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About scikit-bio
================

scikit-bio (canonically pronounced *sigh-kit-buy-oh*) is a library for working with biological data in Python. scikit-bio is open source BSD-licensed software that is currently under active development.


Adoption
--------

Some of the projects that we know of that are using scikit-bio are:

- `QIIME 2 <https://qiime2.org/>`_, `Qiita <https://qiita.ucsd.edu/>`_, `Emperor <https://biocore.github.io/emperor/>`_, `tax2tree <https://github.com/biocore/tax2tree>`_, `ghost-tree <https://github.com/JTFouquier/ghost-tree>`_, `Platypus-Conquistador <https://github.com/biocore/Platypus-Conquistador>`_, `An Introduction to Applied Bioinformatics <https://readiab.org>`_.


License
-------

scikit-bio is available under the new BSD license. See :repo:`LICENSE.txt <blob/main/LICENSE.txt>` for scikit-bio's license, and the :repo:`licenses directory <tree/main/licenses>` for the licenses of third-party software that is (either partially or entirely) distributed with scikit-bio.


Team
----

Our core development team consists of three lead developers: **Dr. Qiyun Zhu** at Arizona State University (ASU) (@qiyunzhu), **Dr. James Morton** at Gutz Analytics (@mortonjt), and **Dr. Daniel McDonald** at the University of California San Diego (UCSD) (@wasade), one software engineer: **Matthew Aton** (@mataton) and one bioinformatician: **Dr. Lars Hunger** (@LarsHunger). **Dr. Rob Knight** at UCSD (@rob-knight) provides guidance on the development and research. **Dr. Greg Caporaso** (@gregcaporaso) at Northern Arizona University (NAU), the former leader of the scikit-bio project, serves as an advisor on the current project.


Credits
-------

We thank the many contributors to scikit-bio. A complete :repo:`list of contributors <graphs/contributors>` to the scikit-bio codebase is available at GitHub. This however may miss the larger community who contributed by testing the software and providing valuable comments, who we hold equal appreciation to.

Wanna contribute? We enthusiastically welcome community contributors! Whether it's adding new features, improving code, or enhancing documentation, your contributions drive scikit-bio and open-source bioinformatics forward. Start your journey by reading the :doc:`Contributor's guidelines <contribute>`.


Funding
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The development of scikit-bio is currently supported by the U.S. Department of Energy, Office of Science under award number `DE-SC0024320 <https://genomicscience.energy.gov/compbioawards2023/#Expanding>`_, awarded to Dr. Qiyun Zhu at ASU (lead PI), Dr. James Morton at Gutz Analytics, and Dr. Rob Knight at UCSD.

.. image:: _static/img/doe_logo_green.png
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   :alt: DOE SC logo

.. image:: _static/img/doe_logo_white.png
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   :alt: DOE SC logo

.. The DOE SC logo was downloaded from: https://science.osti.gov/About/Resources/Logos
.. The webpage stats the following usage policy: "The DOE SC co-Branded logos should only be obtained directly from the download links on this page. Only unaltered usage is permitted. Usage does not require explicit permission. The logos shall not be used in any manner that falsely implies employment by, or affiliation with, the U.S. Department of Energy Office of Science. Additionally, the DOE SC co-Branded logo may not be used for commercial purposes, including but not limited to endorsement of products or services."


Citation
--------

If you use scikit-bio for any published research, please see our `Zenodo page <https://zenodo.org/record/8209901>`_ for how to cite.


Collaboration
-------------

For collaboration inquiries and other formal communications, please reach out to **Dr. Qiyun Zhu** at qiyun.zhu@asu.edu. We welcome academic and industrial partnerships to advance our mission.


Branding
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The logo of scikit-bio was created by `Alina Prassas <https://cargocollective.com/alinaprassas>`_. Vector and bitmap image files are available at the :repo:`logos <tree/main/logos>` directory.


Pre-history
-----------

scikit-bio began from code derived from `PyCogent <https://github.com/pycogent/pycogent>`_ and `QIIME <https://github.com/biocore/qiime>`_, and the contributors and/or copyright holders have agreed to make the code they wrote for PyCogent and/or QIIME available under the BSD license. The contributors to PyCogent and/or QIIME modules that have been ported to scikit-bio are listed below:

.. dropdown::

   Rob Knight (@rob-knight), Gavin Huttley (@gavinhuttley), Daniel McDonald (@wasade), Micah Hamady, Antonio Gonzalez (@antgonza), Sandra Smit, Greg Caporaso (@gregcaporaso), Jai Ram Rideout (@jairideout), Cathy Lozupone (@clozupone), Mike Robeson (@mikerobeson), Marcin Cieslik, Peter Maxwell, Jeremy Widmann, Zongzhi Liu, Michael Dwan, Logan Knecht (@loganknecht), Andrew Cochran, Jose Carlos Clemente (@cleme), Damien Coy, Levi McCracken, Andrew Butterfield, Will Van Treuren (@wdwvt1), Justin Kuczynski (@justin212k), Jose Antonio Navas Molina (@josenavas), Matthew Wakefield (@genomematt) and Jens Reeder (@jensreeder).
