Merge pull request #17 from albarema/webpage

update course

_site/develop/02_DMP.html

@@ -258,7 +258,7 @@ <h1 class="title">2. Data Management Plan</h1>
     <div>
     <div class="quarto-title-meta-heading">Modified</div>
     <div class="quarto-title-meta-contents">
-      <p class="date-modified">May 22, 2024</p>
+      <p class="date-modified">July 30, 2024</p>
     </div>
   </div>
 
@@ -289,7 +289,7 @@ <h1 class="title">2. Data Management Plan</h1>
 </div>
 </div>
 <p>The process of data management involves implementing tailored best practices for your data but how do you ensure comprehensive coverage of the decisions and that data is well-managed throughout its life cycle. To achieve this, a Data Management Plan (DMP) is essential.</p>
-<p>A DMP serves as a comprehensive document detailing strategies for handling project data, code, and documentation across its life cycle. It includes plans for data collection, documentation, organization, and preservation.</p>
+<p>DMP are required for grant applications to ensure research data to be FAIR. A DMP serves as a comprehensive document detailing strategies for handling project data, code, and documentation across its life cycle. It includes plans for data collection, documentation, organization, and preservation.</p>
 <section id="benefits-of-writing-a-dmp" class="level3">
 <h3 class="anchored" data-anchor-id="benefits-of-writing-a-dmp">Benefits of writing a DMP</h3>
 <p>A DMP serves as the initial step toward achieving FAIR principles in a project.</p>

_site/develop/05_VC.html

@@ -261,7 +261,7 @@ <h1 class="title">5. Version Control with Git and GitHub</h1>
     <div>
     <div class="quarto-title-meta-heading">Modified</div>
     <div class="quarto-title-meta-contents">
-      <p class="date-modified">May 22, 2024</p>
+      <p class="date-modified">July 25, 2024</p>
     </div>
   </div>
 
@@ -381,7 +381,7 @@ <h3 class="anchored" data-anchor-id="github-hosting-for-git">GitHub Hosting for
 </div>
 </div>
 <div class="callout-body-container callout-body">
-<p>We will discuss repositories for archiving experimental or large datasets in <a href="../develop/07_repos.html">lesson 7</a>.</p>
+<p>We will discuss repositories for archiving experimental or large datasets in <a href="../develop/07_repos.html">lesson 7</a>. However, if you are interested in version control large files, we recommend the use of <code>git annex</code>. It is important to store files with a checksum (MD5, SHA1, SHA256) to verify that files are not altered or corrupted buy recomputing their signature.</p>
 </div>
 </div>
 <section id="from-project-folders-to-git-repositories" class="level4">

_site/develop/06_pipelines.html

@@ -243,7 +243,7 @@ <h1 class="title">6. Processing and analyzing biodata</h1>
     <div>
     <div class="quarto-title-meta-heading">Modified</div>
     <div class="quarto-title-meta-contents">
-      <p class="date-modified">May 22, 2024</p>
+      <p class="date-modified">July 24, 2024</p>
     </div>
   </div>
 
@@ -340,7 +340,9 @@ <h3 class="anchored" data-anchor-id="connecting-data-organization-and-documentat
 <li>Provide <strong>environment files</strong> for reproducing the computational environment (such as ‘requirements.txt’ for Python or ‘environment.yml’ for Conda). The simplest way is to document the dependencies by reporting the packages and their versions used to run your analysis.</li>
 <li>Data versioning: use <strong>version control systems</strong> (e.g., Git) and upload your code to a <strong>code repository</strong> <a href="../develop/05_VC.html">Lesson 5</a>.</li>
 <li>Integrated development environments (e.g., RStudio, PyCharm) offer tools and features for writing, testing, and debugging code</li>
+<li>Use <code>git submodule</code> for code and software that is reused in several projects</li>
 <li>Leverage curated pipelines such as the ones developed by the <a href="https://nf-co.re/">nf-core community</a>, further ensuring adherence to community standards and guidelines.</li>
+<li>Use <a href="https://www.softwareheritage.org/">Software Heritage</a> an archive for software source code are essential for long-term accessibility and reproducibility</li>
 <li>Add a LICENSE file and perform regular updates: clarifying usage permissions and facilitating collaboration.</li>
 </ul>
 <div class="callout callout-style-default callout-warning callout-titled" title="Practical HPC pipes">

