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Team:Berkeley Software/Team
From 2009.igem.org
The Team
The 2009 University of California Berkeley Software team was composed of seven undergraduate students, one postdoctoral instructor ([http://ddensmore.net Douglas Densmore]) and one faculty advisor ([http://bioeng.berkeley.edu/cv/canderson.php J.Christopher Anderson]). The team was made up of both bioengineering as well as electrical engineering and computer science students. The students were selected from over 100 students which applied in the Spring to be members of the team. Students were selected based on GPA, related research experience, performance on a series of tutorials, letters of recommendation, and short interview sessions.
The team was broken into four projects: Bing Xia focused on revamping the general software infrastructure. Joanna Chen and Richard Mar developed Spectacles. Thien Nguyen and Nina Revko examined assembly protocols and workflow design. Finally, Lesia Bilitchenko and Adam Liu created Eugene.
The team was funded by the [http://www.nsf.gov National Science Foundation], the [http://www.synberc.org Synthetic Biology Engineering Research Center], and the [http://chess.eecs.berkeley.edu Center for Hybrid Embedded Systems Software]. We want to thank all our sponsors and are excited to present our work at the jamboree!
Lesia Bilitchenko Lesia is a 4th year Computer Science major at Cal Poly Pomona. She joined the iGEM 2009 team through the SUPERB program and absolutely enjoyed the experience. Her previous research was in computer vision and place recognition. She intends to pursue graduate studies in parallel computing. Lesia worked on Eugene during the summer. Her non-academic interests include running, reading, watching movies and learning new (both programming and spoken) languages. |
Joanna Chen Joanna is a 4th year Bioengineering major with a concentration in computational bioengineering at UC Berkeley. Last summer, she did research in a lab working on ab initio protein structure prediction. For iGEM this summer, Joanna worked on the Spectacles visualization tool, more specifically, the import/export Eugene functionalities and the ability to get database information to Spectacles through the Clotho Data API. She is also an officer in the [http://tbp.berkeley.edu CA-Alpha chapter of Tau Beta Pi], the Engineering Honor Society. Outside of academics, she enjoys playing the piano, working on crafts projects with beads, and making unit origami. |
Adam Liu Adam is a 4th year [http://www.eecs.berkeley.edu/ Electrical Engineering and Computer Science] major at [http://www.berkeley.edu/ UC Berkeley]. His previous experience includes internships with software companies in Shanghai and Shenzhen, China. After graduating, he hopes to pursue a career in software development or systems administration. For the [http://sourceforge.net/projects/eugene/ Eugene project] this summer, Adam worked on syntax development, XML support, integration with Spectacles, and incremental design functionality. Non-academic interests include ping-pong, volleyball, video games, movies, [http://kippythekakaru.deviantart.com/art/Passionflower-Kenshin-21114770 drawing], [http://www.animemusicvideos.org/members/members_videoinfo.php?v=89505 video editing], and traveling. He was born in Queens, New York, grew up in Livingston, New Jersey, and then moved to Pleasanton, California, where his family now lives. |
Richard Mar Richard is a 4th year Computer Science major at UC Berkeley. He is planning on pursuing a masters degree in computer science. Richard worked on Spectacles this summer, and was responsible for the back end management of the parts workspace. Outside of school, Richard is a member of [http://fsae.berkeley.edu/ UC Berkeley Formula SAE], "the fastest vehicle team on campus." Richard also enjoys fooling around with LEGO bricks, biking around on local trails, and gaming on the PC. School takes a lot of time out of Richard's gaming schedule, so he goes [http://www.digyourowngrave.com to this site] to fill [http://www.littlegrey.net/user_profile/66/ his] gaming needs. |
Thien Nguyen Thien is a 4th year Computer Science "single" major at UC Berkeley. He learns about synthetic biology from this year iGEM experience and love it. He want to pursue graduate research in computer science and life sciences IT. His past computer research was pattern recognition in data processing. This summer he works on Kepler workflows integration. Apart from academic works, he enjoys collecting movies and games, hiking and having fine tea. |
