Research
“I’m going to eat your brains and gain your knowledge….”
The purpose of this page is to provide information regarding my two main areas of research. One is in the development of tools for synthetic biological systems while the other is in the development of system level architectural models for programmable platforms. While both of these areas seem unrelated, they are both rooted in Platform-Based Design and Electronic Design Automation (EDA). I believe that techniques we use in one area will be applicable to the other and each has to deal explicitly with design abstraction, refinement, and characterization.
Platform-Based Design for Synthetic Biological Systems
Participants: Douglas Densmore, J. Christopher Anderson (UCB), Christopher Voigt (UCSF)
Location: UC Berkeley, UCSF
Description:
Genomics has reached the stage at which the amount of DNA sequence information in existing databases is quite large. Moreover, synthetic biology now is using these databases to catalog sequences according to their functionality and therefore creating standard biological parts which can be used to create large systems. What is needed now are flexible tools which not only permit access and modification to that data but also allow one to perform meaningful manipulation and use of that information in an intelligent and efficient way. These tools need to be useful to biologists working in a laboratory environment while leveraging the experience of the larger CAD community.
A Platform-Based Design (PBD) approach looks at how genetic information can be viewed as having a particular functionality and what is now needed is to assemble platforms (collections of DNA elements) to perform this functionality. This work attempts to leverage the same methodology employed by PBD for embedded systems to the design of synthetic biological systems. This work places synthetic biology in a PBD framework, discusses required EDA concepts in biological terms, and develops a toolset named Clotho which will implement the ideas outlined here.
The Clotho project creates a biological parts management, analysis, and deployment framework. In particular it looks at issues related to part interoperability and standardization as well as assembly and manipulation. The project is run by myself and has a number of undergraduates and graduate students working on it as well. For the latest information check out http://www.clothocad.org. Here is a poster from Synthetic Biology 4.0 which provides an overview of the project visually.
Clotho began as an entry in the 2008 iGEM jamboree where it was awarded a gold medal (only 16 of 84 teams received this distinction) and won “Best Software Tool”. For Clotho’s iGEM page, go here.
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System Level Architecture Modeling, Refinement, and Characterization
System Level Architecture Modeling
This work investigates techniques to create models of highly programmable systems (FPGAs, ASIPs, etc) at the system level. Specifically how to capture the services offered by the models. This should be done in a way which is abstract and modular while remaining efficient and accurate. Models of Xilinx’s Virtex II Pro, ARM7, ARM9, and Sparc architectures have explored and Sun Microsystem’s/UC Berkeley’s FLEET architecture has been examined in the past.
Refinement Verification
Unlike equivalence checking, refinement verification traditionally looks to ensure that a refined model contains a subset of an abstract model’s behaviors (not the full set necessarily). This works examines the issues involved in doing refinement verification of architecture models at the system level.
Programmable Platform Characterization
A modular and scalable approach for automatically extracting actual performance information from a set of FPGA-based architecture topologies. We use this information dynamically during simulation to support performance analysis in a System Level Design environment. These topologies capture systems representing common designs using FPGA technologies of interest. Their characterization is done only once; the results are then used during simulation of actual systems being explored by the designer. Our approach allows a rich set of FPGA architectures to be explored accurately at various abstraction levels to seek optimized solutions with minimal effort by the designer.