A compiler for biological networks on silicon chips

Abstract

The explosive growth in semiconductor integrated circuits was made possible in large part by design automation software. The design and/or analysis of synthetic and natural circuits in living cells could be made more scalable using the same approach. We present a compiler which converts standard representations of chemical reaction networks and circuits into hardware configurations that can be used to simulate the network on specialized cytomorphic hardware. The compiler also creates circuit-level models of the target configuration, which enhances the versatility of the compiler and enables the validation of its functionality without physical experimentation with the hardware. We show that this compiler can translate networks comprised of mass-action kinetics, classic enzyme kinetics (Michaelis-Menten, Briggs-Haldane, and Botts-Morales formalisms), and genetic repressor kinetics, thereby allowing a large class of models to be transformed into a hardware representation. Rule-based models are particularly well-suited to this approach, as we demonstrate by compiling a MAP kinase model. Development of specialized hardware and software for simulating biological networks has the potential to enable the simulation of larger kinetic models than are currently feasible or allow the parallel simulation of many smaller networks with better performance than current simulation software.

The Merging of Biological and Electronic Circuits

“…In this paper, we shall only briefly summarize how these cytomorphic chips operate. Readers interested in further details should consult past work over more than Using compilers that have been developed or are currently in development (Medley et al, 2020), we translate biochemical reactions in SBML or in SPICE netlists to programming bits for the cytomorphic chips that have hardware instantiations of chemical reaction circuits. To aid in such programming, MATLAB and Simulink interfaces interact with field programmable gate arrays (FPGAs) on circuit boards composed of many such cytomorphic chips.…”

A Poisson Process Generator Based on Multiple Thermal Noise Amplifiers for Parallel Stochastic Simulation of Biochemical Reactions

“…There have been several attempts to implement hardware specialized for parallel simulation of stochastic biochemical reactions in order to solve the problem of long simulation times in software [14][15][16][17][18][19][20][21][22][23][24]. Ref.…”