Nina Revko Nina Revko is a 4th year undergraduate majoring in Bioengineering at [http://www.berkeley.edu University of California, Berkeley]. After graduation she is planning to go into industry with a possibility of returning to graduate school for her advanced degree several years later. Nina is interested in creation of affordable and useful solutions for currently existing problems. This summer she worked on the integration of a scientific workflow design environment, called Kepler, with the Clotho environment and also on tying Clotho design activities together with liquid handling robots in Prof. [http://bioeng.berkeley.edu/cv/canderson.php Chris Anderson]'s lab. Besides that Nina is collaborating with [http://www.jbei.org/ Joint BioEnergy Institute] on creation of alternative assembly methods. Her non-academic interests include traveling, watching movies, drinking tea, doing yoga and hiking. |
Bing Xia Bing is a 4th year Applied Math, Molecular Biology, and Computer Science triple major at UC Berkeley. He was on the 2008 Berkeley Wet Lab iGEM team and he thoroughly enjoyed the experience. His research interests mainly lie in the area of computational biology, although he isn't sure what subarea he's most interested in. He hopes to pursue graduate studies in this field after he graduates next spring. Bing worked on the data model portion of Clotho this summer, as well as revamping the core Clotho infrastructure. Some of his non-academic interests include running, taekwondo, classical piano, and origami. |
Douglas Densmore Doug is a post doc currently with the [http://www.synberc.org Synthetic Biology Engineering Research Center] (SynBERC). He works with researchers at UC Berkeley, Stanford, the University of Washington, and the [http://www.jbei.org Joint BioEnergy Institute] to develop new tools for [http://cctbio.ece.umn.edu/iwbda/index.html bio-design automation]. He received his Bachelors of Science in Engineering ([http://eecs.umich.edu Computer Engineering]) from the [http://www.umich.edu/ University of Michigan] in 2001. He received his Masters of Science and PhD in [http://www.eecs.berkeley.edu Electrical Engineering] 2004 and 2007 from the [http://www.berkeley.edu University of California at Berkeley]. This summer as the team instructor his duties involved the design of the project, its management, and the design of the core architectural changes to the software infrastructure. These responsibilities built on the experiences he had as team leader for UC Berkeley's 2008 iGEM team. In his spare time he enjoys camping, video games, [http://www.rc411.com radio controlled cars], classic hip hop music, basketball, and movies. |
Other Attribution and Thanks
We would like the thank the following people for their help coding, feedback on Clotho, help testing the software, and infrastructure support. All of these folks were physically present at UC Berkeley this summer and we expect to continue collaborating with them in the future.
- Jenn Brophy - UC Berkeley 2009 "wet team"
- Sherine Cheung - UC Berkeley 2009 "wet team"
- Tim Hsiau - UC Berkeley graduate student
- Josh Kittleson - UC Berkeley graduate student
- Armen Khodaverdian - UC Berkeley undergraduate student
- Nade Sritanyaratana - University of Wisconsin graduate student (former iGEM 2008 UC Berkeley tools team member)
- Evan Yang - UC Berkeley undergraduate student
Also we would like to thank a couple folks which helped with the design of this website and the artistic supporting material developed around our project.
- [http://slifertheskydragon.deviantart.com Christine Tsin] - created much of the beautiful artwork on these pages.
- Marlee Tichenor - helped assemble the videos on this site.
We collaborated with a number of individuals without whom our project would not be nearly as rich:
- The Stanford iGEM team also provided great feedback on Spectacles.
- Cesar Rodriquez at Stanford was very helpful in initial discussions regarding Eugene.
- Emma Weeding from the University of Minnesota helped us work to integrate Eugene with SynBioSS.
We also want to thank Kate Spohr for all her support regarding logistic and financial issues and naturally J.Christopher Anderson for his mentorship and constant support.
