Bio-design and research

Problem

Synthetic biology will require a multidisciplinary, collaborative design environment in order to engineer the complex biological systems of the future. Our teams created a collection of software tools which address specific technical synthetic biology challenges while simultaneously advancing the way in which users interact with computing environments.

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State of the art for biologists is to open a ton of tabs and programs; copying, converting, and pasting heterogeneous data.

Method

To understand our users, we studied their existing workflow in situ, interviewed novices and experts, and tried to become our users via immersive activities and workshops. Once we had a better understanding of their process, we collaborated with our users during ideation and brainstorming sessions, identifying potential opportunities for improvement that could be addressed with technology. Following the collaborative brainstorm, we began the divergent design process, creating many prototypes that might address the problem and sending them to our users for feedback. We iterated on the prototypes with our users’ blessing and reaped what positives we could from those that did not. Increasing the fidelity and regularly requesting feedback from our users, we arrived at something we could evaluate in the wild.

Solutions

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Our 2011 software workflow comprises G-nome Surfer Pro (see video) for research, Trumpet and Optimus Primer for design, and Puppetshow and eLabNotebook for the construction of those designs. In addition, we also incorporate wetlab experimentation into our project to apply these tools to create novel biological systems to investigate tuberculosis.

The 2012 software suite includes the MoClo Planner for mediation of the Golden Gate Molecular Cloning process, SynBio Search for genetic research and planning, and SynFlo for the interactive exposure of basic synthetic biology concepts to students.

Our 2013 focused on supporting collaborative top-down bio-design with an integrated development environment and a visual programming language Eugenie. We also explored 3D visualization of combinatorial DNA libraries with zTree. With Bac to the Future we seek to communicate core ideas in synthetic biology to non-scientists in informal learning environments. The combination of human computer interaction, bio-design automation, and experimental design makes our effort unique in the iGEM experience and closes the loop on the design-build-test methodology.

Publications

O. Shaer, C. Valdes, S. Liu, K. Lu, K. Chang, W. Xu, T. L. Haddock, S. Bhatia, D. Densmore, R. Kincaid. Designing Reality-Based Interfaces for Experiential Bio-Design, Personal and Ubiquitous Computing, November 2013.

O. Shaer, C. Valdes, S. Liu, K. Lu, T. L. Haddock, S. Bhatia, D. Densmore, R. Kincaid. MoClo Planner: Interactive Visualization for Modular Cloning Bio-Design, IEEE BioVis 2013.

K. Chang, W. Xu, N. Francisco, C. Valdes, R. Kincaid, R. Shaer. SynFlo: An Interactive Installation Introducing Synthetic Biology Concepts. ITS’2012, November 2012

W. Xu, K. Chang, N. Francisco, C. Valdes, O. Shaer. From Wet Lab Bench to Tangible Virtual Experiment: SynFlo. TEI 2013, February 2013

S. Liu, K. lu, N. Seifeselassie, C. Grote, N. Francisco, V. Lin, L. Ding, C. Valdes, R. Kincaid, O. Shaer. MoClo Planner: Supporting Innovation in Bio-Design through Multi-touch Interaction. ITS’12, November 2012

W. Xu, K. Chang, N. Francisco, C. Valdes, R. Kincaid, O. Shaer, From Wet Lab Bench to Tangible Virtual Experiment: SynFlo, Extended abstract, ACM SIGCHI TEI 2013 Tangible, Embedded and Embodied Interaction.

S. Liu, K. Lu, N. Seifeselassie, C. Grote, N. Francisco, V. Lin, L. Ding, C. Valdes, R. Kincaid, O. Shaer, MoClo Planner: Supporting Innovation in Bio-Design through Multitouch Interaction, Demo abstract, ACM ITS 2012 Interactive Tabletops and Surfaces.

K. Chang, W. Xu, N.Francisco, C. Valdes, R. Kincaid, O.Shaer, SynFlo: An Interactive lnstallation Introducing Synthetic Biology Concepts, Demo abstract, ACM ITS 2012 Interactive Tabletops and Surfaces.