707 lines
34 KiB
HTML
707 lines
34 KiB
HTML
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<!-- Edit me start! -->
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<title>RDM in Neuroimaging</title>
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<meta name="description" content=" RDM in Neuroimaging ">
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<meta name="author" content=" Adina Wagner ">
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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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<!-- Start of slides -->
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<section>
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<section>
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<h2>Research data management<br />👩💻🧠👨💻<br />for Neuroimagers</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://mas.to/@adswa" target="_blank">@adswa@mas.to</a> <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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</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<br>
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Institute of Experimental Psychology, HHU Düsseldorf</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/QRcode_rdmwin.png" height="200">
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</p>
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<br><br><small>
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Slides: <a href="https://doi.org/10.5281/zenodo.7419377" target="_blank">
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DOI 10.5281/zenodo.7419377</a> (Scan the QR code)
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<br>
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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>Research data management?</h2>
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<div class="r-stack">
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<img class="fragment fade-in-then-out" data-fragment-index="1" width="700" src="../pics/RDM.gif">
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<img class="fragment fade-in-then-out" data-fragment-index="2" height="700" src="../pics/stolenlaptop.jpg">
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<p> <img class="fragment fade-in-then-out" data-fragment-index="3" src="../pics/theverge_excel_genetics_screen1.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/theverge_excel_genetics_screen2.gif" style="box-shadow: 10px 10px 8px #888888;height=300px" height="300"><br>
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<img class="fragment fade-in-then-out" data-fragment-index="3" src="../pics/theverge_excel_genetics_screen3.png" style="box-shadow: 10px 10px 8px #888888;height=200px" height="200"><br>
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</p>
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<p> <img class="fragment fade-in-then-out" data-fragment-index="4" src="../pics/guardian_excel_corona_screen1.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="4" src="../pics/guardian_excel_corona_screen2.png" style="box-shadow: 10px 10px 8px #888888;height=300px" height="300"><br>
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</p>
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<img class="fragment fade-in-then-out" data-fragment-index="5" src="../pics/frontend_vs_backend_paper.png" style="box-shadow: 10px 10px 8px #888888;height=600px">
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</div>
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<p class="fragment fade-in-then-out" data-fragment-index="2">
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<imgcredit> adapted from https://dribbble.com/shots/3090048-Front-end-vs-Back-end</imgcredit>
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</p>
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<small class="fragment fade-in-then-out" data-fragment-index="3"><a href="https://www.theverge.com/2020/8/6/21355674/human-genes-rename-microsoft-excel-misreading-dates" target="_blank">
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www.theverge.com/2020/8/6/21355674/human-genes-rename-microsoft-excel-misreading-dates</a></small>
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</section>
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<section>
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<h2>What exactly is RDM?</h2>
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<img src="../pics/turingway_rdm.png">
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<img src="../pics/datalifecycle_jisc_ccbysand.png">
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<imgcredit>JISC, <a href="https://www.jisc.ac.uk/guides/rdm-toolkit#" target="_blank">www.jisc.ac.uk/guides/rdm-toolkit</a> (CC-BY)</imgcredit>
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</section>
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<section>
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<h2>RDM - for whom?</h2>
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<div class="r-stack">
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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>
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<img src="../pics/wellcome-rdm.png"></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>
