455 lines
20 KiB
HTML
455 lines
20 KiB
HTML
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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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<title>OHBM 2026 Traintrack</title>
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<meta name="description" content=" OHBM 2026 Traintrack ">
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<meta name="author" content=" Adina Wagner ">
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<link rel="stylesheet" href="../reveal.js/dist/reset.css">
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<div class="reveal">
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<div class="slides">
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<!-- Start of slides -->
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<section>
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<section>
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<h2>2026 OHBM Brainhack-Traintrack<br />👩💻👨💻<br />RDM & Version Control</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><img data-src="../pics/mastodon.svg" style="height:30px;margin:0px" /> <a href="https://mas.to/@adswa" target="_blank">@adswa@mas.to</a></small>
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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;vertical-align:middle" data-src="../pics/fzj_logo.svg" /><br>
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</td>
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<td style="vertical-align:middle">
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<small><br> Institute of Neuroscience and Medicine (INM-7)<br>
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<strong>Research Center Jülich</strong></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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<p style="z-index: 100;position: fixed;background-color:#ede6d5;font-size:35px;box-shadow: 10px 10px 8px #888888;margin-top:0px;margin-bottom:100px;margin-left:1000px">
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<img src="../pics/ohbm26.png" height="200">
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</p><small>
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<br>
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Slides: <a href="https://files.inm7.de/adina/talks/html/ohbm26-brainhack.html#/" target="_blank">files.inm7.de/adina/talks/html/ohbm26-brainhack.html</a>
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</small>
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</section>
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</section>
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<section>
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<section>
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<h2>RDM - what and why?</h2>
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<div class="r-stack">
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<p class="fragment fade-out" data-fragment-index="1">
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<img width="1200" src="../pics/turingway_rdm.png">
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<br><br>
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... ideally, as <a href="https://www.go-fair.org/fair-principles/" target="_blank">F.A.I.R.</a> (<a href="https://doi.org/10.1038/sdata.2016.18" target="_blank">Wilkinson et al., 2016</a>) as possible
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</p>
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<img class="fragment fade-in-then-out" data-fragment-index="1" width="700" src="../pics/carrotsandsticks.png">
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<img class="fragment fade-in-then-out" data-fragment-index="2" height="700" src="../pics/sidney_harris_miracle.jpg">
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<p> <img class="fragment fade-in-then-out" data-fragment-index="3" src="../pics/reallifeexample.png" style="box-shadow: 10px 10px 8px #888888;height=200px" height="200"><br>
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<img class="fragment fade-in-then-out" data-fragment-index="3" src="../pics/drive.png" s height="300"><br></p>
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<img class="fragment fade-in-then-out" data-fragment-index="4" src="../pics/ownlegacycode_phd.png" height="400">
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<img class="fragment fade-in-then-out" data-fragment-index="5" src="../pics/frustration2.gif" height="200"><br>
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</div>
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<div class="r-stack">
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<p class="fragment fade-in-then-out" data-fragment-index="1">
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Funders & publishers require it <br></p>
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<p class="fragment fade-in-then-out" data-fragment-index="2">
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Scientific peers & the public increasingly expect it</p>
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<p class="fragment fade-in-then-out" data-fragment-index="3">
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Win over academic staff (librarians, system administrators)</p>
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<p class="fragment fade-in-then-out" data-fragment-index="4">
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Your future self will be grateful</p>
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<p class="fragment fade-in-then-out" data-fragment-index="5">
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Without good RDM, any project becomes dreadful.</p>
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</div>
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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>
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You write a paper and stay up late to generate nice figures.
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But you have to tweak parameters & display options to make it work AND look good.
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<br>The next morning, you have <strong>no idea which parameters produced which figures, and which of the figures
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fits to what you report in the paper</strong>.<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>
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Your research project produces phenomenal results, but your laptop,
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<strong>the only place that stores the source code </strong> for the results, is
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<strong>stolen/breaks</strong> <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>
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A student approaches their supervisor and complains that the
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research idea does not work. But <strong>oral communication doesn't help</strong> - the
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student can't sufficiently explain their environment (data, algorithms,
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...), and <strong>if the supervisor can't explore the students project there's no way to find a fix.</strong>
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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>
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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 <strong>forgot how it worked</strong>.
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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>
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You try to recreate results from another lab's published paper.
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You base your <strong>re-implementation</strong> on everything reported in their paper,
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but the results you obtain <strong>look nowhere like the original</strong>.
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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>Sounds familiar?</h2>
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Show off hands: Did you encounter any of those in your work so far?
