Ack,abs,con,concl,ref of DNA Storage

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ACKNOWLEDGEMENT
I take this opportunity to present my vote of thanks to all those who really acted as
lightening pillars to enlighten my way to successful and satisfactory completion of this
project report.
I have gained immense knowledge about “GI-FI TECHNOLOGY“. I am grateful to the
teachers who guided me and taught me during this training period. I am much obliged to
respected Mr. RakeshSambyal H.O.D INFORMATION TECHNOLOGY for
endowing me this splendiferous opportunity to increase my skillsets.
Name: Khalid Majeed Mir
Roll No.: 321/14

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Abstract
Demand for data storage is growing exponentially, but the capacity of existing storage
media is not keeping up. Using DNA to archive data is an attractive possibility because it
is extremely dense, with a raw limit of 1 exabyte/mm3 (109 GB/mm3), and long-lasting,
with observed half-life of over 500 years. This paper presents an architecture for a DNA-
based archival storage system. It is structured as a key-value store, and leverages
common biochemical techniques to provide random access. We also propose a new
encoding scheme that offers controllable redundancy, trading off reliability for density.
We demonstrate feasibility, random access, and robustness of the proposed encoding
with wet lab experiments involving 151kB of synthesized DNA and a 42kB
randomaccess subset, and simulation experiments of larger sets calibrated to the wet lab
experiments. Finally, we highlight trends in biotechnology that indicate the impending
practicality of DNA storage for much larger datasets.
Categories and Subject Descriptors B.3.2 [Memory Structures]: Design Styles—Mass
storage; J.3 [Life and Medical Sciences]: Biology and genetics

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CONTENT Page No.
CHAPTER-1 INTRODUCTION 1-3
CHAPTER-2 BACKGROUND ON DNA MANIPULATION 4-6
2.1 DNA Basic 4
2.2 Selective DNA amplification with polymerase chain reaction (PCR) 4
2.3DNA Syntheis 5
2.4DNA Sequencing 5
2.5Sequencing and synthesis improvement projections 6
CHAPTER-3 A DNA STORAGE SYSTEM 7-10
3.1 Overview 7-8
3.2 Interface and Addressing 9
3.3 System Operation 9
CHAPTER:-4 REPRESENTINGDATAIN DNA 11-14
4.1 Representation 11
4.2 Data Format 12
4.2.1Address 13
4.2.2Primers. 14
4.2.3Random Access. 14
CHAPTER:-5 ENCODINGS FOR RELIABLE STORAGE 15-18
5.1Existing Encodings 15
5.2Goldman Encoding. 16
5.3 XOR Encoding 16
5.4Tunable Redundancy 17
5.5 Factors in Encoding Design 18

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CHAPTER-6 EXPERIMENTS 19-21
6.1 Materials and Method 19
6.2 Results 20
6.2.1 Fle Recovery. 20
6.2.2 Sequencing Depth. 20
6.2.3Reduced Sequencing Depth. 21
6.2.4Naive Encoding. 21
CHAPTER:-7 SIMULATION 22-25
7.1Reliability and Density. 22
7.2Density and Strand Length. 24
7.3Decay. 24
CHAPTER:-8 DISCUSSION AND FUTURE WORK 26-29
8.1The Real Source of Errors. 26
8.2Synthesis Efficiency. 27
8.3Avoiding Bad Sequences. 28
CHAPTER:-9 RELATED WORK ENCODING 30
ACKNOWLEDGEMENT i
ABSTRACT ii
CONTENTS iii-iv
LIST OF FIGURES v
CONCLUSIONS vi
REFERENCES vii

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LIST OF FIGURES
Fig No. Discription Page No.
1 Carlson curves 6
2 NA storage as the bottom level of the storage hierarchy 7
3 Overview of a DNA storage system. 8
4 Overview of a DNA storage system operation as a key-value store 8
5 Translating binary data to DNA nucleotides via a Huffman code 11
6 Encoding a stream of binary data as a stream of nucleotides 12
7 An overview of the DNA data encoding format 13
8 An encoding proposed by Goldman et al. 16
9 Our proposed encoding incorporates redundancy 16
10 Distribution of sequencing depths over all encoded strands 20
11 Reliability of encoded data 22
12 Density of different encodings as a function 23
13 Average number of copies of sequences required 24
14 Distribution of DNA error 26
15 Expected and observed distributions of strand length from DNA synthesis 27
16 A hairpin, 28

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Conclusion
DNA-based storage has the potential to be the ultimate archival storage solution: it is
extremely dense and durable. While this is not practical yet due to the current state of
DNA synthesis and sequencing, both technologies are improving at an exponential
rate with advances in the biotechnology industry. Given the impending limits of
silicon technology, we believe that hybrid silicon and biochemical systems are worth
serious consideration: time is ripe for computer architects to consider incorporating
biomolecules as an integral part of computer design. DNA-based storage is one clear
example of this direction. Biotechnology has benefited tremendously from progress in
silicon technology developed by the computer industry; perhaps now is the time for
the computer industry to borrow back from the biotechnology industry to advance the
state of the art in computer systems.
References
[1] http://www.nature.com/news/how-dna-could-store-all-the- world-s-data-1.20496
[2]https://homes.cs.washington.edu/~bornholt/papers/dnastorageasplos16.pdf
[3]//www.idc.com/downloads/where_is_storage_infographic_243338.pdf
[4]http://www.synthesis.cc/2014/02/time-for-new-cost-curves-2014.html

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[5]http://www.datacenterknowledge.com/archives/2013/01/18/facebook-builds-
newdata-centers-for-cold-storage/
[6]http://www.extremetech.com/computing/159245-new-optical-laser-canincrease-dvd-
storage-up-to-one-petabyte