R&D: How to Enable Index Scheme for Reducing Writing Cost of DNA Storage on Insertion and Deletion

ACM Transactions on Embedded Computing Systems has published an article written by Yi-Syuan Lin, Department of Computer Science, National Tsing Hua University, Taiwan, Yu-Pei Liang, Tseng-Yi Chen, Department of Computer Science and Information Engineering, National Chung Cheng University, Taiwan, Yuan-Hao Chang, Institute of Information Science, Academia Sinica, Taiwan, Shuo-Han Chen, Department of Computer Science, National Taipei University of Technolgoy, Taiwan, Hsin-Wen Wei, Department of Electrical Engineering, Tamkang University, Taiwan, and Wei-Kuan Shih, Department of Computer Science, National Tsing Hua University, Taiwan.

Abstract: “Recently, the requirement of storing digital data has been growing rapidly; however, the conventional storage medium cannot satisfy these huge demands. Fortunately, thanks to biological technology development, storing digital data into deoxyribonucleic acid (DNA) has become possible in recent years. Furthermore, because of the attractive features (e.g., high storing density, long-term durability, and stability), DNA storage has been regarded as a potential alternative storage medium to store massive digital data in the future. Nevertheless, reading and writing digital data over DNA requires a series of extremely time-consuming processes (i.e., DNA sequencing and DNA synthesis). More specifically, among the two costs, the writing cost is the predominant cost of DNA data storage system. Therefore, to enable efficient DNA storage, this paper proposes an index management scheme for reducing the number of accesses to DNA storage. Additionally, this paper introduces a new DNA data encoding format with VERA (Version Editing Recovery Approach) to reduce the total writing bits while inserting and deleting the data. To the best of our knowledge, this work is the first work to provide a total data management solution for DNA storage. According to the experimental results, the proposed design with VERA can reduce the cost by 77% and improve the performance by 71% compared to the append-only methods.“