Team:BU Wellesley Software/Acknowledgement

Acknowledgements

We would like to thank all of the following people and organizations for their comments, feedback, contribution, and support for our team:

BU

Daniel Dwyer, Jim Collins, and the Collins Lab

Andrew Krueger, James Galagan, and the Galagan Lab

Gretchen Fougere, Assistant Dean of Outreach and Diversity

BBN Technologies

Aaron Aadler

JBEI

Josh Gilmore

JHU

Jef Boeke

Noah Young

MIT

Jonathan Babb and the Weiss Lab

Tiffany Huang, Louis Lamia and the MIT iGEM Team

Joy, Leanna, Paul, Shawn, and Shirley of the MIT iGEM team of 2010

Somerville High School

Chris Angelli

UC Berkeley

J. Christopher Anderson

Wellesley College

Catherine Summa
Wellesley College Science Center Summer Research

Yui Suzuki and the Suzuki Lab

Wyss Institute

Avi Robinson-Mosher

Attributions and Contributions

Computational team

We developed five software applications and deployed most of them in the wet lab. While this was a team effort, we point out key contributors to each of the five applications below:

G-nome Surfer Pro and E-Lab Notebook

Both of these applications were conceived, designed, and implemented by the Human Computer Interaction Laboratory (HCI) at Wellesley College. Michael Lintz, Heidi Wang, Taili Feng, Casey Grote, and Megan Strait contributed to the design and implementation of the G-nome Surfer Pro application, whereas Kathy Liu, Michelle Ferreirae, Consuelo Valdes, and Kelsey Tempel contributed to the design of the E-Lab Notebook application.

Optimus Primer

This application was conceived by Traci Haddock (instructor) and designed and implemented by Jenhan Tao. In parallel, a Microsoft Surface version was also developed by Kelsey Tempel, Casey Grote, and Consuelo Valdes of Wellesley College's HCI Lab.

Trumpet

This application was conceived by Swapnil Bhatia (instructor) and designed and implemented by Craig LaBoda. The application implements two design algorithms, one of which was derived by Craig LaBoda and the other by Swapnil Bhatia. In parallel, a Microsoft Surface version was also designed by Michael Lintz, Michelle Ferreirae, and Alex Pan of Wellesley College's HCI Lab.

PuppetShow, and the Puppeteer Protocol Automation Stack

The Puppeteer Protocol Automation stack was conceived and designed by Swapnil Bhatia and graduate student Viktor Vasilev. The PuppetShow application was designed and implemented by Janoo Fernandes. Resource Management in the Puppeteer stack was implemented by Chenkai Liu. Python glue code was provided by Viktor Vasilev, and a Hardware Abstraction Layer implementation was provided by Viktor Vasilev and Aaron Adler (BBN Technologies).

The Clotho Fabdash skin

The new Fabdash skin for Clotho was originally conceived by Professor Anderson of UC Berkeley. The interface was developed and refined by Jenhan Tao. The current interface is a distinct departure from the original Clotho interface, and offers a more streamlined experience.

The iGEM Team Wiki

The iGEM Team Wiki was designed and implemented by Taili Feng, Consuelo Valdes, and Heidi Wang. The content was provided by the entire team.

Wet lab team

The wet lab team helped the computational team design, implement, deploy, and test their applications.

PuppetShow, and the Puppeteer Protocol Automation Stack

The Puppeteer Protocol Automation Stack was tested in the wet lab on the Tecan Evo 150 robot with the help of Evelyn Orozco, who helped construct several genetic circuits and executed manual controls for each robotic assembly.

Clotho

All DNA samples used over the course of the summer were put into Clotho through the Batterboard Clotho application and through the Spreadit series of Clotho applications, by Vanessa Yanez and Margaux Canevari. Vanessa used Batterboard to input all of the physical DNA samples from the wet lab while Margaux used Spreadit Parts, Spreadit Features, and Spreadit Vectors to input the BioBrick names and DNA sequences attached to those samples. Kyle Jones and Alberto Purwada also met with Rishi Ganguly (graduate student), to give feedback to improve the user interface for Batterboard.

Outreach

The Genekai plan was conceived by the entire team during a group discussion and implemented by Chenkai Liu and Shannon Harrington.

The Wellesley HCI Lab mentored 2 rising seniors in High School and presented in the Wellesley College Science Center Summer Poster Session.

Lab organization

Kyle Jones and Alberto Purwada were the major contributors to the physical organization of various types of samples in the lab including plasmid DNA, gel extractions, ligations, and frozen glycerol stocks. Kyle also designed a spreadsheet for keeping track of samples, which was updated weekly by a different wet lab team member each week during the summer.

Optimus Primer

To study various TB transcription factors and their promoters, primers were designed to generate BioBricks of those parts by Kyle Jones, with Suma Jaini overseeing this process.

E-Lab Notebook

All six wet lab team members participated in multiple discussions on the desired tools and layout designs of the e-notebook as implemented by the HCI lab.

Part construction

The wet lab built new parts comprising various fluorescent proteins and promoters to generate a library of reporter circuits. Each member of the wet lab team contributed to this work under the guidance of Traci Haddock (instructor).

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