Chamaeleo is currently the only collection focused on different codec methods for DNA storage. This kit is mainly developed and operated by Synthetic Platform of BGI-Research, for a detailed list of authors, see authors.md. It provides you a chance to use the classical DNA encoding and decoding methods to save files into DNA sequences or load them from DNA sequences.
Here, we provide guidance for different visitors. We recommend that you read the user manual first and then the contributor manual.
- If you are a learner or a engineer, please pay attention to the user manual, see user_manual.md.
- If you want to be a contributor, please pay attention to the contributor manual, see contributor_manual.md.
Chamaeleo has undergone major adjustments before. Versions smaller than 1.3 are unstable. If you insist on using earlier versions, you may get unexpected results.
You can find the latest version in: (1) GitHub release here, (2) PyPI website here. Simply, installation through the command line (pip install Chamaeleo) is the easiest way to obtain the latest and most stable version of Chamaeleo.
As a kind suggestion, when you first touch this package, pipeline cases in the examples folder (please note here) may help you get started well.
Sometimes the results obtained by Chamaeleo do not meet your expectations. We recommend that you can check by following steps: (1) related length settings include segment length, index length, and error-correction length. (2) the method for calculating information density. For the built-in calculation method, it is bound inside the class AbstractCodingAlgorithm(please note here).
In some cases, you may encounter software errors. If you can't solve the problem, please describe your problem here or sent your problem to zhanghaoling@genomics.cn.
Here we declare the digital file used in our library for testing.
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DNA Fountain Input Files.tar: http://files.teamerlich.org/dna_fountain/dna-fountain-input-files.tar.gz. Erlich, Y., & Zielinski, D. (2017). DNA Fountain enables a robust and efficient storage architecture. Science, 355(6328), 950-954.
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Microsoft Winmine.exe: https://www.microsoft.com/en-us/p/microsoft-minesweeper/9wzdncrfhwcn?activetab=pivot:overviewtab. 2012 Microsoft Corporation.
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A Tale of Two Cities.pdf: https://epdf.pub/a-tale-of-two-cities-penguin.html. Fictionwise.
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The Wandering Earth.pdf: https://epdf.pub/the-wandering-earth.html. Beijing Guomi Digital Technology Co., Ltd.
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For Elise.wma: https://www.youtube.com/watch?v=_mVW8tgGY_w. Youtube.
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Summer.mp3: https://www.youtube.com/watch?v=J7or0noYfMA. Youtube.
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Mona Lisa.jpg: https://en.wikipedia.org/wiki/Mona_Lisa. wiki.
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United Nations Flag.bmp: https://www.britannica.com/topic/flag-of-the-United-Nations
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Exiting the Factory.flv: https://www.youtube.com/watch?v=DEQeIRLxaM4. Youtube.
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I have a Dream.mp4: https://www.youtube.com/watch?v=MgYzJGmBXU8. Youtube.
If you think this repo helps or being used in your research, please consider refer this paper.
Chamaeleo: an integrated evaluation platform for DNA storage
with its English version
Thank you!
English version:
@article{ping2020chamaeleo,
title={Chamaeleo: an integrated evaluation platform for DNA storage},
author={Ping, Zhi and Zhang, Haoling and Chen, Shihong and Zhuang, Qianlong and Zhu, Sha and Shen, Yue},
journal={Synthetic Biology Journal},
year={2020},
pages={1-15},
}
Chinese version:
@article{ping2020chamaeleo,
title={Chamaeleo:DNA存储碱基编解码算法的可拓展集成与系统评估平台},
author={平质, 张颢龄, 陈世宏, 倪鸣, 徐讯, 朱砂, 沈玥},
journal={合成生物学},
year={2020},
pages={1-15},
}