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<br><br>
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<div class="fragment fade-in">
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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><br><br>
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<img src="../pics/munafo_nathumbehav_screenshot.png" style="box-shadow: 10px 10px 8px #888888;height=400px" height="400"><br>
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</div>
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<!--<table>
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<tr>
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<td style="width:40%">
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<ol>
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<li>Forgot how own results were generated</li>
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<li>Lost single source of data</li>
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<li>Miscommunication about analysis with supervisor</li>
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<li>Can't get previous code to run</li>
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<li>Failure to reproduce other's work</li>
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<li>Something else related to reproducibility</li>
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</ol>
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</td>
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<td>
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<iframe src="https://directpoll.com/r?XDbzPBd3ixYqg80MlfkonQrATgiLIMEH4Ji3DzR6Pqd3m",
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style="border: 0" width="1500" height="700"></iframe>
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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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<section>
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<section data-transition="None">
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<h2>The road to reproducibility</h2>
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<img src="../pics/reproduciblejourney.png">
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<imgcredit>CC-BY Scriberia and <a href="https://the-turing-way.netlify.app/reproducible-research/rdm.html" target="_blank">
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The Turing Way</a>
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</imgcredit>
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</section>
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<section data-transition="None">
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<dl>
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<dt>The building blocks of a scientific result are rarely static</dt>
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<table>
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<tr>
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<td style="vertical-align:middle">Analysis code evolves<br>
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<small>(Fix bugs, add functions,
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refactor, ...)</small></td>
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<td>
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<img src="../pics/final.png" height="500">
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<imgcredit>Based on Piled Higher and Deeper
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<a href="https://phdcomics.com/comics/archive_print.php?comicid=1531" target="_blank">
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1531
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</a> </imgcredit></td>
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</tr>
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</table>
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</dl>
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<img src="../pics/findfiles.png" height="400">
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<img src="../pics/projectstack.png" height="350">
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<imgcredit >Scriberia and <a href="https://the-turing-way.netlify.app">The Turing Way </a> (CC-BY)</imgcredit>
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</section>
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<section data-transition="None">
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<h2>Version control</h2>
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<table>
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<tr>
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<td>
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<img src="../pics/turingway/ProjectHistory.png" width="500">
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<imgcredit><a href="https://the-turing-way.netlify.app/reproducible-research/vcs/vcs-data.html" target="_blank">
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CC-BY Scriberia & The Turing Way</a>
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</imgcredit>
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</td>
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<td>
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<ul style="font-size:35px">
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<li>keep things organized</li>
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<li>track changes, revert them or go <br>
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back to previous states</li>
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<li>collect and share digital provenance</li>
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<li>collaborate and distribute</li>
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<li>industry standard: <a href="https://git-scm.com" target="_blank">Git</a></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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<img src="../pics/git.png" height="100px">
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<img src="../pics/git-paper.png">
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</section>
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<section data-transition="None">
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<dl>
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<dt>The building blocks of a scientific result are rarely static</dt>
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<table>
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<tr>
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<td style="vertical-align:middle">Data changes <br>
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<small>(errors are fixed, data is extended,<br>
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naming standards change, an analysis <br>
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requires only a subset of your data...)</small></td>
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<td>
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<div class="r-stack">
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<img src="../pics/phd052810s.png" height="400">
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</div>
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<imgcredit>Piled Higher and Deeper
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<a href="https://phdcomics.com/comics/archive_print.php?comicid=1323" target="_blank">
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1323
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</a> </imgcredit></td>
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</tr>
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</table>
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</dl>
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<p class="fragment fade-in" data-fragment-index="2">
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Large data version control (e.g., <a href="https://git-annex.branchable.com" target="_blank">git-annex</a>,
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<a href="https://datalad.org" target="_blank">DataLad</a>)
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<div class="r-stack">
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<img class="fragment fade-in" data-fragment-index="2" src="../pics/tigdata.png">
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<img class="fragment fade-in" data-fragment-index="3" src="../pics/tigdata3.png">
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<img class="fragment fade-in" data-fragment-index="4" src="../pics/tigdata2.png">
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</div>
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</section>
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<section data-transition="None">
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<h2>Leaving a trace </h2>
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<div class="r-stack">
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<p class="fragment fade-out" data-fragment-index="1">"Shit, which version of which script produced these outputs from which version
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of what data?"</p>
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<p class="fragment fade-in" data-fragment-index="1">
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"Shit, why buttons did I click and in which order did I use all those tools?"</p>
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</div>
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<div class="r-stack">
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<p>
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<img class="fragment fade-in-then-out" data-fragment-index="1" src="../pics/manuallabor.png">
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<img class="fragment fade-out" data-fragment-index="2" src="../pics/findfiles.png" height="300">
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<img class="fragment fade-out" data-fragment-index="2" src="../pics/projectstack.png" height="300">
