612 lines
24 KiB
HTML
612 lines
24 KiB
HTML
<!doctype html>
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<html>
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
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<!-- Edit me start! -->
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<title>This is where your title goes</title>
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<meta name="description" content=" This is where you put a short description ">
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<meta name="author" content=" Your Name ">
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<!-- Edit me end! -->
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<link rel="stylesheet" href="../reveal.js/dist/reset.css">
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<link rel="stylesheet" href="../reveal.js/dist/reveal.css">
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<link rel="stylesheet" href="../reveal.js/dist/theme/beige.css">
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<!-- Theme used for syntax highlighted code -->
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<link rel="stylesheet" href="../reveal.js/plugin/highlight/monokai.css">
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</head>
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<body>
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<div class="reveal">
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<div class="slides">
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<section>
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<section>
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<script src="https://cdn.logwork.com/widget/countdown.js"></script>
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<a href="https://logwork.com/countdown-2zu8" class="countdown-timer"
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data-style="columns" data-timezone="Europe/Berlin" data-date="2022-04-21 09:00">
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Welcome Session starts in</a>
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Have a ☕!
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</section>
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<section>
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<h2>Research data management<br />👩💻👨💻<br />with DataLad</h2>
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<div style="margin-top:1em;text-align:center">
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<table style="border: none;">
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<tr>
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<td>
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Adina Wagner<br><small><a href="https://twitter.com/AdinaKrik" target="_blank">
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<img data-src="../pics/twitter.png" style="height:30px;margin:0px" />@AdinaKrik</a></small>
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</td>
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<td>
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Michał Szczepanik<br>
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</td>
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</tr>
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<tr>
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<td>
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<img style="height:70px;margin-right:10px" data-src="../pics/fzj_logo.svg" /><br>
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</td>
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<td>
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<small><a href="http://psychoinformatics.de" target="_blank">Psychoinformatics lab</a>,
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<br> Institute of Neuroscience and Medicine (INM-7)<br>
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Research Center Jülich</small><br>
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</td>
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</tr>
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</table>
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</div>
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<br><br><small>
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Slides: <a href="https://github.com/datalad-handbook/course/blob/master/talks/PDFs" target="_blank">
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https://github.com/datalad-handbook/course/</a></small>
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</a>
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</section>
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</section>
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<!--...WORKSHOP INTRODUCTION...-->
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<section>
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<section>
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<h2>welcome!</h2>
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A few logistical things first:
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<ul style="font-size:30px">
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<li class="fragment fade-in-then-semi-out">
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An approximate schedule for today is
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<a href="https://adswa.github.io/dl-workshop/content/welcome/" target="_blank">
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on our companion workshop website</a>.
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</li>
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<li class="fragment fade-in-then-semi-out">
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Feel free to take collaborative, public notes at <a href="https://etherpad.wikimedia.org/p/RDM_with_DataLad" target="_blank">
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etherpad.wikimedia.org/p/RDM_with_DataLad</a>. You can also use this pad for anonymous questions.
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</li>
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<li class="fragment fade-in-then-semi-out">
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We are using a JupyterHub. You should have received credentials in advance via email -
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if not, please raise your hand!
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</li>
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<li class="fragment fade-in-then-semi-out">
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Find the workshop contents (and more) at <a href="https://psychoinformatics-de.github.io/rdm-course/" target="_blank">
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psychoinformatics-de.github.io/rdm-course/ </a>
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</li>
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<li class="fragment fade-in-then-semi-out">
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Let us introduce the workshop organizers...
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</li>
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<li class="fragment fade-in-then-semi-out">
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Some guidelines for the virtual workshop venue...
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</li>
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<ul>
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<li class="fragment fade-in">Please mute yourself when you don't speak</li>
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<li class="fragment fade-in">Make use of the "Raise hand" feature</li>
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<li class="fragment fade-in">Drop out and re-join as you please</li>
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<li class="fragment fade-in">Adhere to the <a href="https://adswa.github.io/dl-workshop/coc/" target="_blank">code of conduct</a> </li>
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</ul>
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</ul>
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</section>
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<section>
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<h2>Questions/interaction throughout the workshop</h2>
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<ul style="font-size:30px">
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<li>
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If you have a question during a lecture, please first type your questions in the chat.
