论文标题

在DNA存储中有效启用块语义和数据更新

Efficiently Enabling Block Semantics and Data Updates in DNA Storage

论文作者

Sharma, Puru, Lim, Cheng-Kai, Lin, Dehui, Pote, Yash, Jevdjic, Djordje

论文摘要

我们提出了一种新颖而灵活的DNA储存结构,该体系结构将存储空间分为固定尺寸的单元(块),可以独立有效地随机访问读写操作,并进一步允许有效地对连续数据块进行有效的顺序访问。与先前的工作相反,在我们的体系结构中,一对长度为20的随机访问PCR引物并不定义一个对象,而是一个独立的存储分区,该对象在内部被阻止并独立于其他分区进行管理。我们揭示了可以管理每个分区的内部地址空间的灵活性和约束,并将它们纳入我们的设计中,以提供丰富而功能的存储语义,例如块存储组织,有效的数据更新实现以及顺序访问。为了利用基于前缀的PCR寻址性质的全部功能,我们定义了一种将分区的内部寻址方案转换为与PCR兼容的等效物的方法。这使我们能够使用底漆运行PCR,可以多样地拉长,以包括内部地址的所需部分,从而缩小反应范围,以检索特定的块或分区中的一系列块,以足够高的精度。我们的Wetlab评估证明了提议的思想的实用性,并降低了140倍的测序成本和延迟,以检索分区内各个块。

We propose a novel and flexible DNA-storage architecture, which divides the storage space into fixed-size units (blocks) that can be independently and efficiently accessed at random for both read and write operations, and further allows efficient sequential access to consecutive data blocks. In contrast to prior work, in our architecture a pair of random-access PCR primers of length 20 does not define a single object, but an independent storage partition, which is internally blocked and managed independently of other partitions. We expose the flexibility and constraints with which the internal address space of each partition can be managed, and incorporate them into our design to provide rich and functional storage semantics, such as block-storage organization, efficient implementation of data updates, and sequential access. To leverage the full power of the prefix-based nature of PCR addressing, we define a methodology for transforming the internal addressing scheme of a partition into an equivalent that is PCR-compatible. This allows us to run PCR with primers that can be variably elongated to include a desired part of the internal address, and thus narrow down the scope of the reaction to retrieve a specific block or a range of blocks within the partition with sufficiently high accuracy. Our wetlab evaluation demonstrates the practicality of the proposed ideas and a 140x reduction in sequencing cost and latency for retrieval of individual blocks within the partition.

扫码加入交流群

加入微信交流群

微信交流群二维码

扫码加入学术交流群,获取更多资源