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<section>
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<section>
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<h2>RDM in Neuroimaging</h2>
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<ul>
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Some peculiarities of our field...<br><br>
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<ul style="font-size:30px">
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<li class="fragment fade-in" data-fragment-index="1">
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Depending on acquisition hardware and analysis software, some
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data are in proprietary formats (e.g., Neuromag, brain voyager,
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brain vision)
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</li>
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<li class="fragment fade-in" data-fragment-index="1">
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Depending on field, data can be sizeable (e.g., (f)MRI, CT,
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EEG, PET, MEG)
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</li>
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<li class="fragment fade-in" data-fragment-index="1">
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Heterogenous data from complex acquisitions with multiple data
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channels and modalities
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</li>
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<li class="fragment fade-in" data-fragment-index="1">
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Datasets are getting bigger and bigger
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(<a href="https://sci-hub.se/10.1016/j.neuroimage.2017.04.061" target="_blank">Bzdok
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& Yeo, 2017</a>), e.g. multi-modal imaging, behavioral + genetics
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data in HCP (<a href="http://humanconnectome.org/" target="_blank">humanconnectome.org</a>)
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or UKBiobank (<a href="https://www.ukbiobank.ac.uk" target="_blank">ukbiobank.ac.uk/</a>)
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</li>
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<li class="fragment fade-in" data-fragment-index="1">
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Some data fall under General Data Protection Regulation (GDPR)
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</li>
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<li class="fragment fade-in" data-fragment-index="1">Complex, multi-stepped analyses</li>
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</ul>
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</ul><br><br>
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<img class="fragment fade-in" data-fragment-index="1" src="../pics/dataflow.jpg">
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<p class="fragment fade-in" data-fragment-index="2">
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... make RDM more difficult, but also more relevant</p>
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</section>
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</section>
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<section>
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<section>
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<img src="../pics/BIDS_Logo.png" height="100">
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<div class="r-stack">
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<img src="../pics/bids.png" height="600" data-fragment-index="1" class="fragment fade-out">
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<imgcredit class="fragment fade-out" data-fragment-index="1"><a href="https://bids.neuroimaging.io/" target="_blank">BIDS</a>; CC-BY</imgcredit>
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<p>
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<table data-fragment-index="1" class="fragment fade-in-then-out">
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<tr>
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<td style="font-size:25px">
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<pre><code style="max-height:none" data-trim data-noescape>
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├── memento_001
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│ ├── Move_correc_SSS_alignedinitial_nonfitiso
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│ │ ├── 1_memento_001_ml83_mc_transforminitial.fif
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│ │ ├── 2_memento_001_ml83-1_mc_transforminitial.fif
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│ │ ├── 3_memento_001_ml83-2_mc_transforminitial.fif
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│ │ ├── data_fix1.mat
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│ │ ├── data_fix_ft1.mat
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│ │ ├── data_fix_new1.mat
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│ │ ├── data_fix_reduced1.mat