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There are no stupid questions :)
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</li>
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<li>
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It would be great to have lively discussions - unless its interrupting others,
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please feel encouraged to unmute/turn on your video to interact with us.
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</li>
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<li>
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We're happy to discuss specific use cases at the end. Please make a note about them in
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the "Shared notes"
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</li>
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</ul>
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</section>
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<section>
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<h2>Questions/interaction after the workshop</h2>
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<ul>
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If you have a question after the workshop, you can reach out for help:
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<br>
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<ul style="font-size:30px">
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<dt>Reach out to to the <b>DataLad</b> team via</dt>
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<li>
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<a href="https://matrix.to/#/!NaMjKIhMXhSicFdxAj:matrix.org?via=matrix.waite.eu&via=matrix.org&via=inm7.de" target="_blank">
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Matrix</a> (free, decentralized communication app, no app needed).
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We run a weekly Zoom office hour (Thursday, 4pm Berlin time) from this room as well.
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</li>
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<li>
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<a href="https://github.com/datalad/datalad" target="_blank">
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the development repository on GitHub</a>
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</li>
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<br>
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<dt>Reach out to the user community with</dt>
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<li>A question on <a href="https://neurostars.org/" target="_blank">neurostars.org</a>
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with a <code>datalad</code> tag</li>
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<br>
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<dt>Find more user tutorials or workshop recordings</dt>
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<li>On <a href="https://www.youtube.com/channel/datalad" target="_blank">
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DataLad's YouTube channel</a>
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</li>
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<li>
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In the <a href="http://handbook.datalad.org/en/latest/" target="_blank">
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DataLad Handbook </a>
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</li>
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<li>In the <a href="https://psychoinformatics-de.github.io/rdm-course/" target="_blank">DataLad RDM course</a> </li>
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<li>In the <a href="http://docs.datalad.org" target="_blank">Official API documentation</a> </li>
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</ul>
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</ul>
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</section>
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<section>
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<h2>Resources and Further Reading</h2>
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<table style="font-size:30px">
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<tr>
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<td>
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Comprehensive user documentation in the<br>
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DataLad Handbook
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<a href="http://handbook.datalad.org" target="_blank">(handbook.datalad.org)</a>
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</td>
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<td>
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<img src="../pics/logo.svg" height="150">
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</td>
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</tr>
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</table>
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<table style="font-size:30px">
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<tr>
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<td><img src="../pics/artwork/src/enter.svg" height="100"></a></td>
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<td>
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<ul>
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<li>High-level function/command overviews, <br>
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Installation, Configuration, Cheatsheet</li>
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</ul>
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</td>
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</tr>
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<tr>
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<td><img src="../pics/artwork/src/basics.svg" height="100"></td>
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<td>
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<ul>
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<li>Narrative-based code-along course</li>
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<li>Independent on background/skill level, <br>
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suitable for data management novices</li>
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</ul>
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</td>
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</tr>
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<tr>
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<td><img src="../pics/artwork/src/usecases.svg" height="100"></td>
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<td>
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<ul>
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<li>Step-by-step solutions to common <br>
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data management problems, like<br />how to
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make a reproducible paper</li>
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</ul>
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</td>
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</tr>
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</table>
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<p style="font-size:30px">Overview of most tutorials, talks, videos, ... at
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<a href="https://github.com/datalad/tutorials" target="_blank">github.com/datalad/tutorials</a> </p>
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</section>
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<section>
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<h2>Live polling system</h2>
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Please use your phone to scan to QR code, or open the link in a new browser window <br>
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<iframe src="https://www.directpoll.com/r?XDbzPBd3ixYqg8huKIwKuJ7aj5lQw7fByQ4HgMgN",
