CIF: Small: Fundamental Limits of DNA-Based Storage

CIF：小：基于 DNA 的存储的基本限制

基本信息

批准号：
2007597
负责人：
Ilan Shomorony
金额：
$ 48.41万
依托单位：
University of Illinois at Urbana-Champaign
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2020
资助国家：
美国
起止时间：
2020-07-01 至 2024-06-30
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2007597&HistoricalAwards=false
关键词：
CIF Small Fundamental Limits DNA

项目摘要

The demand for data storage continues to increase at a rapid pace, posing significant challenges to current data centers and spurring significant interest in the development of new storage technologies. DNA, the molecule that carries the genetic information of all living matter, has become a promising medium for long-term archival data storage due to its longevity and very high information density. This new approach to data storage presents unique challenges. Unlike typical hard drives, where data bits are stored in a well-ordered linear fashion, storing data on DNA requires the synthesis of a large number of DNA molecules that are then mixed out of order in a liquid solution. This makes the process of reliably reading the data after storage significantly more expensive and computationally complex. The goal of this project is to understand the fundamental limitations and capabilities of DNA as a storage medium. In particular, this research seeks to characterize basic tradeoffs between cost, information density, reading and writing speeds, and reliability, aiming to develop new coding strategies that can unlock the full potential of this innovative approach to data storage.The project will investigate the fundamental limits of DNA storage systems by focusing on three main objectives. The first objective is to develop an information theory framework to formally analyze these systems. DNA storage systems will be modeled via the abstraction of a shuffling channel, which captures the fact that, in DNA-based storage, many blocks of data are shuffled out of order. The capacity of these channels will be characterized under different noise models and properties of optimal coding schemes will be studied. A particular question of interest is how to design capacity-optimal indexing strategies that allow the proper reordering of the data. Since the cost of synthesizing long DNA strands is the main obstacle to practical DNA storage, the second research objective will deal with systems that store data on many very short DNA strands, each of which is too short to encode any meaningful information. For that reason, new strategies to encode information in the concentration of different DNA molecules in the solution will be proposed, and their fundamental capabilities established. The third research objective will focus on the computational challenges associated with the joint processing of a large set of DNA sequences. In particular, basic tradeoffs between storage capacity and computational requirements will be established, and recent algorithmic advances in large-scale sequence alignment will be leveraged towards the development of computationally efficient decoding algorithms.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

对数据存储的需求继续以快速的速度增加，对当前数据中心构成了重大挑战，并激发了人们对新存储技术发展的重大兴趣。 DNA是携带所有生物遗传信息的分子，由于其寿命和非常高的信息密度，已成为长期档案数据存储的有希望的媒介。这种新的数据存储方法提出了独特的挑战。与典型的硬盘驱动器不同，在以良好的线性方式存储数据位，将数据存储在DNA上需要合成大量DNA分子，然后将其混合在液体溶液中。这使得在存储之后可靠读取数据的过程明显更昂贵且计算复杂。该项目的目的是了解DNA作为存储介质的基本局限性和能力。特别是，这项研究试图表征成本，信息密度，阅读速度和可靠性之间的基本权衡，旨在制定新的编码策略，这些编码策略可以释放这种创新的数据存储方法的全部潜力。该项目将通过专注于三个主要目标来研究DNA存储系统的基本限制。第一个目标是开发信息理论框架以正式分析这些系统。 DNA存储系统将通过改组通道的抽象进行建模，该通道捕获了以下事实：在基于DNA的存储中，许多数据块被逐步推翻。这些通道的容量将在不同的噪声模型和最佳编码方案的特性下进行表征。一个特定的兴趣问题是如何设计容量最佳的索引策略，以适当地重新排序数据。由于合成长DNA链的成本是实用DNA存储的主要障碍，因此，第二个研究目标将处理将数据存储在许多非常短的DNA链上的系统，每个系统都太短了，无法编码任何有意义的信息。因此，将提出解决溶液中不同DNA分子浓度的信息的新策略，并确定其基本能力。第三个研究目标将重点关注与大量DNA序列的联合处理相关的计算挑战。特别是，将建立存储容量和计算要求之间的基本权衡，并将最新的大规模序列比对算法进步用于开发计算高效的解码算法。该奖项反映了NSF的立法任务，并被认为是通过基金会的智力优点和广泛的Cricits和Broaditia的评估来评估。