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│ │ ├── delay_photodiode_subject_long_default_realign_only_ICA1.mat
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│ │ ├── memento_results_ICA_newall_alignedinitial228.mat
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│ │ ├── memento_results_ICA_newall_alignedinitial461.mat
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│ │ ├── memento_results_ICA_newall_alignedinitial511.mat
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│ │ ├── num_trials_old_ICA.mat
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│ │ ├── resultfile_probs-1.mat
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│ │ └── trial_out_ind.mat
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│ ├── Move_correc_SSS_realigneddefault_nonfittoiso
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│ │ ├── 1_memento_001_ml83_mc_realigneddefault.fif
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│ │ ├── 2_memento_001_ml83-1_mc_realigned_default.fif
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│ │ ├── 3_memento_001_ml83-2_mc_realigneddefault.fif
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│ │ ├── memento_results_ICA228.mat
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│ │ ├── memento_results_ICA455.mat
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│ │ ├── memento_results_ICA461.mat
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│ │ ├── memento_results_ICA511.mat
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│ │ ├── memento_results_ICA_newall228.mat
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│ │ ├── memento_results_ICA_newall455.mat
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│ │ ├── memento_results_ICA_newall461.mat
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│ │ ├── memento_results_ICA_newall511.mat
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│ │ ├── mri_aligned.mat
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│ │ ├── num_trials_old_ICA.mat
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│ │ ├── outfile_new_all.mat
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│ │ ├── resultfile_new_all.mat
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│ │ ├── template_grid.mat
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│ │ └── trial_out_ind.mat
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│ └── Raw
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│ ├── 1_memento_001_ml83.fif
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│ ├── 2_memento_001_ml83-1.fif
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│ └── memento_001_ml83-2.fif
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</code></pre>
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</td>
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<td style="font-size:25px">
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<pre><code style="max-height:none" data-trim data-noescape>
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├── dataset_description.json
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├── participants.json
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├── participants.tsv
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├── README
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├── sub-001
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│ ├── meg
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│ │ ├── sub-001_acq-calibration_meg.dat
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│ │ ├── sub-001_acq-crosstalk_meg.fif
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│ │ ├── sub-001_coordsystem.json
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│ │ ├── sub-001_task-memento_channels.tsv
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│ │ ├── sub-001_task-memento_events.tsv
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│ │ ├── sub-001_task-memento_log.tsv
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│ │ ├── sub-001_task-memento_meg.json
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│ │ ├── sub-001_task-memento_split-01_meg.fif
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│ │ ├── sub-001_task-memento_split-02_meg.fif
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│ │ └── sub-001_task-memento_split-03_meg.fif
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│ └── sub-001_scans.tsv
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├── sub-002
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│ ├── meg
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│ │ ├── sub-002_acq-calibration_meg.dat
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│ │ ├── sub-002_acq-crosstalk_meg.fif
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│ │ ├── sub-002_coordsystem.json
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│ │ ├── sub-002_task-memento_channels.tsv
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│ │ ├── sub-002_task-memento_events.tsv
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│ │ ├── sub-002_task-memento_log.tsv
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│ │ ├── sub-002_task-memento_meg.json
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│ │ ├── sub-002_task-memento_split-01_meg.fif
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│ │ ├── sub-002_task-memento_split-02_meg.fif
