Skip to content

Commit

Permalink
Update documentation
Browse files Browse the repository at this point in the history
  • Loading branch information
@mhasoba
mhasoba committed Jan 14, 2025
1 parent 0e93933 commit cfd453e
Show file tree
Hide file tree
Showing 83 changed files with 25,097 additions and 21,906 deletions.
2 changes: 1 addition & 1 deletion .buildinfo
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 40be6e96d990e312dca40f6c890edbc8
config: a69159fed7e1fb0a1e4508b289bb66f4
tags: 645f666f9bcd5a90fca523b33c5a78b7
33 changes: 10 additions & 23 deletions HPC/Instructions/2024_11_16_HPC_worksheet.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>&lt;no title&gt; &#8212; TheMulQuaBio</title>
<title>&lt;no title&gt; &#8212; MulQuaBio</title>



Expand All @@ -32,7 +32,7 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=a3416100" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=3943d584" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
<link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
<link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=01a0bdc2" />
Expand Down Expand Up @@ -153,8 +153,8 @@



<img src="../../_static/logo.png" class="logo__image only-light" alt="TheMulQuaBio - Home"/>
<script>document.write(`<img src="../../_static/logo.png" class="logo__image only-dark" alt="TheMulQuaBio - Home"/>`);</script>
<img src="../../_static/logo.png" class="logo__image only-light" alt="MulQuaBio - Home"/>
<script>document.write(`<img src="../../_static/logo.png" class="logo__image only-dark" alt="MulQuaBio - Home"/>`);</script>


</a></div>
Expand Down Expand Up @@ -188,23 +188,9 @@
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Python.html">Biological Computing in Python</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/R.html">Biological Computing in R</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Maths for Biologists</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture01/01_Making_mathematical_statements.html">01 - Making mathematical statements</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture02/02_Describing_shapes_and_patterns.html">02 - Describing shapes and patterns</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture03/03_Analysing_change%2C_one_step_at_a_time.html">03 - Analysing change, one step at a time</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture04/04_From_table_arrangements_to_powerful_tools.html">04 - From table arrangements to powerful tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture05/05_From_table_arrangements_to_powerful_tools_part2.html">05 - From table arrangements to powerful tools - part 2</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture06/06_Analysing_change_continuously.html">06 - Analysing change, continuously</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture07/07_Analysing_change_continuously_part2.html">07 - Analysing change, continuously (Part 2)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture08/08_Calculating_accumulated_change.html">08 - Calculating accumulated change</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/tutorials/lecture01/Tutorial_01.html">Tutorial 01</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/tutorials/lecture05/Tutorial_05.html">Tutorial 05</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/tutorials/lecture06/Tutorial_06.html">Tutorial 06</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Basic Data Analyses and Statistics</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../../Stats-Intro.html">Basic Data Science and Statistics: Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../intro-Stats.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Data_R.html">Data Management and Visualization</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/ExpDesign.html">Experimental design and Data exploration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/t_F_tests.html">Basic hypothesis testing: <span class="math notranslate nohighlight">\(t\)</span> and <span class="math notranslate nohighlight">\(F\)</span> tests</a></li>
Expand All @@ -217,13 +203,14 @@
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Advanced Data Analyses and Statistics</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/glm.html">Generalised Linear Models</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/ModelFitting-NLLS.html">Model Fitting using Non-linear Least-squares</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/NLLS.html">Model Fitting using Non-linear Least-squares</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Appendices</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-JupyIntro.html">Introduction to Jupyter</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-Data-Python.html">Data analyses with Python &amp; Jupyter</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-Maths.html">Mathematical models in Jupyter</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-MathsForBiologists/MathsForBiologists.html">Maths for Biologists</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-Databases.html">Databases <span class="tocSkip"></span></a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-NLLS-Python.html">Model fitting in Python</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-MiniProj.html">The Computing Miniproject</a></li>
Expand Down Expand Up @@ -283,7 +270,7 @@



<li><a href="https://github.com/mhasoba/TheMulQuaBio" target="_blank"
<li><a href="https://github.com/MulQuaBio/MQB" target="_blank"
class="btn btn-sm btn-source-repository-button dropdown-item"
title="Source repository"
data-bs-placement="left" data-bs-toggle="tooltip"
Expand All @@ -300,7 +287,7 @@



