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Team:Wellesley Desyne/Eugenie
From 2013.igem.org
Wellesley HCI iGEM 2013
Eugenie
TOOL OVERVIEW
Eugenie is a multi touch application which allows synthetic biologists to utilize the programming language Eugene without having to write Eugene code and to create biological circuits. The application consists of three representations of the circuit: “TreeView,” “FlowView,” and “EugeneView.” The user can search through the Clotho and iGEM databases to find the biological parts desired and can drag them to the workspace, edit behavior and properties, and view live-updating Eugene code for the circuit. After the user is finished creating a circuit, they can then view the search results which display the permutations of the circuit. This process is meant to be iterative, so users can go back and add more properties and behavior specifications if they would like to reduce the number of results.
Design
The design process is divided into three main views. In the TreeView, users can specify the order and structure of their design. The behavior between parts in the device is specified in 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. |
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Implementation
We implemented Eugenie using C#, XAML and the Surface SDK 2.0. We also used the MVVM framework and Eugene for the creation of synthetic biology circuits.
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. - Enhancing sensemaking
We implemented sliding panel views, which allow users the option to view multiple sets of information simultaneously and the option to view an individual set of information by itself. - Supporting resource integration
We created a web crawler to load parts from the iGEM parts registry - Fostering collaboration
Results
We conducted user-testing with Eugenie with members of the BU and MIT iGem teams as well as Wellesley College students. In our study, students were given a brief explanation of synthetic biology, Eugene, the visual language we had created and the Eugenie user interface, and our project goals, and were then tasked with first interpreting genetic devices from our visual language and then translating genetic devices represented in SBOL visualization into our visual language. Then, participants were tasked with using our program to create one of the genetic devices they had translated. We asked participants to rate the ease of understanding the visual language and using the program. We also asked participants for their feedback on how the program could be improved. Overall response 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