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│ │ └── sub-002_task-memento_split-03_meg.fif
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│ └── sub-002_scans.tsv
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... <img class="fragment fade-in" src="../pics/bidsfeeling.png" height="100px">
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</code></pre>
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</td>
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</tr>
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</table>
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</p>
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<img src="../pics/bidsapps.png" class="fragment fade-in">
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</div>
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BIDS is an established and evolving community standard for a multitude of
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neuroimaging data (MRI, (i)EEG, MEG, ...).
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It defines a data organization, naming schemes for files,
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and meta data descriptors.<br>
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<a href="https://bids.neuroimaging.io/" target="_blank">bids.neuroimaging.io</a>
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</aside>
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</script>
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</section>
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</section>
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<section>
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<section>
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<h3>Open {software,standards}</h3>
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<div class="r-stack">
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<table class="fragment fade-out" data-fragment-index="1">
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<tr style="vertical-align:middle">
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<td style="vertical-align:middle">
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<img style="height:50px;margin-right:50px" data-src="../pics/ohba_logo.png"/>
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<img style="height:50px;margin-right:50px" data-src="../pics/neurodebian.png"/>
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<img style="height:50px;margin-right:50px" data-src="../pics/jupyter_logo.png"/>
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<img style="height:50px;margin-right:50px" data-src="../pics/neologo.png" />
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<img style=height:50px;margin-left:50px" data-src="../pics/mindboggle_logo.png" />
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<img style="height:50px;margin-left:50px" data-src="../pics/psychopy_logo.png" />
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<img style="height:50px;margin-left:50px" data-src="../pics/fsl_logo.png" />
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<img style="height:50px;margin-left:50px" data-src="../pics/pydra_logo.png" />
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<img style="height:50px;margin-left:50px" data-src="../pics/R_logo.png" />
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<img style="height:50px;margin-left:50px" data-src="../pics/nwblogo.png" />
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<img style="height:50px;margin-left:50px" data-src="../pics/rstudio-logo.png" />
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<img style="height:50px;margin:20px" data-src="../pics/afni_logo.png" />
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<img style="height:50px;margin-left:50px" data-src="../pics/pymvpa_logo.png" />
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<img style="height:50px;margin-left:50px" data-src="../pics/mne_logo.svg" />
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<img style="height:50px;margin-left:50px" data-src="../pics/bids.png" />
|
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<img style="height:50px;margin-left:50px" data-src="../pics/FSlogo.png" />
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<img style="height:50px;margin-left:50px" data-src="../pics/odMLLogo.png" />
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<img style="height:50px;margin-left:50px" data-src="../pics/pysurfer_logo.png" />
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<img style="height:50px;margin-left:50px" data-src="../pics/nix_logo.png" />
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<img style="height:50px;margin:20px" data-src="../pics/nilearn-logo.png" />
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<img style="height:50px;margin:20px" data-src="../pics/elephant_logo.png" />
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<img style="height:50px;margin:20px" data-src="../pics/ants_logo.png" />
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<img style="height:50px;margin:20px" data-src="../pics/brainiak_logo.svg" />
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<img style="height:50px;margin:20px" data-src="../pics/spm.svg" />
|