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style="border: 0" width="900" height="800"></iframe>
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</section>
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<section>
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<h2>What's your mood today?</h2>
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<img src="../pics/sheepscale.png" height="600"><iframe src="https://www.directpoll.com/r?XDbzPBd3ixYqg8huKIwKuJ7aj5lQw7fByQ4HgMgN",
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style="border: 0" width="400" height="600"></iframe>
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</section>
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<section>
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<h2>What's your level of excitement?</h2>
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<img src="../pics/rubberduckscale.png" height="600"><iframe src="https://www.directpoll.com/r?XDbzPBd3ixYqg8huKIwKuJ7aj5lQw7fByQ4HgMgN",
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style="border: 0" width="400" height="600"></iframe>
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</section>
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<section>
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<h2>Video recordings</h2>
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<small>The recording would be edited or stopped to exclude certain or all discussions.<br>
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This poll is unanimous - only if everyone votes "yes" the workshop will be recorded</small>
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<iframe src="https://www.directpoll.com/r?XDbzPBd3ixYqg8huKIwKuJ7aj5lQw7fByQ4HgMgN",
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style="border: 0" width="900" height="800"></iframe>
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</section>
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<section data-background-image="https://www.datalad.org/theme/img/logo/datalad_nav_wide.png"
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data-background-opacity="0.1" data-background-size="400px">
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<h2>What will we do today?</h2>
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<ul style="font-size:30px">
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<li class="fragment fade-in-then-semi-out">
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The workshop centers around
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<a href="http://handbook.datalad.org/r.html?about" target="_blank">DataLad</a> (version 0.16)
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</li>
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<li class="fragment fade-in-then-semi-out">
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We aim to do more than a standard introduction by providing in-depth explanations,
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hands-on exercises, and discussions throughout the workshop
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</li>
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<small><li class="fragment fade-in-then-semi-out">
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(Help us by asking any question that comes up!)<br>
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</li></small>
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<img class="fragment fade-in-then-semi-out" src="../pics/splits.jpg">
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</ul>
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</section>
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</section>
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<!--..Research data management in general..-->
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<section>
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<section>
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<h2>Motivation</h2>
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</section>
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<section data-transition="None">
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<h2>Common problems in science</h2>
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<div class="fragment fade-in" data-fragment-index="1">
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You write a paper about an algorithm, stay up
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late to generate good-looking figures, but you have to tweak parameters and
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display options to make it work AND look good. The next morning, you have no
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idea which parameters produced which figures, and which of the figures
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fits to what you report in the paper.<br>
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<img height="400" src="../pics/turingway/findfiles.png">
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<img height="400" src="../pics/turingway/projectstack.png"</div>
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<imgcredit>Illustration adapted from Scriberia and The Turing Way</imgcredit>
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</section>
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<section data-transition="None">
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<h2>Common problems in science</h2>
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<div class="fragment fade-in" data-fragment-index="1">
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Your research project produces phenomenal results, but your laptop,
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the only place that stores the source code for the results, is
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stolen/breaks<br>
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<img height="700" src="../pics/stolenlaptop.jpg"></div>
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<imgcredit>https://co.pinterest.com/pin/551128073121451139//imgcredit>
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</section>
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<section data-transition="None">
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<h2>Common problems in science</h2>
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<div class="fragment fade-in" data-fragment-index="1">
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A graduate student approaches their supervisor, complaining that the
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supervisors research idea does not work. After weeks of discussion,
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it becomes apparent that oral communication doesn't suffice - the
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student can't sufficiently explain the environment (data, algorithms,
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...) they constructed, and if the supervisor can't enter and use the
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students project there's no way to find a fix.
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<br>
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<img height="500" src="../pics/badsupervision.gif"></div>
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<imgcredit>http://phdcomics.com/comics.php?f=1693</imgcredit>
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</section>
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<section data-transition="None">
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<h2>Common problems in science</h2>
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<div class="fragment fade-in" data-fragment-index="1">
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A Post-doc wrote a script during the PhD that applied a specific
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method to a dataset. Now, with new data and a new project, they
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try to reuse the script, but forgot how it worked.
