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biosustain · Jan 15, 2025 · 9faced2 · 9faced2
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diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/trainings/index.doctree b/.doctrees/trainings/index.doctree
diff --git a/_downloads/dbc9f48b43f7be2ec205fa043a7b03c5/practical_unix_workshop_slides.pdf b/_downloads/dbc9f48b43f7be2ec205fa043a7b03c5/practical_unix_workshop_slides.pdf
diff --git a/_sources/index.md b/_sources/index.md
@@ -13,6 +13,7 @@ is part of the Informatics Platform, see our aims and goals
 :hidden:
 
 about
+trainings/index
 ```
 
 ```{toctree}

diff --git a/_sources/trainings/index.md b/_sources/trainings/index.md
@@ -0,0 +1,35 @@
+# Training
+
+On November 2024, the Data Science platform from DTU Biosustain launched a series of
+hands-on workshops about different subjects related to Data Science for DTU Biosustain 
+and DTU Bioengineering research fellows. In this first edition we covered the subjects 
+below. If interested, stay tuned for future Data Science workshops!
+
+## Introduction the command line with bash
+
+You can find the slides [here](practical_unix_workshop_slides.pdf). Find the associated 
+repository at 
+[github.com/biosustain/dsp_workshop_bash](https://github.com/biosustain/dsp_workshop_bash)
+
+## Demystifying git
+
+Find the instructions for the training [here](https://github.com/biosustain/git-tutorial/blob/HEAD/instructions_241113.md)
+
+You can view a recording with some hints related specifically to the exercises on youtube:
+[![Instructions on youtube](https://img.youtube.com/vi/mX3Il5xvKAs/maxresdefault.jpg
+)](https://www.youtube.com/watch?v=mX3Il5xvKAs)
+
+## Data Visualizaton with R
+
+Find the material in the repository [biosustain/dsp_workshop_datavizR](https://github.com/biosustain/dsp_workshop_datavizR)
+on GitHub.
+
+The material is available as a hmtl document for direct viewing 
+[here](https://html-preview.github.io/?url=https://github.com/biosustain/dsp_workshop_datavizR/blob/main/01_Code/workshop_R.html).
+
+## Nextflow for reproducible workflows
+
+Find the material as a website [here](https://biosustain.github.io/dsp_nextflow_training).
+The repository itself is available at
+[github.com/biosustain/dsp_nextflow_training](https://github.com/biosustain/dsp_nextflow_training).
+
diff --git a/_static/basic.css b/_static/basic.css
@@ -48,7 +48,7 @@ div.sphinxsidebarwrapper {
 
 div.sphinxsidebar {
     float: left;
-    width: 270px;
+    width: 230px;
     margin-left: -100%;
     font-size: 90%;
     word-wrap: break-word;

diff --git a/_static/scripts/pydata-sphinx-theme.js b/_static/scripts/pydata-sphinx-theme.js
diff --git a/_static/scripts/pydata-sphinx-theme.js.map b/_static/scripts/pydata-sphinx-theme.js.map
diff --git a/_static/styles/pydata-sphinx-theme.css b/_static/styles/pydata-sphinx-theme.css
diff --git a/_static/styles/pydata-sphinx-theme.css.map b/_static/styles/pydata-sphinx-theme.css.map
diff --git a/_static/webpack-macros.html b/_static/webpack-macros.html
@@ -5,20 +5,20 @@
 
 {% macro head_pre_assets() %}
   <!-- Loaded before other Sphinx assets -->
-  <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
-<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+  <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=8878045cc6db502f8baf" rel="stylesheet" />
+<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=8878045cc6db502f8baf" rel="stylesheet" />
 {% endmacro %}
 
 {% macro head_js_preload() %}
   <!-- So that users can add custom icons -->
-  <script src="{{ pathto('_static/scripts/fontawesome.js', 1) }}?digest=26a4bc78f4c0ddb94549"></script>
+  <script src="{{ pathto('_static/scripts/fontawesome.js', 1) }}?digest=8878045cc6db502f8baf"></script>
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=26a4bc78f4c0ddb94549" />
-<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=26a4bc78f4c0ddb94549" />
+  <link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=8878045cc6db502f8baf" />
+<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=8878045cc6db502f8baf" />
 {% endmacro %}
 