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<img style="height:50px;margin:20px" data-src="../pics/cpac_logo.png" />
|
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<img style="height:50px;margin:20px" data-src="../pics/fieldtrip_logo.png" />
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<div style="margin:-100px;margin-left:600px;font-size:35px">... and many more!</div>
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</td>
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</tr>
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</table>
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<p>
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<table>
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<tr>
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<td class="fragment fade-in-then-out" data-fragment-index="1" >
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<img height="400px" src="../pics/outside-collab-uk.png">
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<imgcredit><a href="https://royalsociety.org/~/media/royal_society_content/policy/publications/2010/4294970126.pdf" target="_blank">
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The Royal Society, 2010</a></imgcredit>
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</td>
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<td class="fragment fade-in-then-out" data-fragment-index="2">
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<img height="250px" src="../pics/research-abroad-uk.png">
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<imgcredit><a href="https://royalsociety.org/-/media/policy/projects/international-mobility/infographics/RAND-lit-review-visualisation-01.pdf" target="_blank">
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Royal Society, 2017
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</a> </imgcredit>
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</td>
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</tr>
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</table>
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</p>
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<p class="fragment fade-in" data-fragment-index="3">
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<img src="../pics/WOMM2.jpg" width="700px">
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<img src="../pics/software-provenance.png">
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<br><small><a href="https://doi.org/10.1016/j.neuroimage.2022.119738" target="_blank">
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doi.org/10.1016/j.neuroimage.2022.119738</a> </small>
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</p>
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</div>
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<br><br><br><br><ul>
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<li class="fragment fade-in-then-semi-out" data-fragment-index="1">
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remove accessibility barriers</li>
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<li class="fragment fade-in-then-semi-out" data-fragment-index="3">
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allow transparent digital provenance</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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<dl style="font-size:35px">
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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
|
|
<a href="https://phdcomics.com/comics/archive_print.php?comicid=1531" target="_blank">
|
|
1531
|
|
</a> </imgcredit></td>
|
|
</tr>
|
|
</table>
|
|
</dl>
|
|
<img class="fragment fade-in" data-fragment-index="1" src="../pics/findfiles.png" height="400">
|
|
<img class="fragment fade-in" data-fragment-index="1" src="../pics/projectstack.png" height="350">
|
|
<imgcredit class="fragment fade-in" data-fragment-index="1" >Scriberia and <a href="https://the-turing-way.netlify.app">The Turing Way </a> (CC-BY)</imgcredit>
|
|
|
|
</section>
|
|
|
|
<section data-transition="None">
|
|
<h2>Version control</h2>
|
|
<table>
|
|
<tr>
|
|
<td>
|
|
<img class="fragment fade-in" data-fragment-index="1" src="../pics/turingway/ProjectHistory.png" width="600">
|
|
<imgcredit><a href="https://the-turing-way.netlify.app/reproducible-research/vcs/vcs-data.html" target="_blank">
|
|
CC-BY Scriberia & The Turing Way</a>
|
|
</imgcredit>
|
|
</td>
|
|
<td>
|
|
<ul style="font-size:35px">
|
|
<dt class="fragment fade-in" data-fragment-index="1" >Version control</dt>
|
|
<li class="fragment fade-in" data-fragment-index="2">keep things organized</li>
|
|
<li class="fragment fade-in" data-fragment-index="2">keep track of changes</li>
|
|
<li class="fragment fade-in" data-fragment-index="2">revert changes or go <br>
|
|
back to previous states</li>
|
|
<li class="fragment fade-in" data-fragment-index="3">collect and share digital provenance</li>
|
|
<li class="fragment fade-in" data-fragment-index="3">industry standard: Git</li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
<img class="fragment fade-in" data-fragment-index="4" src="../pics/git.png" height="100px">
|
|
<img class="fragment fade-in" data-fragment-index="4" src="../pics/git-paper.png">
|
|
</section>
|
|
|
|
<section data-transition="None">
|
|
