Team:BostonU/Collaborations

We are working closely with the Wellesley Desyne software team this year.

On June 3 and 4, we hosted the Wellesley team for a two day workshop. On June 3, the BU team reviewed some fundamental biology and synthetic biology concepts and held a Eugene tutorial. We went over some famous genetic circuits and wrote Eugene scripts for them. On June 4, both the Wellesley and BU teams presented their iGEM projects to each other and provided constructive feedback. The BU team also held a wet lab tour.

On June 14, we traveled to Wellesley's campus to continue discussing our projects. The BU team broke up into three small groups and met with each Wellesley project team who described their project and tested out some of their initial software. Later, we held an open discussion where each Wellesley project group discussed the feedback and suggestions they received from earlier in the day.

Throughout the summer, we have kept in contact with Wellesley to discuss Eugene and Eugenie. We provided feedback on their existing designs and explained how Eugene is intended to be used and how a visual representation would aid someone who does not understand the Eugene scripting code. We also provided sample Eugene code for some of our experiments so the Wellesley team could have Eugene code to test their prototypes with. Members of the Wellesley team came to some of our weekly Eugene meetings with the Eugene team. They also came to BU to present their paper prototypes of Eugenie and get feedback from the Eugene team and the BU iGEM team. Furthermore, the BU iGEM team took part in user studies for Eugenie.

We are also working closely with the Purdue Biomakers team this year to work on a standardized data sheet.

While working from the 2012 BostonU Team’s start on the Data Sheet app, we learned that the Purdue Biomaker’s team had a very similar concept in mind for creating a standardized way of sharing information about parts.

Early in June, we contacted the Purdue team to let them know that much of the groundwork has already been laid by the 2012 team here at BostonU. We shared our rough draft of the data sheet format with them and inquired if they had any plans to write software to implement the new data sheet. By July, the Purdue replied to us that the would like to use our data sheet draft as the basis for the project. Purdue’s team members had been collecting survey data from over 75 teams around the world to find out what information they thought was essential to a data sheet and showed them a version of our draft. Purdue also video chatted with several teams to demonstrate what the data sheet’s functionality and ask for more feedback. We also video chatted with Purdue to discuss more changes to the data sheet format and how we wanted to propose that we would build a web app to create the datasheets. Each team began to develop a simple mock up of what we envisioned for the user interface and shared them with each other.

In early August, Thomas flew out to Indiana to visit Charlotte Hoo and Chris Thompson from the Purdue team to show them our progress and plans on the web app. At the meeting, we compared programs at talked about what the final product might look like. Both teams mutually agreed that the BostonU team would handle all of the software side of things while Purdue, with their extensive network of team contacts, would continue to refine some of the specific assay data fields for the data sheet and work on distribution and promotion of the new standard. Furthermore, one of our other collaborators, Jake Beal of BBN Technologies heard about our collaboration through iGEM HQ and offered to give some advice on the information that would be needed in the flow cytometry section of the data sheet.

We are collecting large quantities of characterization data from our flow cytometry experiments. To analyze this data, we have been working with BBN Technologies and utilizing their BBN Synthetic Biology Tools. These tools came out of the TASBE project, which was a collaborative effort between BBN Technologies, the Densmore Lab at Boston Univeristy, and the Weiss Lab at MIT.

We have worked closely with Dr. Jacob Beal this summer to characterize constitutively expressed and repressible circuits. Specifically, Dr. Beal helped us design positive controls in order to successfully use the TASBE tools for quantitative fluorescence analysis (see Data Collected).

References

[1] Beal et al. (2012) "An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications." ACS Synthetic Biology, 2012, 1 (8), pp 317–331. DOI: 10.1021/sb300030d