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<br>
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<img height="500" src="../pics/frustration.jpg"></div>
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<imgcredit>http://phdcomics.com/comics.php?f=1693</imgcredit>
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</section>
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<section data-transition="None">
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<h2>common problems in science</h2>
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<div class="fragment fade-in" data-fragment-index="1">
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You try to recreate results from another lab's published paper.
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You base your re-implementation on everything reported in their paper,
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but the results you obtain look nowhere like the original.
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<br>
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<img height="500" src="../pics/turingway/ReadableCode.png"></div>
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<imgcredit>http://phdcomics.com/comics.php?f=1693</imgcredit>
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</section>
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<section>
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<h2><strike>common</strike> old problems in science</h2>
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<div class="fragment fade-in" data-fragment-index="1">
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All these problems were paraphrased from
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<a href="https://sci-hub.se/https://link.springer.com/chapter/10.1007%2F978-1-4612-2544-7_5" target="_blank">
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Buckheit & Donoho, <b>1995</b></a>
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<br></div>
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<div class="fragment fade-in">Let's do better!</div>
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</section>
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</section>
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<!--...WHAT IS DATALAD...-->
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<section>
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<section data-transition="fade">
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<div><table>
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<tr><dl>
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<img src="../pics/datalad_logo_wide.svg" height="150"><br>
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<b><a href="https://www.datalad.org/" target="_blank"> DataLad</a>
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can help <br> with small or large-scale <br> data management </b>
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<dt></dt>
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</dl></tr>
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<tr><dl class="fragment fade-in">Free, <br> open source, <br> command line tool & Python API </dl></tr>
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</table>
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</div>
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<ul style="vertical-align:middle">
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<br>
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<dt></dt>
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</ul>
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</section>
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<section>
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<h2> <img src="../pics/datalad_logo_wide.svg"></h2>
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<ul>
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<li>A command-line tool, available for all major operating systems
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(Linux, macOS/OSX, Windows), MIT-licensed</li>
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<li>Build on top of <a href="https://git-scm.com/" target="_blank">Git</a>
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and <a href="https://git-annex.branchable.com/" target="_blank">Git-annex</a></li>
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<dt><li>Allows...</li></dt>
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<dt>... version-controlling arbitrarily large content </dt>
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<dd>version control data and software alongside to code!</dd>
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<dt>... transport mechanisms for sharing and obtaining data </dt>
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<dd>consume and collaborate on data (analyses) like software</dd>
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<dt>... (computationally) reproducible data analysis</dt>
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<dd>Track and share provenance of all digital objects</dd>
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<dt>... and <i>much</i> more </dt>
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<li>Completely domain-agnostic</li>
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<br>
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</ul>
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</section>
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<section>
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<h2>Acknowledgements</h2>
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<table>
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<tr style="vertical-align:top">
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<td style="vertical-align:top">
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<dl>
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<dt>Software</dt>
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<dd style="margin-left:5px!important">
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<ul style="margin-left:5px!important">
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<li>Joey Hess (git-annex)</li>
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<li>The DataLad team &
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contributors</li>
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</ul>
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</dd>
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<dt style="margin-top:20px">Illustrations </dt>
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<dd style="margin-left:5px!important">
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<ul style="margin-left:5px!important">
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<li>The Turing Way <br>
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project & Scriberia</li>
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<img src="../pics/bannerthanks.svg">
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</ul>
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</dd>
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</dl>
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</td>
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<td style="vertical-align:top">
