Software Overview

Design Automation Tools for Synthetic Biology

 

One of CIDAR’s primary goals is to research technologies that make synthetic biology more effective by integrating concepts from electronic design automation into the specification, design, and assembly of complex biological systems. This includes the development of both computational and experimental tools for synthetic biological engineering.

Specification tools allow synthetic biologists to better define the identity, characteristics, and behavior of the biological parts and devices that they work with. This facilitates collaboration between researchers and allows for the development of software tools built upon standard practices and formats, such as the Synthetic Biology Open Language.

One of CIDAR’s specification projects is the development of Eugene, a domain-specific language for synthetic biology that allows users to define biological parts and the rules that govern how they can be put together to form devices.

The team is also working to develop a formal specification and verification framework for design automation in synthetic biology, which will include software that allows users to specify genetic circuit behavior using a hardware description language (such as Verilog) and assists them in selecting optimal genetic regulatory network topologies.

The design of synthetic biological devices is most commonly performed by hand, involving a large investment of time and effort and requiring extensive knowledge of available biological components. Software tools have the potential to make this process both easier and more effective by assisting users in the storage, selection, and arrangement of biological components, as well as the visualization and verification of finalized designs.

Clotho, which is developed by CIDAR in collaboration with the Anderson Lab at the University of California, Berkeley, provides a way for synthetic biologists to store and interact with biological data, preserving detailed information on biological parts for use in device design. It also provides a framework for applications that act upon this data, which are then able to automate many design tasks.

One example of this is Pigeon, a web-based software tool that renders textual descriptions of genetic circuit designs into graphical images using standardized visual elements. The combination of Eugene, Clotho, and Pigeon allows the rapid design and assessment of genetic circuit libraries, producing results that can be easily recognized and understood by other members of the synthetic biology community.

The process of biological device assembly from plasmid- and oligo-derived DNA components is often composed of many steps, with each step carried out according to established protocols and requiring specific input parts, reagents, and equipment.

Raven generates optimized assembly plans by minimizing the number of steps required to achieve a target DNA sequence, given a set of input devices and a standardized DNA assembly protocol. This not only reduces the time spent planning laboratory work, but also makes the assembly process more cost- and time-efficient.

Puppeteer automates the physical processes involved in DNA assembly by tracking reagents, scheduling tasks, and generating both human-readable and robotic instructions to carry out laboratory processes. This decreases the impact of human error on DNA assembly, and reduces the amount of manual benchwork required to create new biological devices.


Want to see our software in action? Check out the demos on our YouTube channel.