Signal-to-noise ratio measures efficacy of biological computing devices and circuits
Signal-to-noise ratio measures efficacy of biological computing devices and circuits
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DOI：
10.3389/fbioe.2015.00093
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发表时间：
2015-01-01
影响因子：
5.7
通讯作者：
Beal, Jacob
中科院分区：
文献类型：
--
作者：
Beal, Jacob
工程生物细胞进行计算具有广泛的潜在应用，包括精密医疗、生物合成过程控制和环境传感。然而，由于可用部件的可组合性差，以及部件及其与其运行的复杂环境的相互作用的不足，实施可预测和有效的计算一直是极其困难的。在这篇文章中，作者认为，这种情况可以通过定量的信噪比分析计算抽象与生物有机体特有的变异和不确定性之间的关系来改善。这种分析采用每个计算设备的Delta SNRdB函数的形式，该函数可以通过测量设备的输入/输出曲线和表达式噪声来计算。然后，可以将这些功能组合在一起，以预测电路执行预期计算的能力，以及评估生物设备对工程计算电路的一般适用性。将信噪比分析应用于当前的抑制器库表明，目前没有一个库足以用于一般电路工程，但也指出了解决这种情况的关键目标，并极大地提高了可有效用于实现生物应用的计算范围。
Engineering biological cells to perform computations has a broad range of important potential applications, including precision medical therapies, biosynthesis process control, and environmental sensing. Implementing predictable and effective computation, however, has been extremely difficult to date, due to a combination of poor composability of available parts and of insufficient characterization of parts and their interactions with the complex environment in which they operate. In this paper, the author argues that this situation can be improved by quantitative signal-to-noise analysis of the relationship between computational abstractions and the variation and uncertainty endemic in biological organisms. This analysis takes the form of a Delta SNRdB function for each computational device, which can be computed from measurements of a device's input/output curve and expression noise. These functions can then be combined to predict how well a circuit will implement an intended computation, as well as evaluating the general suitability of biological devices for engineering computational circuits. Applying signal-to-noise analysis to current repressor libraries shows that no library is currently sufficient for general circuit engineering, but also indicates key targets to remedy this situation and vastly improve the range of computations that can be used effectively in the implementation of biological applications.