Update documentation

WS1/module_1/0_python_basics.html

@@ -202,8 +202,7 @@
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../module_3/0_intro_module_3.html">Module 3</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/1_operations.html">Operations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Finding the logarithm of a value in Python</a></li>
-
+<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Linear Regression</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/3_stoichiometry.html">Stoichiometry (1)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/4_stoichiometry_solution.html">Stoichiometry (solution)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/5_stoichiometry_pt2.html">Stoichiometry (2)</a></li>

WS1/module_1/4_exercise_1.html

@@ -200,8 +200,7 @@
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../module_3/0_intro_module_3.html">Module 3</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/1_operations.html">Operations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Finding the logarithm of a value in Python</a></li>
-
+<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Linear Regression</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/3_stoichiometry.html">Stoichiometry (1)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/4_stoichiometry_solution.html">Stoichiometry (solution)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/5_stoichiometry_pt2.html">Stoichiometry (2)</a></li>
@@ -622,7 +621,11 @@ <h2>3. Lists and generators<a class="headerlink" href="#lists-and-generators" ti
 <h2>4. Compound statements<a class="headerlink" href="#compound-statements" title="Link to this heading">#</a></h2>
 <p><strong>Exercise</strong>: Translate the following flow chart to check why the unit for the <em>hydrodynamics condition in packed tower</em> experiment is not working.</p>
 <p>Level: <span style="color:green">Easy</span>.</p>
-<p><img alt="alt text" src="WS1/theory/images/Flow_chart.png" /></p>
+<p><img src="../../media/WS1/flow_chart.png" 
+        alt="Picture" 
+        width="400" 
+        height="600" 
+        style="display: block; margin: 0 auto" /></p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Your code here</span>

WS1/module_1/5_exercise_2.html

@@ -200,8 +200,7 @@
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../module_3/0_intro_module_3.html">Module 3</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/1_operations.html">Operations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Finding the logarithm of a value in Python</a></li>
-
+<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Linear Regression</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/3_stoichiometry.html">Stoichiometry (1)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/4_stoichiometry_solution.html">Stoichiometry (solution)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/5_stoichiometry_pt2.html">Stoichiometry (2)</a></li>
@@ -550,7 +549,11 @@ <h2>Exercise: Binary to English translation<a class="headerlink" href="#exercise
 <section id="possible-solutions">
 <h2>Possible solutions<a class="headerlink" href="#possible-solutions" title="Link to this heading">#</a></h2>
 <p><span style="color:red">!!! Do not scroll down if you don’t want to see the solutions…you have been warned!</span>.</p>
-<p><img alt="alt text" src="WS1/theory/images/spoiler.jpg" /></p>
+<p><img src="../../media/WS1/spoiler.jpg" 
+        alt="Picture" 
+        width="400" 
+        height="300" 
+        style="display: block; margin: 0 auto" /></p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">string_a</span> <span class="o">=</span> <span class="s1">&#39;a&#39;</span>

WS1/module_2/0_intro_module_2.html

@@ -200,8 +200,7 @@
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../module_3/0_intro_module_3.html">Module 3</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/1_operations.html">Operations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Finding the logarithm of a value in Python</a></li>
-
+<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Linear Regression</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/3_stoichiometry.html">Stoichiometry (1)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/4_stoichiometry_solution.html">Stoichiometry (solution)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/5_stoichiometry_pt2.html">Stoichiometry (2)</a></li>

WS1/module_2/3_numpy_arrays.html

@@ -200,8 +200,7 @@
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../module_3/0_intro_module_3.html">Module 3</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/1_operations.html">Operations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Finding the logarithm of a value in Python</a></li>
-
+<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Linear Regression</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/3_stoichiometry.html">Stoichiometry (1)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/4_stoichiometry_solution.html">Stoichiometry (solution)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/5_stoichiometry_pt2.html">Stoichiometry (2)</a></li>

WS1/module_3/0_intro_module_3.html

@@ -202,8 +202,7 @@
 </details></li>
 <li class="toctree-l1 current active has-children"><a class="current reference internal" href="#">Module 3</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="1_operations.html">Operations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="2_linear_regression.html">Finding the logarithm of a value in Python</a></li>
-
+<li class="toctree-l2"><a class="reference internal" href="2_linear_regression.html">Linear Regression</a></li>
 <li class="toctree-l2"><a class="reference internal" href="3_stoichiometry.html">Stoichiometry (1)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="4_stoichiometry_solution.html">Stoichiometry (solution)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="5_stoichiometry_pt2.html">Stoichiometry (2)</a></li>