 {% macro body_post() %}
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script defer src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=26a4bc78f4c0ddb94549"></script>
-<script defer src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=26a4bc78f4c0ddb94549"></script>
+  <script defer src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=8878045cc6db502f8baf"></script>
+<script defer src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=8878045cc6db502f8baf"></script>
 {% endmacro %}
diff --git a/about.html b/about.html
@@ -16,8 +16,8 @@
     document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
     document.documentElement.dataset.theme = localStorage.getItem("theme") || "";
   </script>
-  <!-- 
-    this give us a css class that will be invisible only if js is disabled 
+  <!--
+    this give us a css class that will be invisible only if js is disabled
   -->
   <noscript>
     <style>
@@ -27,18 +27,18 @@
   </noscript>
 
   <!-- Loaded before other Sphinx assets -->
-  <link href="_static/styles/theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
-<link href="_static/styles/pydata-sphinx-theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+  <link href="_static/styles/theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
+<link href="_static/styles/pydata-sphinx-theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
 
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="_static/styles/sphinx-book-theme.css?v=a3416100" />
     <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
 
   <!-- So that users can add custom icons -->
-  <script src="_static/scripts/fontawesome.js?digest=26a4bc78f4c0ddb94549"></script>
+  <script src="_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
-<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
+  <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
+<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
     <script src="_static/documentation_options.js?v=9eb32ce0"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
@@ -49,7 +49,7 @@
     <link rel="author" title="About these documents" href="#" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Create Azure resources" href="azure/creating_ressources.html" />
+    <link rel="next" title="Training" href="trainings/index.html" />
     <link rel="prev" title="DTU Biosustain’s Data Science Platform Documentation" href="index.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -157,6 +157,7 @@
     <div class="bd-toc-item navbar-nav active">
         <ul class="current nav bd-sidenav">
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">About</a></li>
+<li class="toctree-l1"><a class="reference internal" href="trainings/index.html">Training</a></li>
 </ul>
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Azure</span></p>
 <ul class="nav bd-sidenav">
@@ -179,9 +180,14 @@
 
 
   <div class="sidebar-primary-items__end sidebar-primary__section">
+      <div class="sidebar-primary-item">
+<div id="ethical-ad-placement"
+      class="flat"
+      data-ea-publisher="readthedocs"
+      data-ea-type="readthedocs-sidebar"
+      data-ea-manual="true">
+</div></div>
   </div>
-
-  <div id="rtd-footer-container"></div>
 
 
       </div>
@@ -359,11 +365,11 @@ <h1>About<a class="headerlink" href="#about" title="Link to this heading">#</a><
       </div>
     </a>
     <a class="right-next"
-       href="azure/creating_ressources.html"
+       href="trainings/index.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Create Azure resources</p>
+        <p class="prev-next-title">Training</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
@@ -417,8 +423,8 @@ <h1>About<a class="headerlink" href="#about" title="Link to this heading">#</a><
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script defer src="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549"></script>
-<script defer src="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549"></script>
+  <script defer src="_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf"></script>
+<script defer src="_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf"></script>
 
   <footer class="bd-footer">
   </footer>

diff --git a/azure/creating_ressources.html b/azure/creating_ressources.html
@@ -16,8 +16,8 @@
     document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
     document.documentElement.dataset.theme = localStorage.getItem("theme") || "";
   </script>
-  <!-- 
-    this give us a css class that will be invisible only if js is disabled 
+  <!--
+    this give us a css class that will be invisible only if js is disabled
   -->
   <noscript>
     <style>
@@ -27,18 +27,18 @@
   </noscript>
 
   <!-- Loaded before other Sphinx assets -->
-  <link href="../_static/styles/theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
-<link href="../_static/styles/pydata-sphinx-theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+  <link href="../_static/styles/theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
+<link href="../_static/styles/pydata-sphinx-theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
 
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css?v=a3416100" />
     <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
 
