Fluigi: Synthetic Biology Based Microfluidic Control Synthesis

Douglas Densmore

Junior Faculty Fellow, Hariri Institute for Computing
Assistant Professor, Department of Electrical and Computer Engineering
Boston University

Abstract: One goal of synthetic biology is to design and build genetic circuits in living cells for a range of applications. Metabolic and cross-talk make it difficult to construct multiple layered logic circuits in a single cell, limiting the calability of engineered biological systems. Microfluidic technologies provide a reliable and scalable construction of synthetic biological systems by allowing compartmentalization of cells encoding simple genetic circuits and  the spatiotemporal control of communication among these cells. This control is achieved via valves on the chip which restrict fluid flow when activated. We describe a Computer Aided Design (CAD) framework called “Fluigi”  for optimizing the layout of genetic circuits on a microfluidic chip, generating the control sequence of the associated signaling fluid valves, and simulating the behavior of the configured biological circuits. We demonstrate the  capabilities of Fluigi on a set of Boolean algebraic benchmark circuits found in both synthetic biology and electrical engineering. The integration of microfluidics and synthetic biology has the capability to produce rapid prototyping platforms.

Bio: Douglas Densmore is a Kern Faculty Fellow and Assistant 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 Center of Synthetic Biology (CoSBI).

His research interests include Computer Architecture, Embedded Systems, Logic Synthesis, Digital Logic Design, System Level Design, and Synthetic Biology.