Mining Biochemical Circuits from Enzyme Databases via Boolean Reasoning

Synthetic biology has become an important technology in biomedical and many other applications. Despite the enormous progress made, engineering biochemical circuits especially from natural reactions in the real world remains challenging. Most prior work on biochemical circuit synthesis either assumed abstract or hypothetical species and reactions that may not be associated with real-world instances, or lacked scalability due to inefficient search procedures. In this work we propose a Boolean reasoning approach to mining biochemical circuits from enzyme databases to implement a design specification. Experimental results show that our method can synthesize desired biosensor circuits from an enzyme database with more than 200 reactions, and outperforms the state-of-the-art tool. ? 2020 Association on Computer Machinery.