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<div style="margin-bottom:-20px;text-align:center"><strong>Funders</strong></div>
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<img style="height:150px;margin-right:50px" data-src="../pics/nsf_2020.png" />
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<img style="height:150px;margin-right:50pxi;margin-left:50px" data-src="../pics/binc.png" />
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<img style="height:150px;margin-left:50px" data-src="../pics/bmbf_2020.png" />
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<img style="height:80px;margin-top:-40px;margin-left:auto;margin-right:auto;width:100%" data-src="../pics/fzj_logo.svg" />
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<div style="margin-top:-20px">
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<img style="height:60px;margin-right:20px" data-src="../pics/erdf.png" />
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<img style="height:60px;margin-right:20px" data-src="../pics/cbbs_logo.png" />
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<img style="height:60px" data-src="../pics/LSA-Logo.png" />
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</div>
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<div style="margin-top:40px;margin-bottom:20px;text-align:center"><strong>Collaborators</strong></div>
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<div style="margin-top:-20px">
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<img style="height:100px;margin:20px" data-src="../pics/hbp_logo.png" />
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<img style="height:100px;margin:20px" data-src="../pics/conp_logo.png" />
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<img style="height:100px;margin:20px" data-src="../pics/vbc_logo.png" />
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</div>
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<div style="margin-top:-40px">
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<img style="height:120px;margin:20px" data-src="../pics/openneuro_logo.png" />
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<img style="height:120px;margin:20px" data-src="../pics/cbrain_logo.png" />
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<img style="height:140px;margin:20px" data-src="../pics/brainlife_logo.png" />
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</div>
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</td>
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</tr>
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</table>
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</section>
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<section>
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<h2>Core concepts & features</h2>
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</section>
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|
|
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<section>
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<h2>Everything happens in DataLad datasets</h2>
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<img src="../pics/artwork/src/dataset.svg" width="600"> <br>
|
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</section>
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|
|
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<section>
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<h2>Dataset = Git/git-annex repository</h2>
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<ul>
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<li>content agnostic</li>
|
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<li>no custom data structures</li>
|
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<li>complete decentralization</li>
|
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<li>Looks and feels like a directory on your computer:</li>
|
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</ul>
|
|
<br>
|
|
<br>
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<img src="../pics/remodnav-ds-nautilus.png" width="500"> <img src="../pics/remodnav-ds-terminal.png" width="500">
|
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<small>File viewer and terminal view of a DataLad dataset</small>
|
|
</section>
|
|
|
|
<section>
|
|
<h2>version control arbitrarily large files</h2>
|
|
<img src="../pics/artwork/src/local_wf.svg" width="600"> <br>
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|
|
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<ul><p class="fragment fade-in">
|
|
Stay flexible:
|
|
<li class="fragment fade-in">Non-complex DataLad core API (easy for data management novices)</li>
|
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<li class="fragment fade-in">Pure Git or git-annex commands (for regular Git or git-annex users, or to use specific functionality)</li>
|
|
</ul></p>
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</section>
|
|
|
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<section>
|
|
<h2>Use a datasets' history</h2>
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|
<img src="../pics/researchlog.png">
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|
<ul>
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<li class="fragment fade-in"> reset your dataset (or subset of it) to a previous state, </li>
|
|
<li class="fragment fade-in"> revert changes or bring them back, </li>
|
|
<li class="fragment fade-in"> find out what was done when, how, why, and by whom </li>
|
|
<li class="fragment fade-in"> Identify precise versions: Use data in the most recent version, or the one from 2018, or... </li>
|
|
</ul>
|
|
</section>
|
|
|
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<section>
|
|
<h2>Consume and collaborate</h2>
|
|
<img src="../pics/artwork/src/collaboration.svg" width="900"> <br>
|
|
</section>
|
|
|
|
<section>
|
|
<h2>machine-readable, re-executable provenance</h2>
|
|
<img src="../pics/artwork/src/reproducible_execution.svg" width="900"> <br>
|
|
</section>
|
|
|
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<section>
|
|
<h2>Seamless nesting and dataset linkage</h2>
|
|
|
|
<img src="../pics/artwork/src/linkage_subds.svg" width="900"> <br>
|
|
<!-- <ul>
|
|
<li class="fragment fade-in" data-fragment-index="2">Overcomes scaling issues with large amounts of files</li>
|
|
<pre class="fragment fade-in" data-fragment-index="2"><code>adina@bulk1 in /ds/hcp/super on git:master❱ datalad status --annex -r
|
|
15530572 annex'd files (77.9 TB recorded total size)
|
|
nothing to save, working tree clean</code></pre>
|
|
<small><a class="fragment fade-in" data-fragment-index="2" href="https://github.com/datalad-datasets/human-connectome-project-openaccess" target="_blank">(github.com/datalad-datasets/human-connectome-project-openaccess)</a></small>
|
|
<li class="fragment fade-in">Modularizes research components for transparency, reuse, and access management</li>
|
|
</ul>
|
|
-->
|
|
</section>
|
|
|
|
<section>
|
|
<h2>Third party integrations</h2>
|
|
<img src="../pics/artwork/src/thirdparty.svg" width="900"> <br>
|
|
<small>Apart from <b>local computing infrastructure</b> (from private laptops to computational clusters),
|
|
datasets can be hosted in major <b>third party repository hosting and cloud storage</b> services.
