Domain-Specific Programming Languages for Computational Nucleic Acid Systems.,ACS Synthetic Biology

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Domain-Specific Programming Languages for Computational Nucleic Acid Systems.
ACS Synthetic Biology ( IF 3.7 ) Pub Date : 2020-06-26 , DOI: 10.1021/acssynbio.0c00050
Matthew R Lakin _{1,

2,

3} , Andrew Phillips ₄

Affiliation

The construction of models of system behavior is of great importance throughout science and engineering. In bioengineering and bionanotechnology, these often take the form of dynamic models that specify the evolution of different species over time. To ensure that scientific observations and conclusions are consistent and that systems can be reliably engineered on the basis of model predictions, it is important that models of biomolecular systems can be constructed in a reliable, principled, and efficient manner. This review focuses on efforts to address this need by using domain-specific programming languages as the basis for custom design tools for researchers working on computational nucleic acid devices, where a domain-specific language is simply a programming language tailored to a particular application domain. The underlying thesis of our review is that there is a continuum of practical implementation strategies for computational nucleic acid systems, which can all benefit from appropriate domain-specific languages and software design tools. We emphasize the need for specialized yet flexible tools that can be realized using domain-specific languages that compile to more general-purpose representations.

中文翻译：

计算核酸系统的领域特定编程语言。

系统行为模型的构建在整个科学和工程中都非常重要。在生物工程和生物纳米技术中，这些通常采用动态模型的形式，该模型指定了不同物种随时间的演变。为了确保科学观察和结论是一致的，并且可以在模型预测的基础上可靠地对系统进行工程设计，重要的是，可以以可靠，有原则和有效的方式构建生物分子系统的模型。这篇综述着重于通过使用领域特定的编程语言作为针对从事计算核酸设备的研究人员的定制设计工具的基础来满足这一需求的努力，其中领域特定的语言只是针对特定应用领域定制的编程语言。我们的综述的基本主题是，对于计算核酸系统而言，存在着一系列实用的实施策略，它们都可以从适当的领域特定语言和软件设计工具中受益。我们强调需要专用但灵活的工具，这些工具可以使用可编译为更多通用表示形式的领域特定语言来实现。

更新日期：2020-07-17

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