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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 XX 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. She is also an officer in the 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 Electrical Engineering and Computer Science major at UC Berkeley. His previous experience includes interships with software companies in Shanghai and Shenzhen, China. After graduating, he hopes to pursue a career in software development or systems administration. Adam worked on Eugene during the summer. Non-academic interests include ping-pong, volleyball, video games, movies, drawing, and traveling. |
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, and gaming. |
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 the 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. Chris Anderson's lab. Besides that Nina is collaborating with JBEI 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. His research interests mainly lie in computational biology, and he hopes to pursue graduate studies in this field after he graduates. Bing worked on the data model portion of Clotho this summer. Some of his non-academic interests include running, taekwondo, 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
Thanks to Evan Yang and Armen Khodaverdian for their help this summer both related to coding and infrastructure support. Also we would like to thank Josh Kittleson, Tim Hsiau, and Sherine Cheung for feedback on Clotho and help testing the software. [http://slifertheskydragon.deviantart.com Christine Tsin] is responsible for much of the beautiful artwork on these pages. The Stanford iGEM team also provided great feedback on Spectacles. Cesar Rodriquez at Stanford was very helpful in initial discussions regarding Eugene along with Emma Weeding from the University of Minnesota. We also want to thank Kate Spohr for all her support regarding logistic and financial issues.
