title: The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module.
abstract: The size of digital data is ever increasing and is expected to grow to 40,000 EB by 2020, yet the estimated global information storage capacity in 2011 is <300 EB, indicating that most of the data are transient. DNA, as a very stable nano-molecule, is an ideal massive storage device for long-term data archive. The two most notable illustrations are from Church et al. and Goldman et al., whose approaches are well-optimized for most sequencing platforms - short synthesized DNA fragments without homopolymer. Here, we suggested improvements on error handling methodology that could enable the integration of DNA-based computational process, e.g., algorithms based on self-assembly of DNA. As a proof of concept, a picture of size 438 bytes was encoded to DNA with low-density parity-check error-correction code. We salvaged a significant portion of sequencing reads with mutations generated during DNA synthesis and sequencing and successfully reconstructed the entire picture. A modular-based programing framework - DNAcodec with an eXtensible Markup Language-based data format was also introduced. Our experiments demonstrated the practicability of long DNA message recovery with high error tolerance, which opens the field to biocomputing and synthetic biology.
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong , Hong Kong , China ; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong , Hong Kong , China ; State Key Laboratory of Argobiotechnology, The Chinese University of Hong Kong , Hong Kong , China ; Department of Computer Science and Engineering, The Chinese University of Hong Kong , Hong Kong , China.
authors.forename: Aldrin Kay-Yuen
authors.initials: AK
authors.lastname: Yim
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong , Hong Kong , China ; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong , Hong Kong , China.
authors.forename: Allen Chi-Shing
authors.initials: AC
authors.lastname: Yu
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong , Hong Kong , China ; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong , Hong Kong , China.
authors.forename: Jing-Woei
authors.initials: JW
authors.lastname: Li
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong , Hong Kong , China.
authors.forename: Ada In-Chun
authors.initials: AI
authors.lastname: Wong
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong , Hong Kong , China.
authors.forename: Jacky F C
authors.initials: JF
authors.lastname: Loo
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong , Hong Kong , China.
authors.forename: King Ming
authors.initials: KM
authors.lastname: Chan
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong , Hong Kong , China.
authors.forename: S K
authors.initials: SK
authors.lastname: Kong
authors.affiliation: Department of Computer Science and Engineering, The Chinese University of Hong Kong , Hong Kong , China.
authors.forename: Kevin Y
authors.initials: KY
authors.lastname: Yip
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong , Hong Kong , China ; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong , Hong Kong , China ; State Key Laboratory of Argobiotechnology, The Chinese University of Hong Kong , Hong Kong , China ; Department of Computer Science and Engineering, The Chinese University of Hong Kong , Hong Kong , China.
authors.forename: Ting-Fung
authors.initials: TF
authors.lastname: Chan
keywords: DNA-based computational process; DNA-based information storage; biocomputing; error-tolerating module; synthetic biology