   <!-- So that users can add custom icons -->
-  <script src="../_static/scripts/fontawesome.js?digest=26a4bc78f4c0ddb94549"></script>
+  <script src="../_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
-<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
+  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
+<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
     <script src="../_static/documentation_options.js?v=9eb32ce0"></script>
     <script src="../_static/doctools.js?v=9bcbadda"></script>
@@ -50,7 +50,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="How to run a nextflow pipleline on Azure" href="running_nextflow_on_azure.html" />
-    <link rel="prev" title="About" href="../about.html" />
+    <link rel="prev" title="Training" href="../trainings/index.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   <meta name="docsearch:version" content="" />
@@ -157,6 +157,7 @@
     <div class="bd-toc-item navbar-nav active">
         <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../about.html">About</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../trainings/index.html">Training</a></li>
 </ul>
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Azure</span></p>
 <ul class="current nav bd-sidenav">
@@ -179,9 +180,14 @@
 
 
   <div class="sidebar-primary-items__end sidebar-primary__section">
+      <div class="sidebar-primary-item">
+<div id="ethical-ad-placement"
+      class="flat"
+      data-ea-publisher="readthedocs"
+      data-ea-type="readthedocs-sidebar"
+      data-ea-manual="true">
+</div></div>
   </div>
-
-  <div id="rtd-footer-container"></div>
 
 
       </div>
@@ -351,12 +357,12 @@ <h1>Create Azure resources<a class="headerlink" href="#create-azure-resources" t
 
 <div class="prev-next-area">
     <a class="left-prev"
-       href="../about.html"
+       href="../trainings/index.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">About</p>
+        <p class="prev-next-title">Training</p>
       </div>
     </a>
     <a class="right-next"
@@ -418,8 +424,8 @@ <h1>Create Azure resources<a class="headerlink" href="#create-azure-resources" t
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script defer src="../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549"></script>
-<script defer src="../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549"></script>
+  <script defer src="../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf"></script>
+<script defer src="../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf"></script>
 
   <footer class="bd-footer">
   </footer>

diff --git a/azure/running_nextflow_on_azure.html b/azure/running_nextflow_on_azure.html
@@ -16,8 +16,8 @@
     document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
     document.documentElement.dataset.theme = localStorage.getItem("theme") || "";
   </script>
-  <!-- 
-    this give us a css class that will be invisible only if js is disabled 
+  <!--
+    this give us a css class that will be invisible only if js is disabled
   -->
   <noscript>
     <style>
@@ -27,18 +27,18 @@
   </noscript>
 
   <!-- Loaded before other Sphinx assets -->
-  <link href="../_static/styles/theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
-<link href="../_static/styles/pydata-sphinx-theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+  <link href="../_static/styles/theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
+<link href="../_static/styles/pydata-sphinx-theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
 
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css?v=a3416100" />
     <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
 
   <!-- So that users can add custom icons -->
-  <script src="../_static/scripts/fontawesome.js?digest=26a4bc78f4c0ddb94549"></script>
+  <script src="../_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
-<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
+  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
+<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
     <script src="../_static/documentation_options.js?v=9eb32ce0"></script>
     <script src="../_static/doctools.js?v=9bcbadda"></script>
@@ -157,6 +157,7 @@
     <div class="bd-toc-item navbar-nav active">
         <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../about.html">About</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../trainings/index.html">Training</a></li>
 </ul>
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Azure</span></p>
 <ul class="current nav bd-sidenav">
@@ -179,9 +180,14 @@
 
 
   <div class="sidebar-primary-items__end sidebar-primary__section">
+      <div class="sidebar-primary-item">
+<div id="ethical-ad-placement"
+      class="flat"
+      data-ea-publisher="readthedocs"
+      data-ea-type="readthedocs-sidebar"
+      data-ea-manual="true">
+</div></div>
   </div>
-
-  <div id="rtd-footer-container"></div>
 
 
       </div>
@@ -417,8 +423,8 @@ <h1>How to run a nextflow pipleline on Azure<a class="headerlink" href="#how-to-
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script defer src="../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549"></script>
-<script defer src="../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549"></script>
+  <script defer src="../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf"></script>
+<script defer src="../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf"></script>
 
   <footer class="bd-footer">
   </footer>
-Original file line number
+Diff line change
@@ Expand Up / @@ -13,6 +13,7 @@ is part of the Informatics Platform, see our aims and goals @@
     :hidden:
     about
+    trainings/index
     ```
     ```{toctree}
@@ Expand Down @@