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DNAQL: a query language for DNA sticker complexes
Natural Computing ( IF 2.1 ) Pub Date : 2021-01-12 , DOI: 10.1007/s11047-020-09839-7
Robert Brijder , Joris J. M. Gillis , Jan Van den Bussche

DNA computing has a rich history of computing paradigms with great expressive power. However, far less expressive power is needed for data manipulation. Indeed, the relational algebra, the yardstick of database systems, is expressible in first-order logic, and thus less powerful than Turing-complete models. Turing-complete DNA computing models have to account for many and varied scenarios. A DNA implementation of data manipulations might be nimbler and perform its operation faster than a Turing-complete DNA computing model. Hence, we propose a restrictive model for implementing data manipulation operations, focused on implementability in DNA. We call this model the sticker complex model. A forte of the sticker complex model, is its ability to detect when hybridization becomes an uncontrolled chain reaction. Such chain reactions make hybridization less predictable and thus less attractive for deterministic computations. Next, we define a query language on sticker complexes, called DNAQL. DNAQL is a typed, applicative functional programming language, powerful enough to simulate the relational algebra on sticker complexes. The type system enjoys a number of desirable properties such as soundness, maximality, and tightness.



中文翻译:

DNAQL:DNA标签复合物的查询语言

DNA计算具有丰富的计算能力,具有丰富的计算范例历史。但是,数据处理所需的表达能力要低得多。确实,关系代数是数据库系统的标准,可以用一阶逻辑表示,因此,其功能不如图灵完备模型那么强大。图灵完备的DNA计算模型必须考虑多种情​​况。数据处理的DNA实现可能比图灵完备的DNA计算模型更灵活,并且其执行速度更快。因此,我们提出了一个用于实施数据操纵操作的限制性模型,重点是DNA的可实施性。我们称此模型为复杂标签模型。贴纸复合物模型的一个优点是它能够检测杂交何时变为不受控制的链反应。这样的链反应使杂交更难以预测,因此对于确定性计算不太有吸引力。接下来,我们在标签复合体上定义一种查询语言,称为DNAQL。DNAQL是一种类型化的,可应用的函数式编程语言,功能强大,足以模拟粘贴复合物上的关系代数。该类型系统具有许多理想的属性,例如稳健性,最大性和紧密性。

更新日期:2021-01-12
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