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[DESCRIPTION]
<p>This is a handout that was created by Code Ocean, Addgene, and protocols.io for the Caltech workshop on reproducibility. For more information and slides from the workshop, please see: <a href="https://codeocean.com/workshop/caltech" target="_blank">https://codeocean.com/workshop/caltech</a>.</p>
<p> </p>
<p>Please feel free to clone and modify it. If you do, would be wonderful to see you share the new resource in this group. Also, please suggest other useful resources.</p>

[GUIDELINES]
<p><span style="font-weight: 400;">Practical tips for reproducibility</span></p>
<p> </p>
<p><strong>1. Plan for reproducibility before you start</strong></p>
<p> </p>
<ul>
<li><strong>Write a study plan or protocol</strong> and track new versions.</li>
<li><strong>Set-up a reproducible project </strong>using an electronic lab notebook to organize and track your work. Avoid saving proprietary file formats.</li>
</ul>
<p> </p>
<p><strong>2. Keep track of things</strong></p>
<p> </p>
<ul>
<li><strong>Preregister</strong> important study design and analysis information. Free tools to help you make your first registration include <a href="https://aspredicted.org/" target="_blank">AsPredicted</a>, <a href="https://osf.io/" target="_blank">Open Science Framework</a>, and <a href="https://cos.io/rr/" target="_blank">Registered Reports</a>. Clinical trials use <a href="https://clinicaltrials.gov/" target="_blank">Clinicaltrials.gov</a>.</li>
<li><strong>Track changes</strong> to your files using version control.</li>
<li><strong>Document</strong> everything done by hand in a README file and data dictionary. <strong>Karl Broman’s Data Organization module:</strong> <a href="http://kbroman.org/dataorg/pages/dictionary.html" target="_blank">http://kbroman.org/dataorg/pages/dictionary.html</a></li>
</ul>
<p> </p>
<p><strong>3. Report your research transparently</strong></p>
<p> </p>
<ul>
<li><strong>Share your protocols and interventions</strong> explicitly and transparently.</li>
<li><strong>Write a transparent report</strong>. Guidelines from the <a href="http://www.equator-network.org/" target="_blank">Equator Network</a> or processes like <a href="https://cos.io/rr/" target="_blank">Registered Reports</a> can help.</li>
</ul>
<p> </p>
<p><strong>4. Archive + share your materials</strong></p>
<p> </p>
<p>   <strong>i. Data</strong></p>
<ul>
<li>Avoid supplementary files, licence, and share your data using a repository. <strong>How to License Research Data</strong>: <a href="http://www.dcc.ac.uk/resources/how-guides/license-research-data" target="_blank">http://www.dcc.ac.uk/resources/how-guides/license-research-data</a>.</li>
</ul>
<p><strong>   ii. Materials &amp; reagents</strong></p>
<ul>
<li>Licence your published materials so they can be reused. <strong>Creative Commons License Picker</strong>: <a href="https://creativecommons.org/choose/" target="_blank">https://creativecommons.org/choose/</a></li>
<li>Deposit reagents with repositories like <a href="https://www.addgene.org/" target="_blank">Addgene</a>, <a href="https://bdsc.indiana.edu/" target="_blank">The Bloomington Drosophila Stock Center</a>, and <a href="https://www.atcc.org/" target="_blank">ATCC</a> to make them easily accessible to other researchers.</li>
</ul>
<p><strong>   iii. Software</strong></p>
<p> </p>
<ul>
<li>Licence your code using <a href="https://codeocean.com/" target="_blank">Code Ocean</a> or <a href="https://github.com/" target="_blank">Github</a>. <strong>Open Source Initiative: About Open Source Licences</strong>: <a href="https://opensource.org/licenses" target="_blank">https://opensource.org/licenses</a>.</li>
</ul>
<p> </p>
<p><strong>5. Further reading:</strong></p>
<p> </p>
<ul>
<li style="font-weight: 400;"><strong>Ten Simple Rules for Reproducible Computational Research</strong><span style="font-weight: 400;">: </span><a href="&quot;http://journals.plos.org/ploscompbiol/article?" target="_blank"><span style="font-weight: 400;">http://journals.plos.org/ploscompbiol/article?</span></a></li>
<li style="font-weight: 400;"><strong>Reproducibility in Science</strong><span style="font-weight: 400;">: </span><a href="http://ropensci.github.io/reproducibility-guide/" target="_blank"><span style="font-weight: 400;">http://ropensci.github.io/reproducibility-guide/</span></a></li>
<li style="font-weight: 400;"><strong>Open Science MOOC</strong><span style="font-weight: 400;">: </span><span style="font-weight: 400;"><a href="https://opensciencemooc.eu/" target="_blank">https://opensciencemooc.eu/</a></span></li>
<li style="font-weight: 400;"><strong>Tools and Resources for Reproducibility Series at protocols.io: </strong><a href="https://www.protocols.io/groups/tools-and-resources-for-reproducibility" target="_blank">https://www.protocols.io/groups/tools-and-resources-for-reproducibility</a></li>
</ul>

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