_site/develop/07_repos.html

@@ -41,6 +41,9 @@
 <link href="../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
 <link href="../site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
 <link href="../site_libs/bootstrap/bootstrap-dark.min.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
+<script src="../site_libs/quarto-contrib/glightbox/glightbox.min.js"></script>
+<link href="../site_libs/quarto-contrib/glightbox/glightbox.min.css" rel="stylesheet">
+<link href="../site_libs/quarto-contrib/glightbox/lightbox.css" rel="stylesheet">
 <script id="quarto-search-options" type="application/json">{
   "location": "navbar",
   "copy-button": false,
@@ -234,7 +237,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#domain-specific-repositories" id="toc-domain-specific-repositories" class="nav-link" data-scroll-target="#domain-specific-repositories">Domain-specific repositories</a></li>
   <li><a href="#general-repositories" id="toc-general-repositories" class="nav-link" data-scroll-target="#general-repositories">General repositories</a>
   <ul class="collapse">
-  <li><a href="#step-by-step-setup-guide" id="toc-step-by-step-setup-guide" class="nav-link" data-scroll-target="#step-by-step-setup-guide">Step-by-Step Setup Guide</a></li>
+  <li><a href="#zenodo" id="toc-zenodo" class="nav-link" data-scroll-target="#zenodo">Zenodo</a></li>
   </ul></li>
   <li><a href="#wrap-up" id="toc-wrap-up" class="nav-link" data-scroll-target="#wrap-up">Wrap up</a></li>
   </ul>
@@ -257,7 +260,7 @@ <h1 class="title">7. Storing and sharing biodata</h1>
     <div>
     <div class="quarto-title-meta-heading">Modified</div>
     <div class="quarto-title-meta-contents">
-      <p class="date-modified">May 22, 2024</p>
+      <p class="date-modified">July 23, 2024</p>
     </div>
   </div>
 
