Team:Wellesley Desyne/Eugenie

Eugenie

Design

The design process is divided into three main views: TreeView, FlowView, and EugeneView. A user starts by searching for parts from the Part Registry or their Clotho database and bringing them into their worskspace. In the TreeView, users can specify the order and structure of their design. The behavior of parts in the device is specified using the FlowView. Users specify structure and behavior using a visual language that we developed specifically for the application; the language utilizes SBOL symbols, an open-source standard for in silico representation of genetic designs. The EugeneView updates automatically throughout the design process, and users may click on individual parts in order to see the corresponding code highlighted in the EugeneView. Finally, users may view and export their results to a CSV or Pigeon files in the ResultsView.

Implementation

We implemented Eugenie using C#, XAML and the Surface SDK 2.0. We also used the MVC framework, Eugene for the creation of synthetic biology circuits, and Pigeon to display the circuits visually.

Goals

We had four goals in creating Eugenie:

• Implementing top-down design
  We utilized the functionality of Eugene, a programming language that is used to implement top-down design of novel genetic circuits—design that begins by specifying devices and then instantiating parts.
• Enhancing sensemaking
  We implemented sliding panel views, which allow users the option to view multiple sets of information simultaneously or one set at a time, helping users understand the connection between the different types of presentation.
• Supporting resource integration
  We give users the option to load parts from the parts registry, access parts in a Clotho database, or use a local database.
• Fostering collaboration
  We used the Microsoft PixelSense, which allows multiple people to use Eugenie simultaneously.

Results

We conducted user studies of Eugenie with members of the BU and MIT iGEM teams as well as with Wellesley College students; the majority of the 15 participants were biology or other science majors. Our study began with a brief introduction to the Eugene programming language, the visual language we had created, and the Eugenie user interface. Users were first tasked with interpreting genetic devices from our visual language and then translating SBOL representations of genetic devices into our visual language.

We next asked participants to use Eugenie to specify one of the genetic devices they had translated. Post task, participants rated the ease of understanding the visual language and of using the program. We also asked participants for their feedback on how the program could be improved.

The majority of users found it easier to create a device using Eugenie than to draw one by hand. Some participants also remarked that the multiple panels were helpful for understanding the device. Overall, users' response to Eugenie was positive, with many testers believing that Eugenie can become a great tool to help other young synthetic biologists with their research work.

Demo

Future Work

• Supplement part information with additional information from previous iGEM projects and other synthetic biology databases
• Allow users to access more parts from other synthetic biology databases
• Expedite the process for synthetic biologists to create genetic circuits
• Further incorporate the visual language we created into Eugenie's interface
• Develop a companion web application to enable widespread access to Eugenie