Electrical Engineering
      and Computer Sciences

Electrical Engineering and Computer Sciences


UC Berkeley


2008 Research Summary

A Platform-Based Approach to the Design of a Bioinformatic System

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Douglas Michael Densmore, Alberto L. Sangiovanni-Vincentelli and Christopher Voigt

Bioinformatics has reached the stage at which the amount of DNA sequence information in existing databases is quite large. 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. This process should be done in a way useful to biologists working in a laboratory environment.

A platform-based approach looks at how sequences can be viewed as having a particular functionality and what is now needed is to assemble platforms (individual DNA elements) to perform this functionality. This work attempts to leverage traditional CAD for VLSI techniques whenever possible.

This project creates an initial toolset which provides a GUI to interact with the DNA databases as well as perform operations to create biological parts and components. This incorporates a variety of input mechanisms and a variety of front-end and back-end tools.

C. A. Voigt, "Genetic Parts to Program Bacteria," Current Opinion in Biotechnololgy, Vol. 17, 2006, pp. 548-557.