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<imgcredit>CC-BY Scriberia and <a href="https://the-turing-way.netlify.app/reproducible-research/rdm.html" target="_blank">
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The Turing Way</a>
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</imgcredit>
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</p>
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<p>
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<img class="fragment fade-in" data-fragment-index="2" height="200px" src="../pics/file-management-manual-with-text.png">
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<img class="fragment fade-in" data-fragment-index="3" height="200px" src="../pics/documentation.png">
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<img class="fragment fade-in" data-fragment-index="4" height="200px" src="../pics/turingway/MachineReadable.png">
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</p>
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</div>
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<div style="font-size:30px">
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<p class="fragment fade-in" data-fragment-index="2">1) Create an intuitive structure (<a href="https://bids-specification.readthedocs.io/en/stable/" target="_blank">BIDS</a>!!!), and </p>
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<p class="fragment fade-in" data-fragment-index="3">2) write (plenty! of) documentation as you go, and<br></p>
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<p class="fragment fade-in" data-fragment-index="4">
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3) make your processes machine-readable <br><small>Tools and tricks: Perkel, 2020,
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<a href="https://www.nature.com/articles/d41586-020-02462-7" target="_blank">
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checklist for computational reproducibility
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</a></small>
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</p></div>
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</section>
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<section data-transition="None">
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<h2>Methods documentation and provenance</h2>
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Analytic flexibility leads to sizeable variations in results
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<br><small>(see e.g., Carp. 2012 and Botvinik-Nezer, 2020 for examples from neuroimaging)</small><br>
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<img src="../pics/sidney_harris_miracle.jpg" style="box-shadow: 10px 10px 8px #888888;height=500px" height="500"><br>
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<ul>
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<li>provide information on how data came into existence</li>
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<li>change data through documented code, not manually</li>
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<li>relate changes in data to changes in code</li>
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</ul>
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</section>
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</section>
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<section>
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<section data-transition="None">
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<img style="height:150px;margin-bottom:30px" data-src="../pics/datalad_logo_wide.svg"><br>
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<ul style="font-size:37px">
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<li>Domain-agnostic <strong>command-line tool</strong> (+ <strong>graphical user interface</strong>),
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built on top of <a href="https://git-scm.com/" target="_blank">Git</a>
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& <a href="https://git-annex.branchable.com/" target="_blank">Git-annex</a></li>
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<li>10+ year open source project (100+ contributors), available for all major OS</li>
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<li>Major features:</li>
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<dt>Version-controlling arbitrarily large content </dt>
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<dd>Version control data & software alongside to code!</dd>
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<dt>Transport mechanisms for sharing, updating & obtaining data </dt>
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<dd>Consume & 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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<br>
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</ul>
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</section>
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<section data-transition="None">
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<h3>Examples of what DataLad can be used for:</h3>
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<ul>
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<li>
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Install yourself a dataset to hack on from <a href="https://openneuro.org/" target="_blank"> OpenNeuro</a>:
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</li>
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</ul>
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<img height="500" src="../pics/openneuro_new_2.gif" alt="a screenrecording of browsing open neuro">
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</section>
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<section data-transition="None">
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<h3>Examples of what DataLad can be used for:</h3>
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<ul>
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<li>
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Or <b>publish or consume datasets</b> from Git Forges - or many other services
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</li>
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</ul>
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<img height="500" src="../pics/getdata_studyforrest.gif" alt="a screenrecording of cloning studyforrest data from github">
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</section>
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<section data-transition="None">
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<h3>Examples of what DataLad can be used for:</h3>
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<ul>
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<li>
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<b>Create and share reproducible science</b>: Data, software, code, and provenance
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</li>
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</ul>
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<img height="500" src="../pics/remodnavpaper_2.gif" alt="a screenrecording of cloning REMODNAV paper dataset from github">
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</section>
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<section>
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<h2>Further Information</h2>
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<ul>
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<br>
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<ul style="font-size:30px">
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<dt>Reach out 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 (Monday, 2pm Berlin time) from this room as well.
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</li>
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<li>the development repositories on
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<a href="https://github.com/datalad/datalad" target="_blank">
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<s>GitHub</s></a> Codeberg: <a href="https://codeberg.org/datalad">codeberg.org/datalad</a>
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</li>
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<li><strong>Talk to me, Michael, Stephan or Yarik right here, or hack with us!</strong></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 DataLad's YouTube channel <a href="https://www.youtube.com/channel/datalad" target="_blank">
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(www.youtube.com/channel/datalad) </a>
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</li>
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<li>
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In the DataLad Handbook<a href="http://handbook.datalad.org/en/latest/" target="_blank">
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(handbook.datalad.org)</a>
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</li>
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<li>In the DataLad RDM course <a href="https://psychoinformatics-de.github.io/rdm-course/" target="_blank">
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(psychoinformatics-de.github.io/rdm-course)</a> </li>
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<li>In the Official API documentation <a href="http://docs.datalad.org" target="_blank">
|
|
(docs.datalad.org)</a> </li>
|
|
<br>
|
|
<li>On the advantages of decentralized research data management:
|
|
<a href="https://www.degruyter.com/document/doi/10.1515/nf-2020-0037/html" target="_blank">
|
|
doi.org/10.1515/nf-2020-0037
|
|
</a></li>
|
|
</ul>
|
|
</ul>
|
|
<br>
|
|
Install it on your own hardware: <a href="http://handbook.datalad.org/r.html?install" target="_blank">handbook.datalad.org/r.html?install</a>
|
|
</section>
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|
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</section>
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