Survey of Engineering Models for Systems Biology

Table 1

Multilayered computing architecture overview.

Level	Function	Implementation in computer	Implementation in a cell
Digital logic	Processing engine	Gate (organized into circuit) as basic element	Amino acid as basic element; Cytoplasmic protein as a logic or signal processor [21]
	Information code	Binary with a base-2 system	Quaternary (Qbits) representing a base-4 system
	Primary (main) memory	Gate (organized into register) as basic element	Ribonucleotide as basic element; Engineered gene circuits [32]
	Latch	Flip-flop
	Timer/oscillator	Ring oscillator	Repressilator for the circadian rhythm [32]
	Secondary (working) memory	Miscellaneous, depending on media	Deoxyribonucleotide as basic element; RNA as a temporary register memory [21]
Microarchitecture	Basic computing structure	Data path (the ALU, a circuit, connected with a number of registers)	Protein
Information system architecture	Instruction specification	Predetermined formatting	The transcribed region of a gene; a gene per CPU instruction [20]
	Instruction function	Controlling the data path	Enabling a chemical reaction; Similarly, a protein, proposed as basic computational elements in living cells [33], is often involved in controlling a step of biochemical reaction through catalysis [20]
	Data specification	Type and format	Substrate specificity
	Memory addressing	Numerical	Promoter and enhancer binding
	Randomly accessed persistent storage	Memory bank or disk drive	Chromosomes [24, 26]; Ribonome (RNA space) [20]
	Low level memory layout	RAM chip
	High level data formatting	Drive formatting	The histone code and its control mechanisms [26]
	Cache (secondary memory) management	Software algorithm to implement a replacement policy	Cellular gene expression regulation: catalysis abundance and how active the catalysis is Protein degradation [20]; Proteome (protein space) to computer cache memory
Operating system	Memory management	Swapping information in and out of primary and secondary memory	Gene transcription and RNA degradation
	Step in a process	Segment of a computer program (e.g., software function)	Many genes of a biochemical pathway are organized into one operon in prokaryote cells [20]; in eukaryotes, functionally related genes share common indexes (transcription factor binding sites)
	Process management	Shared resource such as semaphore	Shared route by pathways
		Interprocess signal	Pathway cross-talk
		CPU time sharing	Pathway bandwidth management
	File system	Continuous or indexed	Discontinuous indexed (transcription factor binding)