School of Computing

Projects

Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies

Synthetic biology involves the design and development of novel, useful biological systems, or the redesign of those systems that exist already. This approach promises to be of major value to society. Potential applications include the production of high-value materials, such as fine chemicals and pharmaceuticals, bio-remediation, sustainable energy, medical diagnostics, and agriculture. In Synthetic Biology novel biological genetic circuits are developed using engineering principles in order to add the new properties to a given organism - called a host or chassis. The type of chassis used will vary according to the application and the circuit. For example, for food and agriculture it is highly desirable to use organisms that have been shown to be safe for human consumption. However, currently, most circuits are designed for, and tested in, a single organism such as the commonly used bacterium Escherichia coli. Moving these circuits to another organism requires the circuit to be re-engineered and retested in the new organism, a process which is very time consuming and costly. This process of 'refactoring' slows down research and costs industry a huge amount of time, effort and money. A major problem is that the connections between the designed genetic circuit and the chassis organism are specific to a given species of chassis. So the genetic circuit ends up being redesigned to meet the new connections required for a different species. In our project we will standardise the connection between a given genetic circuit and the chassis organism. We will develop a set of academically and industrially useful organisms where the plug-in points for the genetic circuit will be the same for each of our organisms, allowing the genetic circuit to be moved from one organism to another with changes. We refer to this standardised plug-in system as a 'bio-adaptor'. This programme grant will initiate a new field in Synthetic Biology, called 'Portabolomics'. This is a highly novel approach that has not been achieved by any other groups to-date. The key to the success of the project is to understand the networks of molecular processes that occur in a cell, since it is these networks that will need to be modified to make the bio-adaptor. We will apply a range of the state-of-the-art computing approaches to this task including many techniques from Computing Science, including network analysis, formal methods and data mining, for which our group has a wide range of world-leading expertise. The results of the Portabolomics project will not only be a new system of major value to UK synthetic biology research and industry, but will enhance the field of computing science as new computational techniques will need to be developed to achieve our goals.