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@@ -292,7 +292,7 @@ <h1 class="title">1. Introduction to RDM</h1>
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     <div class="quarto-title-meta-heading">Modified</div>
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-      <p class="date-modified">August 20, 2024</p>
+      <p class="date-modified">September 13, 2024</p>
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@@ -258,7 +258,7 @@ <h1 class="title">2. Data Management Plan</h1>
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-      <p class="date-modified">August 20, 2024</p>
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@@ -308,7 +308,7 @@ <h1 class="title">3. Data organization and storage</h1>
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-      <p class="date-modified">August 20, 2024</p>
+      <p class="date-modified">September 13, 2024</p>
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diff --git a/develop/04_metadata.html b/develop/04_metadata.html
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@@ -302,7 +302,7 @@ <h1 class="title">4. Documentation for biodata</h1>
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-      <p class="date-modified">August 20, 2024</p>
+      <p class="date-modified">September 13, 2024</p>
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diff --git a/develop/05_VC.html b/develop/05_VC.html
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@@ -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">August 20, 2024</p>
+      <p class="date-modified">September 13, 2024</p>
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@@ -316,25 +316,6 @@ <h2 class="anchored" data-anchor-id="best-practices-in-data-analysis">Best Pract
 </ol>
 </div>
 </div>
-<div class="callout callout-style-default callout-tip callout-titled" title="Take our course on Git &amp; Github">
-<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">
-Take our course on Git &amp; Github
-</div>
-</div>
-<div class="callout-body-container callout-body">
-<p>if you’re interested in delving deeper, explore our course on <a href="https://heads.ku.dk/course/git_github">Git and GitHub</a>.</p>
-<p>Alternatively, here are some examples and online resources to expand your understanding:</p>
-<ul>
-<li><a href="https://docs.github.com/en/get-started/start-your-journey/git-and-github-learning-resources">Git and GitHub online resources</a></li>
-<li><a href="https://docs.github.com/get-started">GitHub documentation</a></li>
-<li><a href="https://git-scm.com/doc">Git documentation</a></li>
-</ul>
-</div>
-</div>
 <section id="version-control-using-git" class="level3">
 <h3 class="anchored" data-anchor-id="version-control-using-git">Version control using Git</h3>
 <p><a href="https://git-scm.com/about">Git</a> is a widely adopted version control system that empowers developers and researchers to efficiently manage their project’s history, collaborate seamlessly, track changes, and ensure data integrity. Git operates on core principles and mechanisms:</p>
@@ -354,6 +335,7 @@ <h3 class="anchored" data-anchor-id="version-control-using-git">Version control
 <section id="github-hosting-for-git" class="level3">
 <h3 class="anchored" data-anchor-id="github-hosting-for-git">GitHub Hosting for Git</h3>
 <p>In addition to exploring Git, we will also explore <a href="https://github.com/">GitHub</a>, a collaborative platform for hosting Git repositories. GitHub enhances Git’s capabilities by offering features like issue tracking, security measures to protect repositories, and GitHub Pages for creating project websites. Additionally, GitHub provides the option to set repositories as private until you are ready to share your work publicly.</p>
+<p>The difference between Git and GitHub is that Git is a version control system used to track changes in code, while GitHub is a cloud-based platform that hosts Git repositories and facilitates collaboration. Essentially, GitHub serves as an online access point for managing and sharing repositories.</p>
 <div class="callout callout-style-default callout-note callout-titled" title="Alternatives flows for collaborative projects">
 <div class="callout-header d-flex align-content-center">
 <div class="callout-icon-container">
@@ -381,7 +363,7 @@ <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>. 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>
+<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 also important to archive 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">
@@ -423,7 +405,7 @@ <h5 class="anchored" data-anchor-id="converting-folders-to-git-repositories">Con
 </div>
 </div>
 <div class="callout callout-style-default callout-exercise callout-titled">
-<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-8-contents" aria-controls="callout-8" aria-expanded="true" aria-label="Toggle callout">
+<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-7-contents" aria-controls="callout-7" aria-expanded="true" aria-label="Toggle callout">
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@@ -432,7 +414,7 @@ <h5 class="anchored" data-anchor-id="converting-folders-to-git-repositories">Con
 </div>
 <div class="callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end"><i class="callout-toggle"></i></div>
 </div>
-<div id="callout-8" class="callout-8-contents callout-collapse collapse show">
+<div id="callout-7" class="callout-7-contents callout-collapse collapse show">
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@@ -500,7 +482,24 @@ <h2 class="anchored" data-anchor-id="wrap-up">Wrap up</h2>
 <p>In this lesson, we explored version control and utilized Git and GitHub to establish data analysis repositories from our Project folders. Additionally, we delved into creating a GitHub organization and leveraging GitHub Pages to showcase data analysis scripts and notebooks publicly. Remember to complete the corresponding exercise from the practical workshop to reinforce your knowledge.</p>
 <section id="sources" class="level3">
 <h3 class="anchored" data-anchor-id="sources">Sources</h3>
+<div class="callout callout-style-default callout-tip callout-titled" title="Take our Git &amp; Github course at KU">
+<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">
+Take our Git &amp; Github course at KU
+</div>
+</div>
+<div class="callout-body-container callout-body">
+<p>If you’re interested in delving deeper, explore our course on <a href="https://heads.ku.dk/course/git_github">Git and GitHub</a>.</p>
