Synthetic Biology @ BBN

TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering

TASBE tool-chain

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: An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications

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