DNA Storage Designer: A practical and holistic design platform for storing digital information in DNA sequence

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/. Author summaryDNA storage technology is an emerging and promising storage technology. At the same time, DNA storage is an interdisciplinary technology that requires researchers to know both computer cryptography and biological experiments knowledge. However, DNA storage experiments are costly and lengthy, many studies have been prevented by the lack of a comprehensive design and evaluation platform to guide DNA storage experiments. Herein, we introduce DNA Storage Designer, the first integrated and practical web server for providing the simulation of the whole process of DNA storage application, from encoding, error simulation during preservation, to decoding. In the encoding process, we not only provided the coding DNA sequences but also analyzed the sequence stability. In the error simulation process, we simulated as many experimental situations as possible, such as different mutation probabilities of DNA sequences due to being stored in different bacteria hosts or different sequencing platforms. The platform provides high freedom in that users could not only encode their files and conduct the entire operation but also could upload FASTA files and only simulate the sustaining process of sequences and imitate the mutation errors together with distribution changes of sequences.