WS1/module_3/2_linear_regression.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Finding the logarithm of a value in Python &#8212; Dig4Bio-workshops</title>
+    <title>Linear Regression &#8212; Dig4Bio-workshops</title>
 
 
 
@@ -202,8 +202,7 @@
 </details></li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="0_intro_module_3.html">Module 3</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="1_operations.html">Operations</a></li>
-<li class="toctree-l2 current active"><a class="current reference internal" href="#">Finding the logarithm of a value in Python</a></li>
-
+<li class="toctree-l2 current active"><a class="current reference internal" href="#">Linear Regression</a></li>
 <li class="toctree-l2"><a class="reference internal" href="3_stoichiometry.html">Stoichiometry (1)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="4_stoichiometry_solution.html">Stoichiometry (solution)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="5_stoichiometry_pt2.html">Stoichiometry (2)</a></li>
@@ -445,7 +444,7 @@
 
 
 <div id="jb-print-docs-body" class="onlyprint">
-    <h1>Finding the logarithm of a value in Python</h1>
+    <h1>Linear Regression</h1>
     <!-- Table of contents -->
     <div id="print-main-content">
         <div id="jb-print-toc">
@@ -455,10 +454,9 @@ <h2> Contents </h2>
             </div>
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#">Finding the logarithm of a value in Python</a></li>
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#simple-linear-regression-in-python-with-scipy-library">Simple linear regression in Python with SciPy library</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#finding-the-logarithm-of-a-value-in-python">Finding the logarithm of a value in Python</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#simple-linear-regression-in-python-with-scipy-library">Simple linear regression in Python with SciPy library</a></li>
 </ul>
-
             </nav>
         </div>
     </div>
@@ -469,7 +467,9 @@ <h2> Contents </h2>
 <div id="searchbox"></div>
                 <article class="bd-article">
 
-  <p>In this notebook, we will explore some more operations, such as calculating the logarithm in numpy and doing a linear regression.</p>
+  <section class="tex2jax_ignore mathjax_ignore" id="linear-regression">
+<h1>Linear Regression<a class="headerlink" href="#linear-regression" title="Link to this heading">#</a></h1>
+<p>In this notebook, we will explore some more operations, such as calculating the logarithm in numpy and doing a linear regression.</p>
 <p>You have the following isothermic reaction:
 <span class="math notranslate nohighlight">\(A+\frac{1}{6}B→\frac{1}{4}C+\frac{1}{2}D\)</span></p>
 <p>During a laboratory experiment you measure in a batch reactor with constant volume and the initial concentration of <span class="math notranslate nohighlight">\(C_A\)</span> is 25 <span class="math notranslate nohighlight">\(mol \cdot m^{-3}\)</span>.</p>
@@ -531,7 +531,7 @@ <h2> Contents </h2>
 </div>
 </div>
 <section id="finding-the-logarithm-of-a-value-in-python">
-<h1>Finding the logarithm of a value in Python<a class="headerlink" href="#finding-the-logarithm-of-a-value-in-python" title="Link to this heading">#</a></h1>
+<h2>Finding the logarithm of a value in Python<a class="headerlink" href="#finding-the-logarithm-of-a-value-in-python" title="Link to this heading">#</a></h2>
 <p>Here we will use the numpy library to calculate the logarithm of the values defined.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
@@ -554,7 +554,7 @@ <h1>Finding the logarithm of a value in Python<a class="headerlink" href="#findi
 </div>
 </section>
 <section id="simple-linear-regression-in-python-with-scipy-library">
-<h1>Simple linear regression in Python with SciPy library<a class="headerlink" href="#simple-linear-regression-in-python-with-scipy-library" title="Link to this heading">#</a></h1>
+<h2>Simple linear regression in Python with SciPy library<a class="headerlink" href="#simple-linear-regression-in-python-with-scipy-library" title="Link to this heading">#</a></h2>
 <p>Here we calculate a linear least-squares regression for two sets of measurements.
 Check the documentation <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.linregress.html">here</a>.</p>
 <p>The unction returns:</p>
@@ -618,6 +618,7 @@ <h1>Simple linear regression in Python with SciPy library<a class="headerlink" h
 </div>
 </div>
 </div>
+</section>
 </section>
 
