Programming language for biochemistry

Computer scientists that think of nature as literally computing, often take the stance that biological organisms are nothing more than protein interaction networks. For example, this is the stance that Leslie Valiant (2009) takes when defining ecorithms: biology is just a specialization of computer science focused on evolvable circuits. User @exploderator summarized the realist computational view of biology on Reddit while answering what theoretical computer science can offer biology:

[B]iology is primarily chemo-computation, chemical information systems and computational hardware.
Theoretical comp sci is the only field that is actually specifically dedicated to studying the mathematics / logic of computation. Therefore, although biology is an incredibly hard programming problem (only a fool thinks nature simple), it is indeed more about programming and less about the hardware it’s running on.

Although it is an easy stance for a theoretician to take, it is a little bit more involved for a molecular biologist, chemist, or engineer. Yet for the last 30 years, even experimentalists have been captivated by this computational realism and promise of engineering molecular devices (Drexler, 1981). Half a year ago, I even reviewed Bonnet et al. (2013) taking steps towards building transcriptors. They are focusing on the hardware side of biological computation and building a DNA-analogue of the von Neumann architecture. However, what we really need is a level of abstraction: a chemical programming language that can be compiled into biocompatible reactions.
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