There is a pressing need for design automation tools for synthetic biological systems. Compared to electronic circuits, cellular information processing has more complex elementary components with a much greater complexity of interactions between components. Moreover, chemical computation within a cell is strongly affected both by other computations taking place within the cell and by the cell's native metabolic processes and its external environment. All this adds up to a design flow that is currently highly iterative, error-prone, and extremely slow: critical problems that must all be addressed in order to realize the potential of synthetic biology.
We have been developing a tool-chain approach to decomposing the
problems of design and assembly into automatable fragments.
Practitioners using our tool-chain will be able to design organisms
using higher level descriptions, which are automatically transformed
into genetic regulatory network designs, then assembled into DNA
samples ready for in vivo execution. At the same time, the tool-chain
is free and open software that will allow researchers to incorporate
their own design tools, thereby disseminating their results to the
community and enhancing the capabilities of the tool-chain.
We have recently published a paper in ACS Synthetic Biology
describing the TASBE tool-chain and its use to design organisms from
End-to-End Workflow for Engineering of Biological Networks from
Work sponsored by DARPA I2O under contract HR0011-10-C-0168; the
views and conclusions contained in this document are those of the
authors and not DARPA or the U.S. Government.
Last Updated: 9/5/2012