousin’s daughter, Sierra, was the flower girl. My sister read a poem she wrote and the officiant was my friend Steve’s dad. It was a lot fun seeing all my friends and family in one place and all dressed up. The whole thing was a blur but we made some great memories (and took some great photos).