<dl style="font-size:35px">
|
|
<dt>The building blocks of a scientific result are rarely static</dt>
|
|
<table>
|
|
<tr>
|
|
<td style="vertical-align:middle">Data changes <br>
|
|
<small>(errors are fixed, data is extended,<br>
|
|
naming standards change, an analysis <br>
|
|
requires only a subset of your data...)</small></td>
|
|
<td>
|
|
<div class="r-stack">
|
|
<img class="fragment fade-out" data-fragment-index="1" src="../pics/phd052810s.png" height="500">
|
|
<img class="fragment fade-in" data-fragment-index="1" src="../pics/abcdtwitter.png">
|
|
|
|
</div>
|
|
<imgcredit class="fragment fade-out" data-fragment-index="1">Piled Higher and Deeper
|
|
<a href="https://phdcomics.com/comics/archive_print.php?comicid=1323" target="_blank">
|
|
1323
|
|
</a> </imgcredit></td>
|
|
</tr>
|
|
</table>
|
|
</dl>
|
|
<p class="fragment fade-in" data-fragment-index="2">
|
|
<img class="fragment fade-in" data-fragment-index="2" src="../pics/gitannex.png" height="100px">
|
|
<a href="https://git-annex.branchable.com" target="_blank">git-annex</a> and
|
|
<a href="https://datalad.org" target="_blank">DataLad</a> version control large data
|
|
<img class="fragment fade-in" data-fragment-index="2" src="../pics/datalad_logo_wide.svg" height="100px"></p>
|
|
<div class="r-stack">
|
|
<img class="fragment fade-in" data-fragment-index="3" src="../pics/tigdata.png">
|
|
<img class="fragment fade-in" data-fragment-index="4" src="../pics/tigdata3.png">
|
|
<img class="fragment fade-in" data-fragment-index="5" src="../pics/tigdata2.png">
|
|
</div>
|
|
</section>
|
|
</section>
|
|
|
|
<section>
|
|
<section data-transition="None">
|
|
<h2>Leaving a trace </h2>
|
|
<div class="r-stack">
|
|
<p class="fragment fade-out" data-fragment-index="1">"Shit, which version of which script produced these outputs from which version
|
|
of what data?"</p>
|
|
<p class="fragment fade-in" data-fragment-index="1">
|
|
"Shit, why buttons did I click and in which order did I use all those tools?"</p>
|
|
</div>
|
|
<br>
|
|
<div class="r-stack">
|
|
<p>
|
|
<img class="fragment fade-in-then-out" data-fragment-index="1" src="../pics/manuallabor.png">
|
|
<img class="fragment fade-out" data-fragment-index="2" src="../pics/findfiles.png" height="400">
|
|
<img class="fragment fade-out" data-fragment-index="2" src="../pics/projectstack.png" height="350">
|
|
<imgcredit>CC-BY Scriberia and <a href="https://the-turing-way.netlify.app/reproducible-research/rdm.html" target="_blank">
|
|
The Turing Way</a>
|
|
</imgcredit>
|
|
</p>
|
|
<p>
|
|
<img class="fragment fade-in" data-fragment-index="2" height="300px" src="../pics/file-management-manual-with-text.png" height="400px">
|
|
<img class="fragment fade-in" data-fragment-index="3" height="300px" src="../pics/documentation.png" height="400px">
|
|
<img class="fragment fade-in" data-fragment-index="4" height="300px" src="../pics/turingway/MachineReadable.png">
|
|
</p>
|
|
</div>
|
|
<div style="font-size:30px">
|
|
<p class="fragment fade-in" data-fragment-index="2">1) Create an intuitive structure, and </p>
|
|
<p class="fragment fade-in" data-fragment-index="3">2) write (plenty! of) documentation as you go, and<br></p>
|
|
<p class="fragment fade-in" data-fragment-index="4">
|
|
3) make your processes machine-readable <br><small>Tools and tricks: Perkel, 2020,
|
|
<a href="https://www.nature.com/articles/d41586-020-02462-7" target="_blank">
|
|
checklist for computational reproducibility
|
|
</a></small>
|
|
</p></div>
|
|
</section>
|
|
</section>
|
|
|
|
<section data-transition="None">
|
|
<h2>Research data management is tied to reproducibility</h2>
|
|
<img src="../pics/fragile.png" height="800">
|
|
<imgcredit>Based on <a href="https://xkcd.com/2347/" target="_blank">
|
|
xkcd.com/2347/</a> (CC-BY)</imgcredit>
|
|
<small><a href="https://www.youtube.com/watch?v=nTVcMDVlyOI" target="_blank">
|
|
Reproducibility Management in Neuroscience -
|
|
Specific Issues and Solutions</a>
|
|
(<a href="https://doi.org/10.5281/zenodo.4285927" target="_blank">DOI 10.5281/zenodo.4285927</a>) </small>
|
|
</section>
|
|
|
|
|
|
<section>
|
|
<h2>Back-Ups and Archival</h2>
|
|
Ensure that your data are regularily backed-up, and eventually
|
|
deposited in an appropriate archive or repository
|
|
<dl>
|
|
<dt>Back-ups</dt>
|
|
<dd>Keep back-ups on different infrastructure,
|
|
ideally even different physical locations</dd>
|
|
<dd>Synchronize regularly</dd>
|
|
<dd>My personal workflow: Distributed version control</dd>
|
|
<dt>Software</dt>
|
|
<dd>E.g., <a href="https://archive.softwareheritage.org/" target="_blank">
|
|
Software Heritage
|
|
</a>, <a href="https://zenodo.org/" target="_blank">Zenodo</a>
|
|
(both have automatic GitHub integrations)</dd>
|
|
<dt>Data</dt>
|
|
<dd>E.g., <a href="https://zenodo.org/" target="_blank">Zenodo</a>,
|
|
<a href="https://gin.g-node.org" target="_blank">Gin.g-node.org</a>
|
|
<a href="https://neurovault.org/" target="_blank">Neurovault</a>,
|
|
<a href="https://dataverse.org/" target="_blank">DataVerse</a>,
|
|
<a href="https://datadryad.org" target="_blank">Data DRYAD</a>,
|
|
<a href="http://figshare.com/" target="_blank">FigShare</a>
|
|
</dd>
|
|
</dl>
|
|
<br><br>
|
|
<small>Further reading: <a href="https://the-turing-way.netlify.app/reproducible-research/rdm/rdm-sharing.html#rr-rdm-sharing" target="_blank">
|
|