|
|
More info: Chapter on <a href="http://handbook.datalad.org/en/latest/basics/basics-thirdparty.html" target="_blank">
|
|
Third party infrastructure</a>.</small>
|
|
</section>
|
|
|
|
<section data-transition="None">
|
|
<h3>
|
|
Examples of what DataLad can be used for:
|
|
</h3>
|
|
<ul>
|
|
<li class="fragment fade-in-then-semi-out">
|
|
Behind-the-scenes <b>infrastructure component for data transport and versioning</b>
|
|
(e.g., used by <a href="https://openneuro.org/" target="_blank"> OpenNeuro</a>,
|
|
<a href="https://brainlife.io/" target="_blank"> brainlife.io </a>,
|
|
the <a href="https://conp.ca/" target="_blank">Canadian Open Neuroscience Platform (CONP)</a>,
|
|
<a href="https://mcin.ca/technology/cbrain/" target="_blank"> CBRAIN</a>)</li>
|
|
<img height="800" class="fragment fade-in" src="../pics/openneuro2.gif" alt="a screenrecording of browsing open neuro">
|
|
</ul>
|
|
</section>
|
|
|
|
<section data-transition="None">
|
|
<h3>
|
|
Examples of what DataLad can be used for:
|
|
</h3>
|
|
<ul>
|
|
<li class="fragment fade-in-then-semi-out"> <b>Creating and sharing reproducible, open science</b>: Sharing data, software, code, and provenance </li>
|
|
<img height="800" class="fragment fade-in" src="../pics/shareresearch2.gif" alt="a screenrecording of cloning REMODNAV paper dataset from github">
|
|
</ul>
|
|
|
|
</section>
|
|
|
|
<section data-transition="None">
|
|
<h3>
|
|
Examples of what DataLad can be used for:
|
|
</h3>
|
|
<ul>
|
|
<li> <b>Creating and sharing reproducible, open science</b>: Sharing data, software, code, and provenance </li>
|
|
<img height="800" class="fragment fade-in" src="../pics/openscience.gif" alt="a screenrecording of cloning REMODNAV paper dataset from github">
|
|
</ul>
|
|
|
|
</section>
|
|
|
|
<section data-transition="None">
|
|
<h3>
|
|
Examples of what DataLad can be used for:
|
|
</h3>
|
|
<ul>
|
|
<li class="fragment fade-in-then-semi-out"><b>Central data management</b> and archival system</li>
|
|
<img height="850" class="fragment fade-in" src="../pics/centralmanagement.gif">
|
|
</ul>
|
|
</section>
|
|
|
|
<section data-transition="None">
|
|
<h3>
|
|
Examples of what DataLad can be used for:
|
|
</h3>
|
|
<ul>
|
|
<li class="fragment fade-in-then-semi-out"><b>Scalable computing framework</b> for reproducible science</li>
|
|
<img height="350" class="fragment fade-in" src="../pics/fairly-big.png">
|
|
<img height="500" class="fragment fade-in" src="../pics/ukb_datasets.svg">
|
|
</ul>
|
|
</section>
|
|
|
|
|
|
<section data-transition="None">
|
|
|
|
<h3>... and many more!</h3>
|
|
<br><br><br>
|
|
Let's fire up a terminal and get started with the Basics
|
|
</section>
|
|
</section>
|
|
|
|
|
|
</div>
|
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</div>
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