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<section id="about-scikit-bio">
<h1>About scikit-bio<a class="headerlink" href="#about-scikit-bio" title="Link to this heading">#</a></h1>
<p>scikit-bio (canonically pronounced <em>sigh-kit-buy-oh</em>) is a library for working with biological data in Python. scikit-bio is open source BSD-licensed software that is currently under active development.</p>
<section id="adoption">
<h2>Adoption<a class="headerlink" href="#adoption" title="Link to this heading">#</a></h2>
<p>Some of the projects that we know of that are using scikit-bio are:</p>
<ul class="simple">
<li><p><a class="reference external" href="https://qiime2.org/">QIIME 2</a>, <a class="reference external" href="https://qiita.ucsd.edu/">Qiita</a>, <a class="reference external" href="https://biocore.github.io/emperor/">Emperor</a>, <a class="reference external" href="https://github.com/biocore/tax2tree">tax2tree</a>, <a class="reference external" href="https://github.com/JTFouquier/ghost-tree">ghost-tree</a>, <a class="reference external" href="https://github.com/biocore/Platypus-Conquistador">Platypus-Conquistador</a>, <a class="reference external" href="https://readiab.org">An Introduction to Applied Bioinformatics</a>.</p></li>
</ul>
</section>
<section id="license">
<h2>License<a class="headerlink" href="#license" title="Link to this heading">#</a></h2>
<p>scikit-bio is available under the new BSD license. See <a class="extlink-repo reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/LICENSE.txt">LICENSE.txt</a> for scikit-bio’s license, and the <a class="extlink-repo reference external" href="https://github.com/scikit-bio/scikit-bio/tree/main/licenses">licenses directory</a> for the licenses of third-party software that is (either partially or entirely) distributed with scikit-bio.</p>
</section>
<section id="team">
<h2>Team<a class="headerlink" href="#team" title="Link to this heading">#</a></h2>
<p>Our core development team consists of three lead developers: <strong>Dr. Qiyun Zhu</strong> at Arizona State University (ASU) (@qiyunzhu), <strong>Dr. James Morton</strong> at Gutz Analytics (@mortonjt), and <strong>Dr. Daniel McDonald</strong> at the University of California San Diego (UCSD) (@wasade), one software engineer: <strong>Matthew Aton</strong> (@mataton) and one bioinformatician: <strong>Dr. Lars Hunger</strong> (@LarsHunger). <strong>Dr. Rob Knight</strong> at UCSD (@rob-knight) provides guidance on the development and research. <strong>Dr. Greg Caporaso</strong> (@gregcaporaso) at Northern Arizona University (NAU), the former leader of the scikit-bio project, serves as an advisor on the current project.</p>
</section>
<section id="credits">
<h2>Credits<a class="headerlink" href="#credits" title="Link to this heading">#</a></h2>
<p>We thank the many contributors to scikit-bio. A complete <a class="extlink-repo reference external" href="https://github.com/scikit-bio/scikit-bio/graphs/contributors">list of contributors</a> 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.</p>
<p>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 <a class="reference internal" href="contribute.html"><span class="doc">Contributor’s guidelines</span></a>.</p>
</section>
<section id="funding">
<h2>Funding<a class="headerlink" href="#funding" title="Link to this heading">#</a></h2>
<p>The development of scikit-bio is currently supported by the U.S. Department of Energy, Office of Science under award number <a class="reference external" href="https://genomicscience.energy.gov/compbioawards2023/#Expanding">DE-SC0024320</a>, awarded to Dr. Qiyun Zhu at ASU (lead PI), Dr. James Morton at Gutz Analytics, and Dr. Rob Knight at UCSD.</p>
<img alt="DOE SC logo" class="only-light" src="_images/doe_logo_green.png" />
<img alt="DOE SC logo" class="only-dark" src="_images/doe_logo_white.png" />
</section>
<section id="citation">
<h2>Citation<a class="headerlink" href="#citation" title="Link to this heading">#</a></h2>
<p>If you use scikit-bio for any published research, please see our <a class="reference external" href="https://zenodo.org/record/8209901">Zenodo page</a> for how to cite.</p>
</section>
<section id="collaboration">
<h2>Collaboration<a class="headerlink" href="#collaboration" title="Link to this heading">#</a></h2>
<p>For collaboration inquiries and other formal communications, please reach out to <strong>Dr. Qiyun Zhu</strong> at <a class="reference external" href="mailto:qiyun.zhu%40asu.edu">qiyun<span>.</span>zhu<span>@</span>asu<span>.</span>edu</a>. We welcome academic and industrial partnerships to advance our mission.</p>
</section>
<section id="branding">
<h2>Branding<a class="headerlink" href="#branding" title="Link to this heading">#</a></h2>
<p>The logo of scikit-bio was created by <a class="reference external" href="https://cargocollective.com/alinaprassas">Alina Prassas</a>. Vector and bitmap image files are available at the <a class="extlink-repo reference external" href="https://github.com/scikit-bio/scikit-bio/tree/main/logos">logos</a> directory.</p>
</section>
<section id="pre-history">
<h2>Pre-history<a class="headerlink" href="#pre-history" title="Link to this heading">#</a></h2>
<p>scikit-bio began from code derived from <a class="reference external" href="https://github.com/pycogent/pycogent">PyCogent</a> and <a class="reference external" href="https://github.com/biocore/qiime">QIIME</a>, 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:</p>
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<p class="sd-card-text">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).</p>
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