<li><a href="https://github.com/mhasoba/TheMulQuaBio/issues/new?title=Issue%20on%20page%20%2FHPC/Instructions/2024_11_16_HPC_worksheet.html&body=Your%20issue%20content%20here." target="_blank"
<li><a href="https://github.com/MulQuaBio/MQB/issues/new?title=Issue%20on%20page%20%2FHPC/Instructions/2024_11_16_HPC_worksheet.html&body=Your%20issue%20content%20here." target="_blank"
class="btn btn-sm btn-source-issues-button dropdown-item"
title="Open an issue"
data-bs-placement="left" data-bs-toggle="tooltip"
Expand Down Expand Up @@ -1336,7 +1323,7 @@ <h2> Contents </h2>
<div class="footer-item">

<p class="component-author">
By TheMulQuaBio collective!
By MulQuaBio collective!
</p>

</div>
Expand Down
33 changes: 10 additions & 23 deletions HPC/Instructions/HPC_practical_mark_scheme_2024.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>&lt;no title&gt; &#8212; TheMulQuaBio</title>
<title>&lt;no title&gt; &#8212; MulQuaBio</title>



Expand All @@ -32,7 +32,7 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=a3416100" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=3943d584" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
<link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
<link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=01a0bdc2" />
Expand Down Expand Up @@ -151,8 +151,8 @@



<img src="../../_static/logo.png" class="logo__image only-light" alt="TheMulQuaBio - Home"/>
<script>document.write(`<img src="../../_static/logo.png" class="logo__image only-dark" alt="TheMulQuaBio - Home"/>`);</script>
<img src="../../_static/logo.png" class="logo__image only-light" alt="MulQuaBio - Home"/>
<script>document.write(`<img src="../../_static/logo.png" class="logo__image only-dark" alt="MulQuaBio - Home"/>`);</script>


</a></div>
Expand Down Expand Up @@ -186,23 +186,9 @@
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Python.html">Biological Computing in Python</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/R.html">Biological Computing in R</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Maths for Biologists</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture01/01_Making_mathematical_statements.html">01 - Making mathematical statements</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture02/02_Describing_shapes_and_patterns.html">02 - Describing shapes and patterns</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture03/03_Analysing_change%2C_one_step_at_a_time.html">03 - Analysing change, one step at a time</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture04/04_From_table_arrangements_to_powerful_tools.html">04 - From table arrangements to powerful tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture05/05_From_table_arrangements_to_powerful_tools_part2.html">05 - From table arrangements to powerful tools - part 2</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture06/06_Analysing_change_continuously.html">06 - Analysing change, continuously</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture07/07_Analysing_change_continuously_part2.html">07 - Analysing change, continuously (Part 2)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/lecture08/08_Calculating_accumulated_change.html">08 - Calculating accumulated change</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/tutorials/lecture01/Tutorial_01.html">Tutorial 01</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/tutorials/lecture05/Tutorial_05.html">Tutorial 05</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../mathscourse/tutorials/lecture06/Tutorial_06.html">Tutorial 06</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Basic Data Analyses and Statistics</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../../Stats-Intro.html">Basic Data Science and Statistics: Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../intro-Stats.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Data_R.html">Data Management and Visualization</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/ExpDesign.html">Experimental design and Data exploration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/t_F_tests.html">Basic hypothesis testing: <span class="math notranslate nohighlight">\(t\)</span> and <span class="math notranslate nohighlight">\(F\)</span> tests</a></li>
Expand All @@ -215,13 +201,14 @@
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Advanced Data Analyses and Statistics</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/glm.html">Generalised Linear Models</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/ModelFitting-NLLS.html">Model Fitting using Non-linear Least-squares</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/NLLS.html">Model Fitting using Non-linear Least-squares</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Appendices</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-JupyIntro.html">Introduction to Jupyter</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-Data-Python.html">Data analyses with Python &amp; Jupyter</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-Maths.html">Mathematical models in Jupyter</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-MathsForBiologists/MathsForBiologists.html">Maths for Biologists</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-Databases.html">Databases <span class="tocSkip"></span></a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-NLLS-Python.html">Model fitting in Python</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../notebooks/Appendix-MiniProj.html">The Computing Miniproject</a></li>
Expand Down Expand Up @@ -281,7 +268,7 @@



<li><a href="https://github.com/mhasoba/TheMulQuaBio" target="_blank"
<li><a href="https://github.com/MulQuaBio/MQB" target="_blank"
class="btn btn-sm btn-source-repository-button dropdown-item"
title="Source repository"
data-bs-placement="left" data-bs-toggle="tooltip"
Expand All @@ -298,7 +285,7 @@



