Rule based constraints for the construction of genetic devices

The construction of composite genetic devices from primitive parts is a key activity in synthetic biology. Currently there does not exist a formal method to specify constraints on the construction of these devices. These constraints would help enable an automated design flow from device specification to physical assembly. This paper examines the laboratory creation of variations of a particular genetic device called a phagemid. We illustrate how lessons learned empirically from the non-functional designs can be captured formally as constraints in a newly created domain specific language called “Eugene”. These constraints will prevent many faulty constructions automatically in the future saving time and money while increasing design abstraction and productivity.