From 2009.igem.org

Latest revision as of 23:24, 1 July 2011

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The Team

Left to right: Richard, Bing, Lesia, Adam, Thien, Nina, Joanna; Seated: Douglas

The 2009 [http://www.berkeley.edu 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 [http://bioeng.berkeley.edu bioengineering] as well as [http://www.eecs.berkeley.edu electrical engineering and computer science] students. The participants were selected from over 100 applicants which applied in the Spring of 2009 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], [http://qb3.org qb3], the [http://www.cdc-computing.org Coalition to Diversify Computing], 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 Bilitchenko Lesia is a 4th year [http://www.csupomona.edu/~cs Computer Science] major at [http://www.csupomona.edu Cal Poly Pomona]. She joined the iGEM 2009 team through the [http://www.eecs.berkeley.edu/Programs/ugrad/superb/superb.html SUPERB program] and absolutely enjoyed the experience. Her previous research was in [http://en.wikipedia.org/wiki/Computer_vision computer vision] and place recognition. She intends to pursue graduate studies in [http://en.wikipedia.org/wiki/Parallel_computing 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 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 also did most of the layout for the team's wiki. In other extracurricular activities, Joanna is an officer of 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 when she has free time. Joanna was born and raised in [http://en.wikipedia.org/wiki/San_Jose,_California San Jose, CA].
Adam Liu 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 [http://en.wikipedia.org/wiki/Shanghai Shanghai] and [http://en.wikipedia.org/wiki/Shenzhen 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 [http://en.wikipedia.org/wiki/Queens Queens, New York], grew up in [http://en.wikipedia.org/wiki/Livingston,_New_Jersey Livingston, New Jersey], and then moved to [http://en.wikipedia.org/wiki/Pleasanton,_California Pleasanton, California], where his family now lives.	Richard Mar Richard Mar Richard is a 4th year Computer Science major at UC Berkeley, and is an officer of the [http://upe.cs.berkeley.edu Nu Chapter of Upsilon Pi Epsilon], the Computer Science Honor Society. 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 [http://www.lm-software.com/mlcad/ LEGO bricks], biking around on local trails, and gaming on the PC.
Thien Nguyen Thien Nguyen Thien is a 4th year Computer Science major at UC Berkeley. He is learning about synthetic biology from this year's iGEM experience and is excited about this emerging field. With his iGEM project, he enjoyed seeing how his computer knowledge can be useful when applied to a more real topic in the life sciences, as his past research has only been CS related (e.g. [http://en.wikipedia.org/wiki/Pattern_recognition pattern recognition] and chat analysis). He wants to pursue graduate research in computer science and life sciences IT, although he is not sure about the exact topic yet. This summer he worked on Kepler workflows integration, was responsible for Kepler back end and the Clotho [http://en.wikipedia.org/wiki/Java_remote_method_invocation RMI] tool. Thien believes in the effectiveness of peer tutoring, and has been a computer & math tutor while at Berkeley, in junior college and during high school. Apart from academic work, he enjoys collecting movies and games, computer stuffs, hiking, music from different cultures, and having fine but affordable [http://damnfinetea.com tea].	Nina Revko 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 the 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 her work this summer, Nina is collaborating with the [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 Xia Bing is a 4th year [http://math.berkeley.edu/ Applied Math], [http://mcb.berkeley.edu/ 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 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.

• [http://openwetware.org/wiki/User:Jennifer_Bophy Jenn Brophy] - UC Berkeley 2009 "wet team"
• Sherine Cheung - UC Berkeley 2009 "wet team"
• [http://www.epernicus.com/th2 Tim Hsiau] - UC Berkeley graduate student
• [http://openwetware.org/wiki/User:Josh_Kittleson 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.
• [http://openwetware.org/wiki/User:Marlee_Tichenor 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.
• [http://openwetware.org/wiki/User:Cesar_A._Rodriguez Cesar Rodriquez] at Stanford was very helpful in initial discussions regarding Eugene.
• [http://openwetware.org/wiki/User:Emma_M._B._Weeding Emma Weeding] from the University of Minnesota helped us work to integrate Eugene with [http://synbioss.sourceforge.net 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.

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