<li><a href="https://github.com/mhasoba/TheMulQuaBio/issues/new?title=Issue%20on%20page%20%2FHPC/Instructions/HPC_practical_mark_scheme_2024.html&body=Your%20issue%20content%20here." target="_blank"
<li><a href="https://github.com/MulQuaBio/MQB/issues/new?title=Issue%20on%20page%20%2FHPC/Instructions/HPC_practical_mark_scheme_2024.html&body=Your%20issue%20content%20here." target="_blank"
class="btn btn-sm btn-source-issues-button dropdown-item"
title="Open an issue"
data-bs-placement="left" data-bs-toggle="tooltip"
Expand Down Expand Up @@ -550,7 +537,7 @@ <h2> Contents </h2>
<div class="footer-item">

<p class="component-author">
By TheMulQuaBio collective!
By MulQuaBio collective!
</p>

</div>
Expand Down
22 changes: 4 additions & 18 deletions Stats-Intro.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Data Management and Visualization" href="notebooks/Data_R.html" />
<link rel="prev" title="Tutorial 06" href="mathscourse/tutorials/lecture06/Tutorial_06.html" />
<link rel="prev" title="Biological Computing in R" href="notebooks/R.html" />
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
</head>
Expand Down Expand Up @@ -186,20 +186,6 @@
<li class="toctree-l1"><a class="reference internal" href="notebooks/Python.html">Biological Computing in Python</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks/R.html">Biological Computing in R</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Maths for Biologists</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="mathscourse/lecture01/01_Making_mathematical_statements.html">01 - Making mathematical statements</a></li>
<li class="toctree-l1"><a class="reference internal" href="mathscourse/lecture02/02_Describing_shapes_and_patterns.html">02 - Describing shapes and patterns</a></li>
<li class="toctree-l1"><a class="reference internal" href="mathscourse/lecture03/03_Analysing_change%2C_one_step_at_a_time.html">03 - Analysing change, one step at a time</a></li>
<li class="toctree-l1"><a class="reference internal" href="mathscourse/lecture04/04_From_table_arrangements_to_powerful_tools.html">04 - From table arrangements to powerful tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="mathscourse/lecture05/05_From_table_arrangements_to_powerful_tools_part2.html">05 - From table arrangements to powerful tools - part 2</a></li>
<li class="toctree-l1"><a class="reference internal" href="mathscourse/lecture06/06_Analysing_change_continuously.html">06 - Analysing change, continuously</a></li>
<li class="toctree-l1"><a class="reference internal" href="mathscourse/lecture07/07_Analysing_change_continuously_part2.html">07 - Analysing change, continuously (Part 2)</a></li>
<li class="toctree-l1"><a class="reference internal" href="mathscourse/lecture08/08_Calculating_accumulated_change.html">08 - Calculating accumulated change</a></li>
<li class="toctree-l1"><a class="reference internal" href="mathscourse/tutorials/lecture01/Tutorial_01.html">Tutorial 01</a></li>
<li class="toctree-l1"><a class="reference internal" href="mathscourse/tutorials/lecture05/Tutorial_05.html">Tutorial 05</a></li>
<li class="toctree-l1"><a class="reference internal" href="mathscourse/tutorials/lecture06/Tutorial_06.html">Tutorial 06</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Basic Data Analyses and Statistics</span></p>
<ul class="current nav bd-sidenav">
<li class="toctree-l1 current active"><a class="current reference internal" href="#">Basic Data Science and Statistics: Introduction</a></li>
Expand All @@ -215,7 +201,7 @@
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Advanced Data Analyses and Statistics</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="notebooks/glm.html">Generalised Linear Models</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks/ModelFitting-NLLS.html">Model Fitting using Non-linear Least-squares</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks/NLLS.html">Model Fitting using Non-linear Least-squares</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Appendices</span></p>
<ul class="nav bd-sidenav">
Expand Down Expand Up @@ -485,12 +471,12 @@ <h2>Readings &amp; Resources<a class="headerlink" href="#readings-resources" tit

<div class="prev-next-area">
<a class="left-prev"
href="mathscourse/tutorials/lecture06/Tutorial_06.html"
href="notebooks/R.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">Tutorial 06</p>
<p class="prev-next-title">Biological Computing in R</p>
</div>
</a>
<a class="right-next"
Expand Down
Binary file added _images/0e3205167ee6fe026989b4ed40257f1e3dd61651f3a9d9a9350f32e0b5ebc84a.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file removed _images/func_diff1.png
View file
Binary file not shown.
Binary file modified _images/log_base_02.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading

0 comments on commit cfd453e

Please sign in to comment.