@@ -299,10 +302,23 @@ <h2 class="anchored" data-anchor-id="data-repositories-and-archives">Data Reposi
 <li><strong>Amplification of Research Impact and Contribution</strong>: Archiving data elevates research quality and extends its impact within the scientific community.</li>
 <li><strong>Fulfilling Scholarly Obligations</strong>: Compliance with requirements set by scientific journals and funding agencies ensures adherence to scholarly standards.</li>
 </ul>
+<div class="callout callout-style-default callout-important callout-titled" title="re3data.org">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-title-container flex-fill">
+re3data.org
+</div>
+</div>
+<div class="callout-body-container callout-body">
+<p>Check the <strong>registry of research data repositories</strong>–<a href="https://www.re3data.org/">re3data.org</a> for a full overview. You can <a href="https://www.re3data.org/browse/by-subject/">browse by subject</a> if you are looking within a specific field.</p>
+</div>
+</div>
 <p>There are two types of repositories:</p>
 <ul>
 <li><strong>General repositories</strong>: relevant to a wide range of disciplines (e.g.&nbsp;Zenodo).</li>
-<li><strong>Domain-specific</strong>: repositories are customized for specific fields, providing specialized curation and context-specific features (e.g.&nbsp;ENA, GEO, Annotare, etc.).</li>
+<li><strong>Domain-specific</strong>: repositories are customized for specific fields, providing specialized curation and context-specific features (e.g.&nbsp;ENA, GEO, Annotare, etc.)</li>
 </ul>
 <div class="callout callout-style-default callout-note callout-titled">
 <div class="callout-header d-flex align-content-center">
@@ -341,7 +357,7 @@ <h2 class="anchored" data-anchor-id="domain-specific-repositories">Domain-specif
 <p>This tailored approach ensures alignment with standards and maximizes the utility and impact of research findings. By catering to particular research areas, these repositories offer researchers a more focused audience, deeper domain expertise, and increased visibility within their specific research community.</p>
 <p>Explore some examples of NGS data repositories below:</p>
 <div class="callout callout-style-default callout-definition no-icon callout-titled">
-<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-3-contents" aria-controls="callout-3" aria-expanded="false" aria-label="Toggle callout">
+<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-4-contents" aria-controls="callout-4" aria-expanded="false" aria-label="Toggle callout">
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@@ -350,7 +366,7 @@ <h2 class="anchored" data-anchor-id="domain-specific-repositories">Domain-specif
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@@ -361,7 +377,7 @@ <h2 class="anchored" data-anchor-id="domain-specific-repositories">Domain-specif
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+<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-5-contents" aria-controls="callout-5" aria-expanded="false" aria-label="Toggle callout">
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@@ -370,7 +386,7 @@ <h2 class="anchored" data-anchor-id="domain-specific-repositories">Domain-specif
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-<div id="callout-4" class="callout-4-contents callout-collapse collapse">
+<div id="callout-5" class="callout-5-contents callout-collapse collapse">
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@@ -381,7 +397,7 @@ <h2 class="anchored" data-anchor-id="domain-specific-repositories">Domain-specif
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-<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-5-contents" aria-controls="callout-5" aria-expanded="false" aria-label="Toggle callout">
+<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-6-contents" aria-controls="callout-6" aria-expanded="false" aria-label="Toggle callout">
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@@ -390,7 +406,7 @@ <h2 class="anchored" data-anchor-id="domain-specific-repositories">Domain-specif
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-<div id="callout-5" class="callout-5-contents callout-collapse collapse">
+<div id="callout-6" class="callout-6-contents callout-collapse collapse">
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@@ -420,18 +436,37 @@ <h2 class="anchored" data-anchor-id="domain-specific-repositories">Domain-specif
 </div>
 <div class="callout-body-container callout-body">
 <p>Keep in mind that these repositories are not intended for downstream analysis data and associated code. However, you should already have those versions controlled by GitHub, which eliminates any concerns. You can then archive such repositories in a general repository like Zenodo.</p>
+<p>Archives for software source code are essential for long-term accessibility and reproducibility and are becoming very popular. Check <a href="https://www.softwareheritage.org/">Software Heritage</a> if you are developing software.</p>
 </div>
 </div>
 </section>
 <section id="general-repositories" class="level2">
 <h2 class="anchored" data-anchor-id="general-repositories">General repositories</h2>
+<p>There are plenty of data archiving repositories. We recommend to check the <a href="https://datamanagement.hms.harvard.edu/share-publish/data-repositories">Longwood Research Data management</a> website at Harvard for a quick overview. Some of the most well-known are:</p>
+<ul>
+<li>Dataverse</li>
+<li>Dryad</li>
+<li>figshare</li>
+<li>Open Science Framework (OSF)</li>
+<li>Zenodo</li>
+</ul>
+<p>We will be using Zenodo for our practical workshop. However, please review the table provided by the Longwood, Harvard Biomedical Data Management team, which outlines the differences between various repositories.</p>
+<div class="quarto-figure quarto-figure-center">
+<figure class="figure">
+<p><a href="./images/longwood_repos.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" data-glightbox="description: .lightbox-desc-1" title="Click to enlarge"><img src="./images/longwood_repos.png" class="img-fluid figure-img" alt="Click to enlarge"></a></p>
+<figcaption>Click to enlarge</figcaption>
+</figure>
+</div>
+<section id="zenodo" class="level3">
+<h3 class="anchored" data-anchor-id="zenodo">Zenodo</h3>
 <p><a href="https://zenodo.org/">Zenodo</a> is one of the widely used repositories for a variety of research outputs. It is an open-access digital platform supported by the European Organization for Nuclear Research (CERN) and the European Commission. It caters to various research outputs, including datasets, papers, software, and multimedia files, making it a valuable resource for researchers worldwide. With its user-friendly platform, researchers can easily upload, share, and preserve their research data. Each deposited item receives a unique Digital Object Identifier (DOI), ensuring citability and long-term accessibility. Additionally, Zenodo offers robust metadata capabilities for enriching submissions with contextual information. Moreover, researchers can <a href="(https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content)">link their GitHub</a> accounts to Zenodo, simplifying the process of archiving the GitHub repository releases for long-term accessibility and citation.</p>
 <p>Once your accounts are linked, creating a Zenodo archive becomes as straightforward as tagging a release in your GitHub repository. Zenodo automatically detects the release and generates a corresponding archive, complete with a unique Digital Object Identifier (DOI) for citable reference. Therefore, before submitting your work to a journal, link your data analysis repository to Zenodo, obtain a DOI, and cite it in your manuscript which enhances reproducibility in research.</p>
-<section id="step-by-step-setup-guide" class="level3">
-<h3 class="anchored" data-anchor-id="step-by-step-setup-guide">Step-by-Step Setup Guide</h3>
+<section id="step-by-step-setup-guide" class="level4">
+<h4 class="anchored" data-anchor-id="step-by-step-setup-guide">Step-by-Step Setup Guide</h4>
 <p>Check the practical material where we demonstrate how to link Zenodo and Github (see <strong>Exercise 6</strong> in the <a href="../develop/practical_workshop.html">practical material</a>).</p>
 </section>
 </section>
+</section>
 <section id="wrap-up" class="level2">
 <h2 class="anchored" data-anchor-id="wrap-up">Wrap up</h2>
 <p>In this concluding lesson, we’ve covered the process of submitting your data to a domain-specific repository and archiving your data analysis GitHub repositories in Zenodo. By applying the lessons from this workshop, you’ll significantly enhance the FAIRness of your data and improve its organization for future use. These benefits extend beyond yourself to your teammates, group leader, and the wider scientific community.</p>
@@ -448,6 +483,9 @@ <h2 class="anchored" data-anchor-id="wrap-up">Wrap up</h2>
 -->
 
 
+<div class="hidden" aria-hidden="true">
+<span class="glightbox-desc lightbox-desc-1">Click to enlarge</span>
+</div>
 </section>
 
 <div id="quarto-appendix" class="default"><section class="quarto-appendix-contents" id="quarto-copyright"><h2 class="anchored quarto-appendix-heading">Copyright</h2><div class="quarto-appendix-contents"><div>CC-BY-SA 4.0 license</div></div></section></div></main> <!-- /main -->
@@ -983,6 +1021,31 @@ <h2 class="anchored" data-anchor-id="wrap-up">Wrap up</h2>
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