     <script type="text/x-thebe-config">
@@ -684,10 +685,9 @@ <h1>Simple linear regression in Python with SciPy library<a class="headerlink" h
   </div>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#">Finding the logarithm of a value in Python</a></li>
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#simple-linear-regression-in-python-with-scipy-library">Simple linear regression in Python with SciPy library</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#finding-the-logarithm-of-a-value-in-python">Finding the logarithm of a value in Python</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#simple-linear-regression-in-python-with-scipy-library">Simple linear regression in Python with SciPy library</a></li>
 </ul>
-
   </nav></div>
 
 </div></div>

WS1/module_4/0_intro_module_4.html

@@ -202,8 +202,7 @@
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../module_3/0_intro_module_3.html">Module 3</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/1_operations.html">Operations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Finding the logarithm of a value in Python</a></li>
-
+<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Linear Regression</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/3_stoichiometry.html">Stoichiometry (1)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/4_stoichiometry_solution.html">Stoichiometry (solution)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/5_stoichiometry_pt2.html">Stoichiometry (2)</a></li>

WS1/module_4/2_combining_balances.html

@@ -202,8 +202,7 @@
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../module_3/0_intro_module_3.html">Module 3</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/1_operations.html">Operations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Finding the logarithm of a value in Python</a></li>
-
+<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Linear Regression</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/3_stoichiometry.html">Stoichiometry (1)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/4_stoichiometry_solution.html">Stoichiometry (solution)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/5_stoichiometry_pt2.html">Stoichiometry (2)</a></li>
@@ -462,8 +461,12 @@ <h1>Energy balance for a laboratory equipment batch reactor for chemical synthes
 <p>In this programming exercise you will also have from a chemical engineering point of view the task to develop the energy balance for a batch reactor. This is a task, we have not yet investigated in the lectures or group exercises.
 We consider the following Reaction taking place in a laboratory sized reactor using a liquid phase:</p>
 <p><span class="math notranslate nohighlight">\(A→B\)</span></p>
-<p>The setup is described in the following:
-<img alt="alt text" src="WS1/module_4/assignment2_system.png" /></p>
+<p>The setup is described in the following:</p>
+<p><img src="../../media/WS1/system.png" 
+        alt="Picture" 
+        width="500" 
+        height="500" 
+        style="display: block; margin: 0 auto" /></p>
 <p>You can assume that the reaction order follows an elementary reaction and you have found in literature the rate velocity coefficient at 298 K to be 0.005 min-1.
 Please perform with help the following analysis:</p>
 <ol class="arabic simple">

WS1/module_4/3_combining_balances_solution.html

@@ -202,8 +202,7 @@
 </details></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../module_3/0_intro_module_3.html">Module 3</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/1_operations.html">Operations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Finding the logarithm of a value in Python</a></li>
-
+<li class="toctree-l2"><a class="reference internal" href="../module_3/2_linear_regression.html">Linear Regression</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/3_stoichiometry.html">Stoichiometry (1)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/4_stoichiometry_solution.html">Stoichiometry (solution)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../module_3/5_stoichiometry_pt2.html">Stoichiometry (2)</a></li>
@@ -463,7 +462,11 @@ <h1>Energy balance for a laboratory equipment batch reactor for chemical synthes
 We consider the following Reaction taking place in a laboratory sized reactor using a liquid phase:</p>
 <p><span class="math notranslate nohighlight">\(A→B\)</span></p>
 <p>The setup is described in the following:
-<img alt="alt text" src="WS1/module_4/assignment2_system.png" /></p>
+<img src="../../media/WS1/system.png" 
+        alt="Picture" 
+        width="500" 
+        height="500" 
+        style="display: block; margin: 0 auto" /></p>
 <p>You can assume that the reaction order follows an elementary reaction and you have found in literature the rate velocity coefficient at 298 K to be 0.005 min-1.
 Please perform with help the following analysis:</p>
 <ol class="arabic simple">

_sources/WS1/module_1/4_exercise_1.ipynb

@@ -335,7 +335,12 @@
     "\n",
     "Level: <span style=\"color:green\">Easy</span>.\n",
     "\n",
-    "![alt text](../theory/images/Flow_chart.png)"
+    "<img src=\"../../media/WS1/flow_chart.png\" \n",
+    "        alt=\"Picture\" \n",
+    "        width=\"400\" \n",
+    "        height=\"600\" \n",
+    "        style=\"display: block; margin: 0 auto\" />\n",
+    "\n"
    ]
   },
   {