SBOLDesigner: A Hierarchical Genetic Design Editor


Synthetic biology, as a field of research, applies electrical engineering, systems biology, and bioinformatics to genetic circuit design. Software tools are leveraged to provide rapid iteration through the design space, and data standards are used to encode and characterize complicated genetic circuit designs. Specifically, genetic design automation workflows centered around standards, abstraction, and decoupling are utilized to help experimental biologists accomplish their goals. Unfortunately, the software tools that support this workflow are lacking in some critical features such as combinatorial design and support for an extended range of glyphs. These inadequacies hinder the adoption of data standards, and therefore hurt the reproducibility of experiments and results. Necessary details of experiments are not recorded, and the resulting conclusions are therefore not trusted. SBOLDesigner, a sequence-based computer aided design tool, addresses these issues. This thesis will focus on SBOLDesigner’s implementation of combinatorial design and the SBOL Visual 2 standard using the SBOL 2 data model. Using SBOLDesigner, experimental biologists are able to visualize their genetic circuits unambiguously and express the full state of their design robustly. This results in higher productivity when designing genetic circuits, more comprehensive circuit descriptions, and most importantly, enhanced reproducibility in the field of synthetic biology.

Michael Zhang
Michael Zhang
Google, Engineer