High-level programming language for Bio-molecular systems

In electronic computing, high-level languages hide much of the details, allowing non-experts and sometimes even children to program and cre- ate systems. High level languages for bio-molecular systems aim to achieve a similar level of abstraction, so that a system might be de- signed on the basis of the behaviors that are desired, rather than the particulars of the genetic code that will be used to implement these behaviors. The drawback to this sort of high-level approach is that it generally means giving up control over some aspects of the system and having decreased efficiency relative to hand-tuned designs. Different languages make different tradeoffs in which aspects of design they em- phasize and which they automate, so we expect that for biology, there will be no single “right language,” just as there is not for electronic com- puting. Because synthetic biology is a new area, no mature languages have yet emerged. In this chapter, we present an in-depth survey of four representative languages currently in development—GenoCAD, Eugene, GEC, and Proto—as well as a brief overview of other related high-level design tools.