This file gives instructions on encoding and decoding information on DNA segments. The code was written for the publication:
``Robust chemical preservation of digital information on DNA in silica with error-correcting codes'', by R. N. Grass, R. Heckel, M. Puddu, D. Paunescu, and W. J. Stark, Angewandte Chemie International Edition, Vol. 54, Nr. 8, pp. 2552–2555, February 2015.
In the following, we describe an example workflow that takes part of Archimedes Book, encodes it to DNA segments, and decodes it in order to recover the information.
To start, change to the folder ./simulate and execute the following commands:
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compile texttodna: (make sure that the correct path to BOOST_LIB is provided in the Makefile)
`make texttodna'
The program texttodna can be used to encode data, map it to DNA segments, and to recover the data from the DNA segments as follows.
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The following command takes the text in the file archimedes_short.txt, encodes it on DNA segments, and stores the segments in arch_short_dna.txt:
./texttodna --encode --input=../data/archimedes_short.txt --output=../data/arch_short_dna.txt -
The following command takes random lines (DNA segments) from arch_short_dna.txt, introduces errors, and saves the resulting file to arch_short_drawnseg.txt:
./texttodna --disturb --input=../data/arch_short_dna.txt --output=../data/arch_short_drawnseg.txt -
The following command decodes the perturbed data in arch_short_dna.txt, and writes the result to arch_short_rec.txt; this should recover the original text:
./texttodna --decode --numblocks=3 --input=../data/arch_short_drawnseg.txt --output=../data/arch_short_rec.txt
The code is written in C++, and compillation requires installation of the boost libary.
sudo apt-get install gcc
sudo apt-get install make
sudo apt-get install libboost-all-dev
All files are provided under the terms of the Apache License, Version 2.0, see the included file "apache_licence_20" for details.