Visualizing genetic circuits is essential in the field of synthetic biology. These genetic designs often involve complex representation of modular and hierarchical biosystems. The representations are standardized through the Synthetic Biology Open Language (SBOL) in the form of glyphs. To make the visualization of biocircuits more efficient and amenable to automation, my goal is to upgrade DNAplotlib to support highly customizable visualizations of genetic circuits from SBOL version 2 files. I will achieve this by integrating DNAplotlib with the pySBOL2 library to support reading and writing of SBOL2 files. The current DNAplotlib only support SBOL 1.0 documentation, and thus is only capable of manifesting DNA components consisted of DNA sequence and sequence annotation. It cannot represent complex interactions between different subcomponents, and thus has poor connectivity with other genetic platforms. Through my work this summer, DNAplotlib will (1) incorporate non-DNA components / partially complete design sequences (2) document and link to external models such as SBML and CellML (3) visualize hierarchical and modular biosystems (4) save customization into SBOL file.

Student

Sunwoo Kang

Mentors

  • Bryan Bartley
  • Thomas Gorochowski
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2018