UVA Computer Science Distinguished Speaker Series*
Doug Densmore, Electrical and Computer Engineering, Boston University
Date: Friday, October 14th, 2016
Time: 2:20 PM
Place: Thornton Hall E316
Host: Samira Khan
Circuits in Cells, Bits in Bugs How (Synthetic) Biology is a Computing Platform
Successful computing systems leverage their underlying technologies to solve problems humans simply cannot. Electronic systems harness the power of electrons and semiconductors. Mechanical systems use physical force and physical interactions. Biological systems represent a computing paradigm that can harness evolution/adaptation, redundancy/replication, chemistry/natural processing, and living material/organisms. Engineered, living biological systems which make decisions, process “data,” record events, adapt to specific inputs/outputs, and communicate to one another will deliver exciting new solutions in bio-therapeutics, bio-materials, bio-energy, and bio-remediation. This is engineering of biological systems has been dubbed “Synthetic Biology.” In this talk, I will outline my vision for “Bio-Design Automation” for synthetic biology. Specifically I will highlight my research’s efforts in the specification, design, assembly, verification, and data management involved in automating synthetic biology. These challenges are addressed by a suite of software tools which draw inspiration from Electronic Design Automation. I will discuss how to leverage traditional logic synthesis techniques to create genetic circuits for synthetic biology using a tool called “Cello.” I will also outline hybrid microfluidic bio-computation captured in a workflow called “Fluigi.”I will close by discussing community and commercial involvement mechanisms via the Bio-Design Automation Consortium, the Nona Research Foundation, and Lattice Automation, Inc.
Douglas Densmore is a Kern Faculty Fellow, a Hariri Institute for Computing and Computational Science and Engineering Faculty Fellow, and Associate Professor in the Department of Electrical and Computer Engineering at Boston University. His research focuses on the development of tools for the specification, design, and assembly of synthetic biological systems, drawing upon his experience with embedded system level design and electronic design automation (EDA). Extracting concepts and methodologies from these fields, he aims to raise the level of abstraction in synthetic biology by employing standardized biological part-based designs which leverage domain-specific languages, constraint-based device composition, visual editing environments, and automated assembly.
He is the director of the Cross-disciplinary Integration of Design Automation Research (CIDAR) group at Boston University, where his team of staff and postdoctoral researchers, undergraduate interns, and graduate students develop computational and experimental tools for synthetic biology. His research facilities include both a computational workspace in the Department of Electrical and Computer Engineering as well as experimental laboratory space in the Boston University Biological Design Center (BDC). Currently he is also the lead PI for the NSF Expeditions in Computing’s “Living Computing Project.”
*This seminar is jointly sponsored by the departments of Computer Science, Biomedical Engineering, and Electrical and Computing Engineering