the-turing-way.netlify.app/reproducible-research/rdm/rdm-sharing.html
|
|
</a> </small>
|
|
</section>
|
|
|
|
<section>
|
|
<h2>Digital Object Identifiers</h2>
|
|
<ul style="font-size:30px">
|
|
<li >Example: 10.5281/zenodo.7419377 (uniquely & persistently identifies this talk)</li>
|
|
<li >Provide a persistent, trusted reference. Resolve any DOI at <a href="https://doi.org" target="_blank">doi.org</a> </li>
|
|
<li class="fragment fade-in" data-fragment-index="3">Make your work citeable</li>
|
|
</ul>
|
|
<div class="r-stack">
|
|
<img class="fragment fade-out" data-fragment-index="2" src="../pics/turingway/doi.png" height="600px">
|
|
<p><img class="fragment fade-in" data-fragment-index="3" src="../pics/zenodo-citation1.png">
|
|
<img class="fragment fade-in" data-fragment-index="3" src="../pics/zenodo-citation2.png"></p>
|
|
</div>
|
|
<imgcredit class="fragment fade-out" data-fragment-index="2"><a href="https://the-turing-way.netlify.app/reproducible-research/rdm.html" target="_blank">
|
|
The Turing Way</a> </imgcredit>
|
|
<ul class="fragment fade-in" data-fragment-index="1" style="font-size:30px">Get a DOI from
|
|
<li>free academic services and archives that you already use,
|
|
such as <a href="https://zenodo.org" target="_blank">Zenodo</a>,
|
|
<a href="https://FigShare.org" target="_blank">FigShare</a>, or
|
|
<a href="osf.com" target="_blank">OSF</a> </li>
|
|
<li>your own institutions (e.g., library, DataVerse, ...) </li>
|
|
<li>Preprint servers, publishers </li>
|
|
<li>My tip for large datasets: <a href="https://gin.g-node.org" target="_blank">Gin.g-node.org</a> </li>
|
|
</ul>
|
|
</section>
|
|
|
|
<section>
|
|
<h2>Licenses</h2>
|
|
<ul style="font-size:30px">
|
|
<li>Everything you (co-)create has a copyright, and you're a/the copyright holder</li>
|
|
<li><strong>Without a license your work is unusable by others</strong></li>
|
|
<li class="fragment fade-in" data-fragment-index="1">Use an established license rather creating one yourself</li>
|
|
<li class="fragment fade-in" data-fragment-index="1">Different licenses are suitable for different types of work</li>
|
|
<table class="fragment fade-in">
|
|
<tr>
|
|
<td>
|
|
<strong>Software</strong>
|
|
</td>
|
|
<td>
|
|
<strong>Data (e.g., comics, text)</strong>
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td style="vertical-align:top">
|
|
<a href="https://choosealicense.com/no-permission/" target="_blank">License picker</a><br>
|
|
<img width="450" src="../pics/software-licenses.png">
|
|
<imgcredit><a href="https://the-turing-way.netlify.app/reproducible-research/rdm.html" target="_blank">
|
|
The Turing Way</a> </imgcredit>
|
|
</td>
|
|
<td style="vertical-align:top">
|
|
<a href="https://creativecommons.org/choose/" target="_blank">Creative Commons <br></a>
|
|
<img width="400" src="../pics/cc-licenses.png">
|
|
<imgcredit><a href="https://www.homoempresarius.com/2013/08/tipos-de-licencia-creative-commons.html" target="_blank">
|
|
www.homoempresarius.com
|
|
</a></imgcredit>
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
<p class="fragment fade-in" style="z-index: 100;position: fixed;background-color:#ede6d5;font-size:20px;box-shadow: 10px 10px 8px #888888;margin-top:-285px;margin-bottom:500px;margin-left:930px;text-align:center">
|
|
<strong>Beware!</strong><br> "Non-commercial" <br>
|
|
can have undesired side-effects
|
|
</p>
|
|
</ul>
|
|
<small>Further reading: <a href="https://the-turing-way.netlify.app/reproducible-research/licensing" target="_blank">
|
|
the-turing-way.netlify.app/reproducible-research/licensing
|
|
</a> </small>
|
|
</section>
|
|
</section>
|
|
|
|
<section>
|
|
<section data-transition="None">
|
|
<h2>FAIR</h2>
|
|
<p style="font-size:25px"> Wilkinson et al., 2016:
|
|
"The FAIR Guiding Principles for scientific data management and stewardship",
|
|
<a href="https://doi.org/10.1038/sdata.2016.18" target="_blank">doi.org/10.1038/sdata.2016.18</a>
|
|
|
|
</p>
|
|
<img src="../pics/../pics/turingway/fairprinciples.png">
|
|
<imgcredit>Scriberia and <a href="https://the-turing-way.netlify.app">The Turing Way </a> (CC-BY)</imgcredit>
|
|
</section>
|
|
|
|
<section data-transition="None">
|
|
<h2>Data Management Plans (DMP)</h2>
|
|
<img height="400px" src="../pics/turingway/data-management-plan-with-text.png">
|
|
<imgcredit>Scriberia and <a href="https://the-turing-way.netlify.app">The Turing Way </a> (CC-BY)</imgcredit>
|
|
<ul style="font-size:30px">A Data Management Plan (DMP) is a brief plan to define:
|
|
<li>how the data will be created or used</li>
|
|
<li>how it will be documented</li>
|
|
<li>who will be able to access it</li>
|
|
<li>where it will be stored</li>
|
|
<li>who will back it up</li>
|
|
<li>whether (and how) it will be shared and preserved.</li>
|
|
</ul>
|
|
<br><br><br>
|
|
<small>Further reading: <a href="https://ukdataservice.ac.uk/learning-hub/research-data-management/plan-to-share/data-management-planning-overview/" target="_blank">
|
|
https://ukdataservice.ac.uk/learning-hub/research-data-management</a> </small>
|
|
|
|
</section>
|
|
</section>
|
|
|
|
<section>
|
|
<section>
|
|
<h2>Take home messages</h2>
|
|
<ul>
|
|
<li class="fragment fade-in">RDM is a continuous process</li>
|
|
<li class="fragment fade-in">There is an ecosystem of resources, infrastructure, and experts to assist you at every step.
