R&D: DNA Storage Designer, Practical and Holistic Design Platform for Storing Digital Information in DNA Sequence

biorxiv.org has published an article written by Likun Jiang, Department of Computer Science, Xiamen University, Xiamen 361005, China, and National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, China, Ziyun Zou, Xinru Ruan, Xinyi Zhang, Xinyu Yu, Yinghao Lan, Department of Computer Science, Xiamen University, Xiamen 361005, China, Xiangrong Liu, Department of Computer Science, Xiamen University, Xiamen 361005, China, and National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, China.

Abstract: “DNA molecules, as natural information carriers, have several benefits over conventional digital storage mediums, including high information density and long-term durability. It is expected to be a promising candidate for information storage. However, despite significant research in this field, the pace of development has been slow due to the lack of complete encoding-decoding platform and simulaton-evaluation system. And the mutation in DNA sequences during synthesis and sequencing requires multiple experiments, and wet experiments can be costly. Thus, a silicon-based simulation platform is urgently needed for promoting research. Therefore, we proposed DNA Storage Designer, the first online platform to simulate the whole process of DNA storage experiments. Our platform offers classical and novel technologies and experimental settings that simulate three key processes: encoding, error simulation, and decoding for DNA storage system. Fisrt, 8 mainstream encoding methods were embedded in the encoding process to convert files to DNA sequences. Secondly, to uncover potential mutations and sequence distribution changes in actual experiments we integrate the simulation setting for five typical experiment sub-processes (synthesis, decay, PCR, sampling, and sequencing) in the error simulation stage. Finally, the corresponding decoding process realizes the conversion of DNA sequence to binary sequence. All the above simulation processes correspond to an analysis report will provide guides for better experiment design for researchers’ convenience. In short, DNA Storage Designer is an easy-to-use and automatic web-server for simulating DNA storage experiments, which could advance the development of DNA storage-related research. And it is freely available for all users at: https://dmci.xmu.edu.cn/dna/.“