High-Level Programming Languages for Biomolecular Systems
High-Level Programming Languages for Biomolecular Systems
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DOI：
10.1007/978-1-4419-6766-4_11
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发表时间：
2011-01-01
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影响因子：
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通讯作者：
Cai, Yizhi
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文献类型：
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作者：
Beal, Jacob;Phillips, Andrew;Cai, Yizhi
在电子计算中，高级语言隐藏了许多细节，允许非专业人士，有时甚至是儿童编程和创建系统。生物分子系统的高级语言旨在达到类似的抽象水平，这样系统就可以根据所期望的行为来设计，而不是根据将用于实现这些行为的遗传密码的细节。这种高级方法的缺点是，它通常意味着放弃对系统某些方面的控制，并且相对于手动调整的设计降低了效率。不同的语言在它们强调的设计方面和自动化的设计方面做出了不同的权衡，所以我们预计，对于生物学来说，不会有单一的“正确的语言”，就像电子计算没有一样。因为合成生物学是一个新领域，还没有成熟的语言出现。在本章中，我们对目前正在开发的四种代表性语言进行了深入的调查，包括GenoCAD、Eugene、GEC和Proto，以及其他相关高级设计工具的简要概述。
In electronic computing, high-level languages hide much of the details, allowing non-experts and sometimes even children to program and create systems. High level languages for biomolecular systems aim to achieve a similar level of abstraction, so that a system might be designed on the basis of the behaviors that are desired, rather than the particulars of the genetic code that will be used to implement these behaviors. The drawback to this sort of high-level approach is that it generally means giving up control over some aspects of the system and having decreased efficiency relative to hand-tuned designs. Different languages make different tradeoffs in which aspects of design they emphasize and which they automate, so we expect that for biology, there will be no single 'right language', just as there is not for electronic computing. Because synthetic biology is a new area, no mature languages have yet emerged. In this chapter, we present an in-depth survey of four representative languages currently in development GenoCAD, Eugene, GEC, and Proto as well as a brief overview of other related high-level design tools.