DNA

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This is a Python script to encode/decode arbitrary computer files into DNA sequences. It is a straight implementation of a method published in this_ Nature’s paper. The details of the method can be found in the Supplementary Information_ report. Another version of report can be found here_. The source code organization follows the article steps and nomenclature, so it should be easy to understand.

How to use

Install it using pip:

.. code-block:: console

$ sudo pip install file2dna

The installed script will be called dna and accepts four types of operations passed as arguments together with the file name:

.. code-block:: console

$ dna -h
usage: dna [-h] [-e | -s | -d | -j] file

positional arguments:
  file        File to be encoded/decoded.

optional arguments:
  -h, --help  show this help message and exit
  -e          encode file and save it as .dna
  -s          encode file and save it as .splitted.zip
  -d          decode .dna file and save as .decoded
  -j          decode .splitted.zip file and save it as .decoded

As an example, we can decode one the files_ encoded by the authors of the paper. Suppose you have cloned this repo with its examples folder:

.. code-block:: console

$ dna -d examples/DNA_versions/wssnt10.txt.dna

To see the decoded file:

.. code-block:: console

$ cat examples/DNA_versions/wssnt10.txt.decoded

Additional information about this work

Nick Goldman talking about DNA Hard Drivers at the WEF2015_

Goldman group DNA storage_

Emily Leprous talking about DNA storage_

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA_

Additional information about DNA storage in general

Hidding messages in DNA microdots_

An improved Huffman coding method for archiving text, images, and music characters in DNA_

Bacterial based storage and encryption device_

The Xenotext Experiment_

If You Were a Secret Message, Where in the Human Genome Would You Hide?_

Store digital files for eons in silica-encased DNA_

.. _this: http://www.nature.com/nature/journal/v494/n7435/full/nature11875.html .. _Supplementary Information: http://www.nature.com/nature/journal/v494/n7435/extref/nature11875-s2.pdf .. _files: http://www.ebi.ac.uk/goldman-srv/DNA-storage/orig_files/ .. _found here: http://www.ebi.ac.uk/sites/ebi.ac.uk/files/groups/goldman/file2features_2.0.pdf .. _Goldman group DNA storage: http://www.ebi.ac.uk/research/goldman/dna-storage .. _Emily Leprous talking about DNA storage: https://vimeo.com/119612296 .. _Nick Goldman talking about DNA Hard Drivers at the WEF2015: https://www.youtube.com/watch?v=tBvd7OSDGgQ .. _Hidding messages in DNA microdots: http://www.researchgate.net/profile/Carter_Bancroft/publication/12921709_Hiding_messages_in_DNA_microdots/links/0922b4f2ac1d18eb73000000.pdf .. _An improved Huffman coding method for archiving text, images, and music characters in DNA: http://www.biotechniques.com/multimedia/archive/00055/Supplementary_Materi_55848a.pdf .. _Towards practical, high-capacity, low-maintenance information storage in synthesized DNA: http://courses.cs.vt.edu/cs2104/Spring13Onufriev/LectureNotes/DNA.storage.pdf .. _Bacterial based storage and encryption device: http://2010.igem.org/files/presentation/Hong_Kong-CUHK.pdf .. _The Xenotext Experiment: http://triplehelixblog.com/2014/01/the-xenotext-experiment/ .. _If You Were a Secret Message, Where in the Human Genome Would You Hide?: http://nautil.us/blog/-if-you-were-a-secret-message-where-in-the-human-genome-would-you-hide .. _Store digital files for eons in silica-encased DNA: http://hackaday.com/2015/02/21/store-digital-files-for-eons-in-silica-encased-dna