Schwarz Peter Michael, Freisleben Bernd
Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany.
Comput Struct Biotechnol J. 2024 Oct 26;23:3878-3896. doi: 10.1016/j.csbj.2024.10.038. eCollection 2024 Dec.
Fountain codes, originally developed for reliable multicasting in communication networks, are effectively applied in various data transmission and storage systems. Their recent use in DNA data storage systems has unique challenges, since the DNA storage channel deviates from the traditional Gaussian white noise erasure model considered in communication networks and has several restrictions as well as special properties. Thus, optimizing fountain codes to address these challenges promises to improve their overall usability in DNA data storage systems. In this article, we present several methods for optimizing fountain codes for DNA data storage. Apart from generally applicable optimizations for fountain codes, we propose optimization algorithms to create tailored distribution functions of fountain codes, which is novel in the context of DNA data storage. We evaluate the proposed methods in terms of various metrics related to the DNA storage channel. Our evaluation shows that optimizing fountain codes for DNA data storage can significantly enhance the reliability and capacity of DNA data storage systems. The developed methods represent a step forward in harnessing the full potential of fountain codes for DNA-based data storage applications. The new coding schemes and all developed methods are available under a free and open-source software license.
喷泉码最初是为通信网络中的可靠多播而开发的，目前已有效地应用于各种数据传输和存储系统。它们最近在DNA数据存储系统中的应用面临着独特的挑战，因为DNA存储通道不同于通信网络中考虑的传统高斯白噪声擦除模型，有多种限制以及特殊属性。因此，优化喷泉码以应对这些挑战有望提高其在DNA数据存储系统中的整体可用性。在本文中，我们提出了几种针对DNA数据存储优化喷泉码的方法。除了喷泉码普遍适用的优化方法外，我们还提出了优化算法来创建喷泉码的定制分布函数，这在DNA数据存储背景下是新颖的。我们根据与DNA存储通道相关的各种指标对所提出的方法进行评估。我们的评估表明，针对DNA数据存储优化喷泉码可以显著提高DNA数据存储系统的可靠性和容量。所开发的方法代表了在充分发挥喷泉码在基于DNA的数据存储应用中的全部潜力方面向前迈出的一步。新的编码方案和所有开发的方法都在免费和开源软件许可下提供。
