GEC

Summary

The Genetic Engineering of Cells language (GEC) is a programming language for designing and simulating genetic circuits to reprogram cell behaviour. The language can be used to write a program describing the desired behaviour of the cell, and automatically generates the DNA code that is needed to achieve this behaviour. The language allows logical interactions between potentially undetermined proteins and genes to be expressed in a modular manner, and generates sequences of biological parts using logic programming techniques and prototype databases containing known biological parts and protein interactions. GEC is a first step towards the automatic translation of high-level behavioural designs to low-level DNA code.

Download

• Web Simulator (requires Silverlight 4.0 for Windows or Mac).

Related publications

• Michael Pedersen and Andrew Phillips, Towards programming languages for genetic engineering of living cells, in Journal of the Royal Society Interface, 15 April 2009
• Coming Soon to a Lab Near You: Drag-and-Drop Virtual Worlds. Science 331:669-671. February 2011.

People

• Matthew Lakin, Filippo Polo, Neil Dalchau, Matthew Smith and Andrew Phillips. Microsoft Research.
• Michael Pedersen, James Brown. Microsoft Research & University of Edinburgh.

Acknowledgements

• GEC was developed by Michael Pedersen, Matthew Lakin, Filippo Polo and Andrew Phillips at Microsoft Research.
• GEC uses a Language for Biological Systems (LBS) as a target for compilation. LBS was developed by Michael Pedersen under a Microsoft PhD scholarship supervised by Gordon Plotkin, Centre for Systems Biology at Edinburgh, University of Edinburgh.
• A prototype Windows Simulator for GEC was developed by Michael Pedersen during a Microsoft Internship.
• Neil Dalchau assisted with the development of an ODE solver for GEC.
• The core GEC language was developed in F#.
• GEC uses Dynamic Data Display for visualising simulation plots.
• GEC uses Microsoft Automatic Graph Layout for visualising networks.