+</div>
+</div>
+<p>Alternatively, here are some examples and online resources to expand your understanding:</p>
 <ul>
+<li><a href="https://docs.github.com/en/get-started/start-your-journey/git-and-github-learning-resources">Git and GitHub online resources</a></li>
+<li><a href="https://docs.github.com/get-started">GitHub documentation</a></li>
+<li><a href="https://git-scm.com/doc">Git documentation</a></li>
 <li><a href="https://guides.library.jhu.edu/c.php?g=1096705&amp;p=8066729">Version Control and Code Repository Link</a></li>
 <li><a href="https://education.github.com/git-cheat-sheet-education.pdf">Git cheat sheet</a></li>
 </ul>

diff --git a/develop/06_pipelines.html b/develop/06_pipelines.html
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@@ -243,7 +243,7 @@ <h1 class="title">6. Processing and analyzing biodata</h1>
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     <div class="quarto-title-meta-heading">Modified</div>
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+      <p class="date-modified">September 13, 2024</p>
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diff --git a/develop/07_repos.html b/develop/07_repos.html
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@@ -235,6 +235,7 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#data-repositories-and-archives" id="toc-data-repositories-and-archives" class="nav-link active" data-scroll-target="#data-repositories-and-archives">Data Repositories and Archives</a></li>
   <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="#software-and-computations-archives" id="toc-software-and-computations-archives" class="nav-link" data-scroll-target="#software-and-computations-archives">Software and computations archives</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="#zenodo" id="toc-zenodo" class="nav-link" data-scroll-target="#zenodo">Zenodo</a></li>
@@ -260,7 +261,7 @@ <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">August 20, 2024</p>
+      <p class="date-modified">September 13, 2024</p>
     </div>
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@@ -289,7 +290,16 @@ <h1 class="title">7. Storing and sharing biodata</h1>
 </ol>
 </div>
 </div>
-<p>While platforms like GitHub excel in version control and collaborative coding, repositories like Zenodo, Gene Expression Omnibus, and Annotare specialize in archiving and sharing scientific data, ensuring long-term accessibility for the global research community.</p>
+<p>While platforms like GitHub excel in version control and collaborative coding, repositories specialize in archiving and sharing scientific data (e.g.&nbsp;Zenodo), ensure long-term accessibility for the global research community.</p>
+<p><strong>What to archive and how?</strong></p>
+<p>A framework for reproducibility in computational research can generally be divided into three key, though sometimes overlapping, categories:</p>
+<ol type="1">
+<li><strong>Readable Components</strong>: This includes elements such as literature reviews, code documentation, data documentation, and workflow descriptions outlining how the code interacts with the data.</li>
+<li><strong>Executable Components</strong>: These are the actual code, scripts, and software that need to be compiled and run to reproduce results.</li>
+<li><strong>Interpretable Components</strong>: This refers to the data itself—raw or processed—that the code and scripts work on.</li>
+</ol>
+<p>Researchers are typically more accustomed to archiving readable components, such as papers or data documentation, compared to executable components like scripts and code. However, for research to be fully reproducible, it is crucial that all key components, including executable ones, are properly archived.</p>
+<p>When choosing an archival solution, it’s important to recognize that there is no one-size-fits-all option. Several factors must be considered, including data size, format requirements, licensing conditions, cost, and tools for data attribution and citation. Each of these features plays a crucial role in selecting the most suitable archive for your needs.</p>
 <section id="data-repositories-and-archives" class="level2">
 <h2 class="anchored" data-anchor-id="data-repositories-and-archives">Data Repositories and Archives</h2>
 <p>Specialized repositories and archives securely store, curate, and disseminate scientific data, ensuring long-term preservation, transparency, and citability of research findings through standardized formats and rigorous curation processes.</p>
@@ -312,7 +322,7 @@ <h2 class="anchored" data-anchor-id="data-repositories-and-archives">Data Reposi
 </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>
+<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>
@@ -425,24 +435,15 @@ <h2 class="anchored" data-anchor-id="domain-specific-repositories">Domain-specif
 </ol>
 <p>By adhering to standards, repositories ensure that submitted data is high quality, well-documented, and compliant with community best practices, promoting data discovery, reproducibility, and interoperability within the scientific community.</p>
 <p>Following all the recommendations in this course makes it straightforward to provide the necessary documentation and information for these repositories. For instance, repositories specific to NGS data will require the raw FASTQ files, sample metadata, and protocols as well as final pre-processing results (for instance, read count matrices in BED files).</p>
-<div class="callout callout-style-default callout-warning callout-titled">
-<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">
-Warning
-</div>
-</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>
+</section>
+<section id="software-and-computations-archives" class="level2">
+<h2 class="anchored" data-anchor-id="software-and-computations-archives">Software and computations archives</h2>
+<p>Keep in mind that data 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>
+<p>There are plenty of general 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>
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@@ -156,7 +156,7 @@ <h1 class="title">Practical material</h1>
     <div>
     <div class="quarto-title-meta-heading">Modified</div>
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-      <p class="date-modified">August 20, 2024</p>
+      <p class="date-modified">September 13, 2024</p>
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