Platform-Based Design: From Cruise Control to Cancer Killer
February 24,2010
University of Notre Dame
Department of Computer Science & Engineering
SEMINAR
Dr. Douglas Densmore
Synthetic Biology Engineering Research Center Postdoctoral Fellow
"Platform-Based Design: From Cruise Control to Cancer Killer"
Abstract:
Platform-Based Design (PBD) is a design methodology within Computer Aided Design which at its core promotes the separation of functionality from implementation. Rigorous and formal applications of PBD have been shown to be very useful in the design of embedded electronic systems. This philosophy has manifested itself in the development of the Polis, Metropolis, and Metro II design environments at UC Berkeley. The emerging field of synthetic biology has the ability to leverage many of the concepts in PBD while at the same time presenting a unique set of challenges and obstacles. If applied correctly, PBD has the potential to intelligently increase the design space of synthetic biological systems and create an entire "Bio-Design Automation" field which will help to create more robust, re-usable, and reliable designs.
This talk will discuss the evolution of PBD from embedded electronics to synthetic biology. Specifically the creation of biological devices from standard, modular parts will be outlined along with the challenges of applying traditional design automation techniques.
Abstract functional biological specification, design constraint enforcement, data exchange and retrieval, and automated assembly together form the core of a bio-design automation framework. These concepts will be illustrated via several design examples using the Clotho design platform and the Eugene domain specific language. These tools lay the foundation for a fully automatic path from synthetic biological device specification to physical assembly which in many ways parallels the ASIC design flow developed by the electronics community and opens a tremendous interdisciplinary opportunity for biological and computer engineers.
Bio:
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in 2001. He received his Masters of Science and his PhD both in Electrical Engineering in 2004 and 2007 from UC Berkeley. He was a UC Chancellor's postdoctoral fellow at UC Berkeley with Prof. Alberto Sangiovanni-Vincentelli from 2007 to 2009 and now is a postdoctoral research fellow in the Synthetic Biology Engineering Research Center.
His current research centers on extracting design techniques from electronic design automation (EDA) and applying them to the design of synthetic biological systems. Specifically he examines how 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. These research agendas find a home in the "Clotho" unified toolset. Clotho is a two time winner of the "best software tool" at MIT's International Genetically Engineered Machine Competition and the first tool of its kind to employ EDA approaches to synthetic biology. He is also the co-founder of the International Workshop on Bio-Design Automation (IWBDA) which is co-located at the Design Automation Conference. His other research interests include system level design, computer architecture, embedded systems, and logic synthesis.
Thursday, February 25, 2010
3:30 p.m.
356 Fitzpatrick
Department of Computer Science & Engineering
SEMINAR
Dr. Douglas Densmore
Synthetic Biology Engineering Research Center Postdoctoral Fellow
"Platform-Based Design: From Cruise Control to Cancer Killer"
Abstract:
Platform-Based Design (PBD) is a design methodology within Computer Aided Design which at its core promotes the separation of functionality from implementation. Rigorous and formal applications of PBD have been shown to be very useful in the design of embedded electronic systems. This philosophy has manifested itself in the development of the Polis, Metropolis, and Metro II design environments at UC Berkeley. The emerging field of synthetic biology has the ability to leverage many of the concepts in PBD while at the same time presenting a unique set of challenges and obstacles. If applied correctly, PBD has the potential to intelligently increase the design space of synthetic biological systems and create an entire "Bio-Design Automation" field which will help to create more robust, re-usable, and reliable designs.
This talk will discuss the evolution of PBD from embedded electronics to synthetic biology. Specifically the creation of biological devices from standard, modular parts will be outlined along with the challenges of applying traditional design automation techniques.
Abstract functional biological specification, design constraint enforcement, data exchange and retrieval, and automated assembly together form the core of a bio-design automation framework. These concepts will be illustrated via several design examples using the Clotho design platform and the Eugene domain specific language. These tools lay the foundation for a fully automatic path from synthetic biological device specification to physical assembly which in many ways parallels the ASIC design flow developed by the electronics community and opens a tremendous interdisciplinary opportunity for biological and computer engineers.
Bio:
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in 2001. He received his Masters of Science and his PhD both in Electrical Engineering in 2004 and 2007 from UC Berkeley. He was a UC Chancellor's postdoctoral fellow at UC Berkeley with Prof. Alberto Sangiovanni-Vincentelli from 2007 to 2009 and now is a postdoctoral research fellow in the Synthetic Biology Engineering Research Center.
His current research centers on extracting design techniques from electronic design automation (EDA) and applying them to the design of synthetic biological systems. Specifically he examines how 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. These research agendas find a home in the "Clotho" unified toolset. Clotho is a two time winner of the "best software tool" at MIT's International Genetically Engineered Machine Competition and the first tool of its kind to employ EDA approaches to synthetic biology. He is also the co-founder of the International Workshop on Bio-Design Automation (IWBDA) which is co-located at the Design Automation Conference. His other research interests include system level design, computer architecture, embedded systems, and logic synthesis.
Thursday, February 25, 2010
3:30 p.m.
356 Fitzpatrick