|
|
Befriend your local librarian!</li>
|
|
<li class="fragment fade-in">The biggest beneficiary of RDM? Yourself</li>
|
|
<li class="fragment fade-in">The second biggest beneficiary of RDM? Yourself in 6 months</li>
|
|
<li class="fragment fade-in">The consequence of good RDM? Better science</li>
|
|
|
|
<br><br><br>
|
|
<ul class="fragment fade-in" style="font-size:30px;align:left">
|
|
<strong>Resources</strong>
|
|
<li><a href="" target="_blank">The Turing Way Handbook for Reproducible Science</a> </li>
|
|
<li><a href="https://www.openaire.eu/rdm-handbook" target="_blank">OpenAIRE Research Data Management Handbook</a></li>
|
|
<li><a href="https://www.tudelft.nl/en/library/research-data-management" target="_blank">RDM resources TU Delft</a></li>
|
|
<li><a href="https://f1000researchdata.s3.amazonaws.com/resources/FAIR_Open_GettingStarted.pdf" target="_blank">Guide to FAIR</a>
|
|
</li>
|
|
<li><a href="https://zenodo.org/record/5111307#.Y8WzbkjMLaE" target="_blank">Checklist: How FAIR are your data?</a>
|
|
</li>
|
|
<li><a href="https://ukdataservice.ac.uk/learning-hub/research-data-management/plan-to-share/checklist/" target="_blank">
|
|
Checklist for Writing a Data Management Plan
|
|
</a></li>
|
|
</ul>
|
|
</ul>
|
|
</section>
|
|
|
|
<section>
|
|
<h2>Thanks for your attention</h2>
|
|
<img src="../pics/QRcode_rdmwin.png" height="400"><br>
|
|
<small>Slides at
|
|
<a href="https://doi.org/10.5281/zenodo.7419377" target="_blank">
|
|
DOI 10.5281/zenodo.7419377 </small>
|
|
<br><br>
|
|
<div style="margin-top:1em;text-align:center">
|
|
<small>
|
|
<table>
|
|
<tr>
|
|
</tr>
|
|
<tr style="vertical-align:middle">
|
|
<td>
|
|
<img src="../pics/winrepo.png">
|
|
</td>
|
|
<td style="font-size: 18px">
|
|
<br><br>
|
|
Women neuroscientists are <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/ejn.14397" target="_blank">
|
|
underrepresented in neuroscience</a>. You can use the <br>
|
|
<a href="https://www.winrepo.org/" target="_blank"> Repository for Women in Neuroscience</a> to find
|
|
and recommend neuroscientists for <br>
|
|
conferences, symposia or collaborations, and help making neuroscience more open & divers.
|
|
</td>
|
|
</tr>
|
|
|
|
</table>
|
|
</small>
|
|
</div>
|
|
</section>
|
|
</section>
|
|
|
|
<!-- End of slides -->
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|
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|
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