ClothoCAD

From Clotho

This page is under construction. This should be done by January 2010. In the meantime, the older, more complete site can be found at http://biocad-server.eecs.berkeley.edu/wiki


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 electronic systems to the design of synthetic biological systems. This work places synthetic biology in a PBD framework, discusses required electronic design automation concepts in biological terms, and describes toolsets which will implement the ideas outlined here.

2008 UC Berkeley Comp. Team
Clotho Design Environment
2009 UC Berkeley Comp. Team


Introduction and Overview of Platform-Based Design

Platform-Based Design

Want to learn more about "Platform-Based Design"? Want to learn more about our vision of how this can be applied to synthetic biological systems? Then you want to start with these links:



Software Tools and Design Environments

2008 iGEM Jamboree Best Software Tool Winner (Clotho Classic)
2009 iGEM Jamboree Best Software Tool Winner (Clotho, Eugene, Spectacles, Kepler)

Did you come here to learn more about our software projects? Want to download the software? Check out these links:





Related Work and Materials

Synthetic Biology Tool Landscape

Want to learn more about other efforts related to our project? Want some papers to read? Check out these links: