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<!DOCTYPE html>
<html lang="en"><head>
<script src="RDM_IntroRDM_files/libs/clipboard/clipboard.min.js"></script>
<script src="RDM_IntroRDM_files/libs/quarto-html/tabby.min.js"></script>
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<script src="RDM_IntroRDM_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="RDM_IntroRDM_files/libs/quarto-html/tippy.css" rel="stylesheet">
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<meta name="generator" content="quarto-1.5.57">
<meta name="author" content="Daniel Manrique-Castano, Ph.D">
<title>Introduction to Research Data Management (RMD)</title>
<meta name="apple-mobile-web-app-capable" content="yes">
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</head>
<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="title-slide" class="quarto-title-block center">
<h1 class="title">Introduction to Research Data Management (RMD)</h1>
<p class="subtitle">A primer for researchers</p>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
Daniel Manrique-Castano, Ph.D
</div>
<div class="quarto-title-author-email">
<a href="mailto:daniel.manrique-castano@alliancecan.ca">daniel.manrique-castano@alliancecan.ca</a>
</div>
<p class="quarto-title-affiliation">
Digital Research Alliance of Canada
</p>
</div>
</div>
<p class="date">Wednesday, December 11, 2024</p>
</section>
<section>
<section id="contextualizaing-research-data-management-rdm" class="title-slide slide level1 agenda-slide center">
<h1>Contextualizaing Research Data Management (RDM)</h1>
<div class="agenda-heading">
<p>Agenda</p>
</div>
<div class="agenda">
<ol>
<li><div class="agenda-active">
<p>Contextualizaing Research Data Management (RDM)</p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Understanding RDM</p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Research project life cycle</p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Data as the new oil</p>
</div></li>
</ol>
</div>
</section>
<section id="why-bother-with-rdm" class="slide level2 center">
<h2>Why “bother” with RDM?</h2>
<p><span style="color:green;">Data</span> is the <span style="text-decoration: underline;">foundation of scientific research</span>. We want to best manage this source for modeling, workflow automation, quality control, and data sharing with our field to produce meaningful scientific work.</p>
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>The 80/20 rule</strong></p>
</div>
<div class="callout-content">
<p>Researchers spend <span style="color:green;">80%</span> of their time finding, producing, cleaning, and organizing data.</p>
</div>
</div>
</div>
</section>
<section id="we-want-our-research-de-be-reproducile" class="slide level2 center">
<h2>We want our research de be reproducile</h2>
<div style="text-align: center; font-size: 70%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/crisis1.png" width="1200" height="500"></p>
<figcaption>Reports on the reproducibility crisis</figcaption>
</figure>
</div>
</div>
</section>
<section id="some-well-known-causes" class="slide level2">
<h2>Some well-known causes</h2>
<div style="text-align: center; font-size: 70%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/crisis.png"></p>
<figcaption>Causes of the reproducibility crisis</figcaption>
</figure>
</div>
</div>
</section>
<section id="creating-reproducible-science" class="slide level2 center">
<h2>Creating reproducible science</h2>
<p><i class="bi-file-earmark-text " style="" role="img" aria-hidden="true"></i> <span style="color:green;">Document data provenance</span> (samples, software, instruments, other tools).</p>
<p><i class="bi-gear " style="" role="img" aria-hidden="true"></i> Define <span style="color:green;">standard procedures and methods</span> (i.e., how measurements were made).</p>
<p><i class="bi-funnel " style="" role="img" aria-hidden="true"></i> <span style="color:green;">Quality control</span> measures (data evaluation, organization and cleaning).</p>
<p><i class="bi-file-earmark-text " style="" role="img" aria-hidden="true"></i> <span style="color:green;">Comprehensive documentation</span> to enable understanding and reuse of data.</p>
</section>
<section id="therefore-research-needs-to-move-towards" class="slide level2 center">
<h2>Therefore, research needs to move towards</h2>
<ul>
<li><p><span style="color:green;">Competent</span> researchers in <span style="text-decoration: underline;">RDM</span> and data analysis.</p></li>
<li><p><span style="color:green;">Standardized approaches</span> to <span style="text-decoration: underline;">sharing</span> raw data and analysis code to support research findings.</p></li>
<li><p>Researchers with a <span style="color:green;">commitment to transparency</span> and best scientific practice practices to ensure <span style="text-decoration: underline;">research integrity</span>.</p></li>
</ul>
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>RDM competences</strong></p>
</div>
<div class="callout-content">
<p>Think of RDM competencies as a matter of professional responsibility, ethical conduct, and commitment to best scientific practices.</p>
</div>
</div>
</div>
</section>
<section id="tri-agency-research-data-management-policy" class="slide level2 center">
<h2>Tri-Agency Research Data Management Policy</h2>
<p>The <a href="https://science.gc.ca/site/science/en/interagency-research-funding/policies-and-guidelines/research-data-management">Goverment of Canada</a> promotes RDM in its <a href="https://science.gc.ca/site/science/en/interagency-research-funding/policies-and-guidelines/research-data-management/tri-agency-research-data-management-policy-frequently-asked-questions">Tri-Agency Research Data Management Policy</a>.</p>
<p>Through its federal funding agencies, the the Government of Canada seeks to implement <span style="text-decoration: underline;">data management plans (DMPs)</span> and <span style="text-decoration: underline;">sharing</span> of research data to maximize the benefits to society.</p>
</section>
<section id="we-can-define-rdm-as" class="slide level2 center">
<h2>We can define RDM as:</h2>
<p><span style="color:green;">RDM</span> encompasses the organization/handling, storage, sharing and preservation of research data, including physical objects/files, documents, images, audio, digital databases, etc.</p>
</section></section>
<section>
<section id="understanding-rdm" class="title-slide slide level1 agenda-slide center">
<h1>Understanding RDM</h1>
<div class="agenda-heading">
<p>Agenda</p>
</div>
<div class="agenda">
<ol>
<li><div class="agenda-inactive agenda-pre-active">
<p>Contextualizaing Research Data Management (RDM)</p>
</div></li>
<li><div class="agenda-active">
<p>Understanding RDM</p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Research project life cycle</p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Data as the new oil</p>
</div></li>
</ol>
</div>
</section>
<section id="where-does-data-end-up" class="slide level2 center">
<h2>Where does data end up?</h2>
<div>
</div>
<div class="quarto-layout-panel" data-layout-ncol="4">
<div class="quarto-layout-row">
<div id="first-column" class="quarto-layout-cell" style="flex-basis: 25.0%;justify-content: flex-start;">
<div style="text-align: center;font-size: 60%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/Laptop.jpg" style="width:100.0%"></p>
<figcaption>Laptop of students and postdocs</figcaption>
</figure>
</div>
</div>
</div>
<div id="second-column" class="quarto-layout-cell" style="flex-basis: 25.0%;justify-content: flex-start;">
<div style="text-align: center;font-size: 60%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/Network.jpg" style="width:100.0%"></p>
<figcaption>Institute network</figcaption>
</figure>
</div>
</div>
</div>
<div id="third-column" class="quarto-layout-cell" style="flex-basis: 25.0%;justify-content: flex-start;">
<div style="text-align: center;font-size: 60%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/Cloud.jpg" style="width:100.0%"></p>
<figcaption>The cloud (Google drive)</figcaption>
</figure>
</div>
</div>
</div>
<div id="forth-column" class="quarto-layout-cell" style="flex-basis: 25.0%;justify-content: flex-start;">
<div style="text-align: center;font-size: 60%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/HighCompuating.jpg" style="width:100.0%"></p>
<figcaption>HPC cluster</figcaption>
</figure>
</div>
</div>
</div>
</div>
</div>
</section>
<section id="considerations-for-storing-data" class="slide level2 center">
<h2>Considerations for storing data</h2>
<p><i class="bi-clock " style="" role="img" aria-hidden="true"></i> In most cases, data must be retained for <span style="color:green;">10 years</span>.</p>
<p><i class="bi-safe " style="" role="img" aria-hidden="true"></i> What do we need to <span style="color:green;">store</span>?</p>
<p><i class="bi-file-earmark-text " style="" role="img" aria-hidden="true"></i> What <span style="color:green;">data formats</span> provide access?</p>
<p><i class="bi-gear " style="" role="img" aria-hidden="true"></i> What <span style="color:green;">technical requirements</span> do I need?</p>
<p><i class="bi-unlock " style="" role="img" aria-hidden="true"></i> How <span style="color:green;">secure</span> is the data and how can I access it?</p>
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Tip</strong></p>
</div>
<div class="callout-content">
<p>These are all aspects of good scientific practice!</p>
</div>
</div>
</div>
</section>
<section id="what-research-data-we-needcould-store" class="slide level2 center">
<h2>What research data we need/could store?</h2>
<p><i class="bi-thermometer-snow " style="" role="img" aria-hidden="true"></i> <span style="color:green;">Experimental samples</span> (physical samples and files, and the methods for generating them).</p>
<p><i class="bi-robot " style="" role="img" aria-hidden="true"></i> <span style="color:green;">Scientific instruments</span> (model, version, setup).</p>
<p><i class="bi-journals " style="" role="img" aria-hidden="true"></i> <span style="color:green;">Experimental data</span> (raw and processed data, plots, tables and figures).</p>
<p><i class="bi-code " style="" role="img" aria-hidden="true"></i> <span style="color:green;">Code and analysis pipelines</span> (processing and analysis workflows, software and libraries, machine learning classifiers, statistical models).</p>
</section>
<section id="section" class="slide level2 center">
<h2></h2>
<div style="text-align: center; font-size: 70%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/FAIR_Principles.png" width="700" height="350"></p>
<figcaption>Image by https://biosistemika.com/</figcaption>
</figure>
</div>
</div>
</section>
<section id="section-1" class="slide level2 center">
<h2></h2>
<div style="text-align: left;font-size: 80%">
<p><i class="bi-search " style="" role="img" aria-hidden="true"></i> <span style="color:green;"><strong>Findable:</strong></span> Data with <span style="text-decoration: underline;">identifiers and metadata</span> that facilitate its discovery.</p>
<p><i class="bi-unlock " style="" role="img" aria-hidden="true"></i> <span style="color:orange;"><strong>Accessible:</strong></span> To the community and research under clear <span style="text-decoration: underline;">permissions</span> (i.e <a href="https://creativecommons.org/share-your-work/cclicenses/">Creative Commons Licenses</a>).</p>
<p><i class="bi-upc-scan " style="" role="img" aria-hidden="true"></i> <span style="color:blue;"><strong>Interoperable:</strong></span> Data conforming to <span style="text-decoration: underline;">specific standards</span> (i.e. standardized vocabularies) and <span style="text-decoration: underline;">formats</span> (i.e. CSV, TIFF).</p>
<p><i class="bi-recycle " style="" role="img" aria-hidden="true"></i> <span style="color:magenta;"><strong>Reusable:</strong></span> Data <span style="text-decoration: underline;">sufficiently described</span> (and licensed) to allow reuse by interested parties.</p>
</div>
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Tip</strong></p>
</div>
<div class="callout-content">
<p>Additional information and guidelines can be found <a href="https://www.go-fair.org/fair-principles/">here</a></p>
</div>
</div>
</div>
</section></section>
<section>
<section id="research-project-life-cycle" class="title-slide slide level1 agenda-slide center">
<h1>Research project life cycle</h1>
<div class="agenda-heading">
<p>Agenda</p>
</div>
<div class="agenda">
<ol>
<li><div class="agenda-inactive agenda-pre-active">
<p>Contextualizaing Research Data Management (RDM)</p>
</div></li>
<li><div class="agenda-inactive agenda-pre-active">
<p>Understanding RDM</p>
</div></li>
<li><div class="agenda-active">
<p>Research project life cycle</p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Data as the new oil</p>
</div></li>
</ol>
</div>
</section>
<section id="research-project-life-cycle-1" class="slide level2 center">
<h2>Research project life cycle</h2>
<div style="text-align: center; font-size: 70%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/DataCycle.webp" width="600" height="400"></p>
<figcaption>Image by SZF TU Berlin</figcaption>
</figure>
</div>
</div>
</section>
<section id="planning-phase" class="slide level2 center">
<h2>Planning phase</h2>
<div style="text-align: left;font-size: 70%">
<p>Planning includes <span style="color:green;">clear perspectives</span> on how researchers will <span style="text-decoration: underline;">manage, store, and share</span> their data. This step may include:</p>
<p><i class="bi-clipboard-data " style="" role="img" aria-hidden="true"></i> <strong>Identify data needs:</strong> Determine what <span style="text-decoration: underline;">type of data</span> is needed or available to answer the research question.</p>
<p><i class="bi-file-earmark-text " style="" role="img" aria-hidden="true"></i> <strong>Create a Data Management Plan (DMP):</strong> Outline how data will be <span style="text-decoration: underline;">collected, documented, and preserved</span>, file formats, appropriate <span style="text-decoration: underline;">metadata standards</span>, and long-term data <span style="text-decoration: underline;">sharing and preservation</span>.</p>
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>DMP assistants</strong></p>
</div>
<div class="callout-content">
<p>The <a href="https://alliancecan.ca/en/services/research-data-management/dmp-assistant">DMP Assistant</a> from the <span style="color:orange;">Digital Research Alliance of Canada</span> is an example of a DMP tool.</p>
</div>
</div>
</div>
<p><i class="bi-file-person " style="" role="img" aria-hidden="true"></i> <strong>Ethical considerations:</strong> Address any ethical requirements related to the data <span style="text-decoration: underline;">privacy, consent, and security</span>.</p>
</div>
</section>
<section id="collection-phase" class="slide level2 center">
<h2>Collection phase</h2>
<div style="text-align: left;font-size: 80%">
<p>Researchers focus on <span style="text-decoration: underline;">collecting research data</span> from:</p>
<ul>
<li><p><strong>Experiments:</strong> laboratory procedures or clinical trials.</p></li>
<li><p><strong>Fieldwork:</strong> population surveys or environmental measurements.</p></li>
<li><p><strong>Existing datasets:</strong> secondary data from repositories or historical archives).</p></li>
</ul>
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Consider:</strong></p>
</div>
<div class="callout-content">
<ul>
<li>Standards for data collection.</li>
<li>Technical elements (what data is stored and how).</li>
<li>Adequate documentation and relevant metadata.</li>
</ul>
</div>
</div>
</div>
</div>
</section>
<section id="storing-phase" class="slide level2 center">
<h2>Storing phase</h2>
<div style="text-align: left;font-size: 80%">
<p>Properly store research data to prevent loss, corruption, or unauthorized access. Some <span style="color:green;">best practices</span> include:</p>
<p><i class="bi-database " style="" role="img" aria-hidden="true"></i> <strong>Systematic backups:</strong> Having <span style="color:green;">multiple copies</span> of the data in multiple physical and digital locations.</p>
<p><i class="bi-file-lock2 " style="" role="img" aria-hidden="true"></i> <strong>Security:</strong> Sensitive data must be <span style="color:green;">protected</span> from unauthorized access by encrypting files or restricting access to authorized personnel.</p>
<p><i class="bi-bar-chart-steps " style="" role="img" aria-hidden="true"></i> <strong>File organization:</strong> Appropriate and consistent <span style="color:green;">naming conventions</span> to facilitate the location and understanding of records.</p>
</div>
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Active RDM platforms</strong></p>
</div>
<div class="callout-content">
<p>Consider using active data management platforms suah as the <a href="https://osf.io/">Open Science Framework</a> (OSF) or <a href="https://openbis.ch/">OpenBis</a>.</p>
</div>
</div>
</div>
</section>
<section id="section-2" class="slide level2 center">
<h2></h2>
<div>
</div>
<div class="quarto-layout-panel" data-layout-ncol="2">
<div class="quarto-layout-row quarto-layout-valign-center">
<div id="first-column" class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<div style="text-align: left;font-size: 80%">
<p>For example, <a href="https://www.projecttier.org/tier-protocol/protocol-4-0/root/">TIER 4.0</a> is <span style="color:green;">systemic template</span> to standardize an appropriate folder structure for research data.</p>
<p>You can download the template <a href="https://github.com/Alliance-RDM-GDR/RDM_IntroRDM/tree/main/resources">here</a>.</p>
</div>
</div>
<div id="second-column" class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<div style="text-align: center;font-size: 50%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/tier.png" style="width:35.0%"></p>
<figcaption>Folder tree</figcaption>
</figure>
</div>
</div>
</div>
</div>
</div>
</section>
<section id="analyze-phase" class="slide level2 center">
<h2>Analyze phase</h2>
<div style="text-align: left;font-size: 80%">
<p>Analyzing data to draw scientific conclusions. This may include:</p>
<p><i class="bi-clipboard-data " style="" role="img" aria-hidden="true"></i> <strong>Data cleaning:</strong> Using <span style="color:green;">reproducible workflows</span> to handle and clean data, removing possible errors, duplicates, and inconsistencies.</p>
<p><i class="bi-code-square " style="" role="img" aria-hidden="true"></i> <strong>Statistical analysis:</strong> Use theoretically motivated <span style="color:green;">statistical models</span> to make scientific inference and identify patterns or relationships in the data.</p>
<p><i class="bi-image " style="" role="img" aria-hidden="true"></i> <strong>Visualization:</strong> Create visualizations to <span style="color:green;">present scientific results</span>.</p>
</div>
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Analysis notebooks</strong></p>
</div>
<div class="callout-content">
<p>Approximations using open source <a href="https://jupyter.org/">Jupyter</a> (Python) or <a href="https://quarto.org/">Quarto</a> (R and Python) notebooks are recommended for replication purposes.</p>
</div>
</div>
</div>
</section>
<section id="partners-to-handle-analysis-workflows" class="slide level2 center">
<h2>Partners to handle analysis workflows</h2>
<div>
</div>
<div class="quarto-layout-panel" data-layout-ncol="2">
<div class="quarto-layout-row quarto-layout-valign-center">
<div id="first-column" class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<h3 id="r-studioquarto-r-python"><i class="bi-code-square " style="" role="img" aria-hidden="true"></i> R-studio/Quarto (R + Python)</h3>
<div style="text-align: center;font-size: 100%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/R-studio_Screen.jpg" width="500" height="300"></p>
<figcaption>R-studio/quarto screen</figcaption>
</figure>
</div>
</div>
</div>
<div id="second-column" class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<h3 id="github-version-control"><i class="bi-github " style="" role="img" aria-hidden="true"></i> GitHub (Version control)</h3>
<div style="text-align: center;font-size: 100%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/GitHub_screen.jpg" width="500" height="300"></p>
<figcaption>GitHub screen</figcaption>
</figure>
</div>
</div>
</div>
</div>
</div>
</section>
<section id="with-r-studio-r-and-python-you-can" class="slide level2 center">
<h2>With R-studio (R and Python) you can</h2>
<div>
</div>
<div class="quarto-layout-panel" data-layout-ncol="2">
<div class="quarto-layout-row quarto-layout-valign-center">
<div id="first-column" class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<h3 id="r-studioquarto-r-python-1"><i class="bi-code-square " style="" role="img" aria-hidden="true"></i> R-studio/Quarto (R + Python)</h3>
<div style="text-align: center;font-size: 100%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/R-studio_Screen.jpg" width="500" height="300"></p>
<figcaption>R-studio/quarto screen</figcaption>
</figure>
</div>
</div>
</div>
<div id="second-column" class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<div style="text-align: left;font-size: 75%">
<p><i class="bi-file-earmark-spreadsheet-fill " style="" role="img" aria-hidden="true"></i> Handle <a href="https://github.com/elalilab/Stroke_PDGFR-B_Reactivity/blob/main/Widefield_10x_ROIs_CD31-Pdgfrb_Coloc.qmd">data tables and variables</a> using the R <a href="https://www.tidyverse.org/">Tidyverse</a>.</p>
<p><i class="bi-images " style="" role="img" aria-hidden="true"></i> Analyze <a href="https://github.com/elalilab/Stroke_PDGFR-B_Reactivity/blob/main/Confocal_40x_ROIs_Pdgfrb_Morpho_BatchScript.qmd">images</a> using Python <a href="https://scikit-image.org/">skimage</a>.</p>
<p><i class="bi-wallet-fill " style="" role="img" aria-hidden="true"></i> Process <a href="https://github.com/elalilab/Stroke_PDGFR-B_Reactivity/blob/main/FlowCytometry_Pdgfrb_Processing.qmd">Flow cytometry</a> files/data using R <a href="https://bioconductor.org/packages/release/bioc/html/flowCore.html">FlowCore</a> from <a href="https://bioconductor.org/">BioConductor</a>.</p>
<p><i class="bi-bandaid " style="" role="img" aria-hidden="true"></i> Analyze <a href="https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html">RNS-seq</a> data using R <a href="https://bioconductor.org/packages/release/bioc/html/DESeq2.html">DESeq2</a> from <a href="https://bioconductor.org/">BioConductor</a>.</p>
<p><i class="bi-bar-chart-line-fill " style="" role="img" aria-hidden="true"></i> Do state-of-the-art <a href="https://github.com/elalilab/Stroke_PDGFR-B_Reactivity/blob/main/Widefield_5x_Ipsilateral_Gfap_IntDen.qmd">statistical modeling</a> using <a href="https://paulbuerkner.com/brms/">brms</a>.</p>
<p>And anything else you can think of…</p>
</div>
</div>
</div>
</div>
</section>
<section id="description-phase" class="slide level2 center">
<h2>Description phase</h2>
<div style="text-align: left;font-size: 80%">
<p>Document the <span style="text-decoration: underline;">content of the dataset</span> to make it easier to <span style="text-decoration: underline;">understand and reuse</span>. This comprises the generation of a readme file containing <span style="color:green;">Metadata</span> schemes (information about the data).</p>
</div>
<div>
</div>
<div class="quarto-layout-panel" data-layout-ncol="2">
<div class="quarto-layout-row quarto-layout-valign-center">
<div id="first-column" class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<div style="text-align: center; font-size: 50%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/readme.webp" width="700" height="300"></p>
<figcaption>From https://github.com/twbs/bootstrap-rubygem</figcaption>
</figure>
</div>
</div>
</div>
<div id="second-column" class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<div style="font-size: 70%;">
<p>There are templates/resources to guide the generation of readme files:</p>
<ul>
<li><p><a href="https://blog.datadryad.org/2023/10/18/for-authors-creating-a-readme-for-rapid-data-publication/">Creating a README file</a></p></li>
<li><p>FRDR readme file <a href="https://www.frdr-dfdr.ca/docs/txt/README.txt">template</a>.</p></li>
<li><p><a href="https://readme.so/">Readme.so</a></p></li>
<li><p><a href="https://readme-ai.streamlit.app/">Readme.ai</a></p></li>
</ul>
</div>
</div>
</div>
</div>
</section>
<section id="contents-of-a-readme-file" class="slide level2 center">
<h2>Contents of a readme file</h2>
<div class="r-fit-text">
<p>In general, a dataset readme file shows:</p>
<p><i class="bi-database-fill " style="" role="img" aria-hidden="true"></i> <span style="color:green;">Dataset identifier</span> showing information such as title, authors, data collection date, geographic information.</p>
<p><i class="bi-folder-fill " style="" role="img" aria-hidden="true"></i> A <span style="color:green;">map of files/folders</span> defining the contents and hierarchy of folders and subfolders, along with naming conventions.</p>
<p><i class="bi-gear-fill " style="" role="img" aria-hidden="true"></i> <span style="color:green;">Methodological information</span> presenting methods for data collection/generation, analysis, and experimental conditions.</p>
<p><i class="bi-sd-card-fill " style="" role="img" aria-hidden="true"></i> A set of <span style="color:green;">instructions and software</span> for opening, handling and reproducing research and analysis workflows.</p>
<p><i class="bi-credit-card-2-front-fill " style="" role="img" aria-hidden="true"></i> <span style="color:green;">Sharing and access information</span> detailing permissions and terms of use.</p>
</div>
<div class="callout callout-caution callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Caution</strong></p>
</div>
<div class="callout-content">
<p>A dataset is a <span style="text-decoration: underline;">standalone object</span>. Methodological information <span style="color:red;">MUST NOT</span> be relegated to associated research articles.</p>
</div>
</div>
</div>
</section>
<section id="archiving-and-sharing-phase" class="slide level2 center">
<h2>Archiving and Sharing Phase</h2>
<div style="text-align: left;font-size: 90%">
<p>Archiving and sharing research data involves its long-term preservation in trusted data repositories, ensuring that the data are:</p>
<p><i class="bi-search " style="" role="img" aria-hidden="true"></i> <strong>Accessible:</strong> Data is <span style="color:green;">findable and accessible</span> for reuse.</p>
<p><i class="bi-database " style="" role="img" aria-hidden="true"></i> <strong>Preserved:</strong> To <span style="color:green;">prevent data loss</span> due to software or hardware obsolescence. Repositories have systematic process to ensure that data is always accessible.</p>
<p><i class="bi-safe2 " style="" role="img" aria-hidden="true"></i> <strong>Licensed:</strong> to define how others can <span style="color:green;">use the data</span>.</p>
<p><i class="bi-link-45deg " style="" role="img" aria-hidden="true"></i> <strong>Cited:</strong> with a <span style="color:green;">DOI</span> or other associated unique identifier.</p>
</div>
</section>
<section id="we-can-do-better-science" class="slide level2 center">
<h2>We can do better science</h2>
<div>
</div>
<div class="quarto-layout-panel" data-layout-ncol="2">
<div class="quarto-layout-row quarto-layout-valign-center">
<div id="first-column" class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<div style="text-align: left; font-size: 70%">
<p><strong>Data availability statement</strong></p>
<p>“The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.”</p>
</div>
</div>
<div id="second-column" class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<div style="text-align: center; font-size: 70%">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/NoData.png" width="600" height="100"></p>
<figcaption>Researchers do not share data</figcaption>
</figure>
</div>
</div>
</div>
</div>
</div>
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Tip</strong></p>
</div>
<div class="callout-content">
<p>We need to be more aware of our responsibilities and duties as scientists!</p>
</div>
</div>
</div>
</section>
<section id="sharing-data-in-repositories" class="slide level2 center">
<h2>Sharing data (in repositories)</h2>
<div style="text-align: left;font-size: 80%">
<p>When you share data, <span style="color:green;">make sure</span> that it meets these characteristics:</p>
<p><i class="bi-diagram-2-fill " style="" role="img" aria-hidden="true"></i> <span style="color:green;">Folders and files</span> are organized in a <span style="text-decoration: underline;">structured way</span>: Use <span style="color:green;">standardized file formats</span> (e.g., CSV, TIFF) and check for consistency in <span style="color:green;">naming conventions</span>.</p>
<p><i class="bi-file-earmark-text-fill " style="" role="img" aria-hidden="true"></i> <span style="color:green;">The metadata/readme</span> allow the dataset to be understood as a standalone object, providing <span style="text-decoration: underline;">collection methods, processing steps, and relevant context</span>.</p>
<p><i class="bi-code-square " style="" role="img" aria-hidden="true"></i> It is <span style="color:green;">desirable</span> that it contains reproducible workflows used to process and generate the <span style="text-decoration: underline;">research results</span>.</p>
</div>
</section>
<section id="section-3" class="slide level2 center">
<h2></h2>
<p>Be aware that datasets are research elements that <span style="color:green;">serve the public and the scientific community</span>, and that can be used (and cited) <span style="color:green;">independently</span> of a research article.</p>
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Why not?</strong></p>
</div>
<div class="callout-content">
<p>Think of research articles as additions to your dataset!</p>
</div>
</div>
</div>
</section>
<section id="reuse" class="slide level2">
<h2>Reuse</h2>
<div style="text-align: left;font-size: 70%">
<p>Researchers and the public can reuse data to:</p>
<ul>
<li><p><strong>Avoid unnecessary or costly experiments</strong> by using previous research results.</p></li>
<li><p><strong>Validate research findings:</strong> <span style="color:green;">Independent verification</span> of scientific results and conclusions (by replicating research workflows).</p></li>
<li><p><strong>Repurpose data:</strong> Use the data for <span style="color:green;">new research questions</span> or in combination with other datasets. They are also extremely valuable as <span style="color:green;">educational resources</span>.</p></li>
<li><p><strong>Build upon previous work:</strong> to <span style="color:green;">accelerate scientific discovery</span> and meta-analysis by avoiding duplication of efforts or reliance on <span style="color:red;">irreproducible research</span>.<br>
</p></li>
</ul>
</div>
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Discovering services</strong></p>
</div>
<div class="callout-content">
<p>Use portals like <a href="https://www.frdr-dfdr.ca/repo/">FRDR</a> or <a href="https://www.lunaris.ca/">Lunaris</a> to discover and reuse research data.</p>
</div>
</div>
</div>
</section></section>
<section>
<section id="data-as-the-new-oil" class="title-slide slide level1 agenda-slide center">
<h1>Data as the new oil</h1>
<div class="agenda-heading">
<p>Agenda</p>
</div>
<div class="agenda">
<ol>
<li><div class="agenda-inactive agenda-pre-active">
<p>Contextualizaing Research Data Management (RDM)</p>
</div></li>
<li><div class="agenda-inactive agenda-pre-active">
<p>Understanding RDM</p>
</div></li>
<li><div class="agenda-inactive agenda-pre-active">
<p>Research project life cycle</p>
</div></li>
<li><div class="agenda-active">
<p>Data as the new oil</p>
</div></li>
</ol>
</div>
</section>
<section id="data-is-a-valuable-resource" class="slide level2 center">
<h2>Data is a valuable resource</h2>
<p><i class="bi-columns " style="" role="img" aria-hidden="true"></i> Simulation-based approaches, machine learning and artificial intelligence.</p>
<p><i class="bi-gear " style="" role="img" aria-hidden="true"></i> Build workflows based on existing data and pipelines.</p>
<p><i class="bi-share-fill " style="" role="img" aria-hidden="true"></i> Share and reuse data with the scientific community to build collaborations.</p>
</section>
<section id="how-do-we-get-there" class="slide level2">
<h2>How do we get there?</h2>
<ul>
<li><span style="color:green;">FAIR</span> data: Making our data useful to others.</li>
<li>Adequate and comprehensive <span style="color:green;">documentation</span> that contextualizes and describes our data.</li>
<li>Sharing <span style="color:green;">reproducible workflows</span> that ensure the reproducibility of results (protocols, open file formats, analysis workflows).</li>
<li>Incorporate an <span style="color:green;">open science culture</span> into research environments, focusing on transparent reporting of research results and open data sharing.</li>
</ul>
</section>
<section id="find-more-supporting-material" class="slide level2 center">
<h2>Find more supporting material</h2>
<ul>