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microbiome · Jan 3, 2025 · 981d075 · 981d075
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diff --git a/docs/404.html b/docs/404.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Page not found | Microbiome Data Science &amp; Multi-Omics with R/Bioconductor</title>
   <meta name="description" content="Course material" />
-  <meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Page not found | Microbiome Data Science &amp; Multi-Omics with R/Bioconductor" />
   <meta property="og:type" content="book" />
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-11-14" />
+<meta name="date" content="2025-01-03" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -63,7 +63,6 @@
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   clear: both;
-  margin-bottom: 0em;
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diff --git a/docs/course_material.pdf b/docs/course_material.pdf
diff --git a/docs/course_material.tex b/docs/course_material.tex
@@ -36,7 +36,7 @@
 \IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
 \IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
 \hypersetup{
-  pdftitle={Microbiome data science with R/Bioconductor},
+  pdftitle={Microbiome Data Science \& Multi-Omics with R/Bioconductor},
   hidelinks,
   pdfcreator={LaTeX via pandoc}}
 \urlstyle{same} % disable monospaced font for URLs
@@ -75,16 +75,16 @@
 \usepackage[]{natbib}
 \bibliographystyle{apalike}
 
-\title{Microbiome data science with R/Bioconductor}
+\title{Microbiome Data Science \& Multi-Omics with R/Bioconductor}
 \usepackage{etoolbox}
 \makeatletter
 \providecommand{\subtitle}[1]{% add subtitle to \maketitle
   \apptocmd{\@title}{\par {\large #1 \par}}{}{}
 }
 \makeatother
-\subtitle{Oulu, June 2024}
+\subtitle{Oulu, December 2024}
 \author{}
-\date{\vspace{-2.5em}2024-10-20}
+\date{\vspace{-2.5em}2025-01-03}
 
 \begin{document}
 \maketitle
@@ -128,13 +128,22 @@ \section{How to apply}\label{how-to-apply}}
 \begin{itemize}
 \tightlist
 \item
-  Send a brief motivation letter to Anna Kaisanlahti \href{mailto:[email protected]}{\nolinkurl{[email protected]}}
+  Send a brief motivation letter to Anna Kaisanlahti \href{mailto:[email protected]}{\nolinkurl{[email protected]}}. In your letter, please describe your skill level in R coding using scale 1-5 (1 = no previous experience, 5 = advanced level), and your previous experience related to bioinformatics.
 \item
-  Applications from local students, and applications sent before Nov 15 will be given priority
+  Applications from local students, and applications sent before 11 November 2024 will be given priority.
 \item
   The course has maximum capacity of 20 participants.
+\item
+  The enrollment to the course will be confirmed within few days after the application deadline (Nov 11).
+\item
+  Applications received after 11.11 will also be considered in case there are slots still available.
 \end{itemize}
 
+\hypertarget{before-the-course}{%
+\section{Before the course}\label{before-the-course}}
+
+For self-learning, visit \href{https://microbiome.github.io/OMA/docs/devel/pages/training.html}{this site}.
+
 \hypertarget{teachers-and-organizers}{%
 \section{Teachers and organizers}\label{teachers-and-organizers}}
 
@@ -164,7 +173,7 @@ \section{Code of Conduct}\label{code-of-conduct}}
 \hypertarget{acknowledgments}{%
 \section{Acknowledgments}\label{acknowledgments}}
 
-\textbf{Citation}: We thank all \href{https://microbiome.github.io}{developers and contributors} who have contributed open resources that supported the development of the training material. Kindly cite the course material as \citet{miacourse}.
+\textbf{Citation}: We thank all \href{https://microbiome.github.io}{developers and contributors} who have contributed open resources that supported the development of the training material. Kindly cite the course material as \citet{miacourse}. This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 952914 (FindingPheno).
 
 \textbf{Contact}: Refer to \url{https://microbiome.github.io}.
 

diff --git a/docs/index.html b/docs/index.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Microbiome Data Science &amp; Multi-Omics with R/Bioconductor</title>
   <meta name="description" content="Course material" />
-  <meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Microbiome Data Science &amp; Multi-Omics with R/Bioconductor" />
   <meta property="og:type" content="book" />
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-11-14" />
+<meta name="date" content="2025-01-03" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -63,7 +63,6 @@
 div.csl-bib-body { }
 div.csl-entry {
   clear: both;
-  margin-bottom: 0em;
 }
 .hanging div.csl-entry {
   margin-left:2em;
@@ -145,7 +144,7 @@ <h1>
 <div id="header">
 <h1 class="title">Microbiome Data Science &amp; Multi-Omics with R/Bioconductor</h1>
 <h2 class="subtitle"><em>Oulu, December 2024</em></h2>
-<p class="date"><em>2024-11-14</em></p>
+<p class="date"><em>2025-01-03</em></p>
 </div>
 <div id="overview" class="section level1 hasAnchor" number="1">
 <h1><span class="header-section-number">1</span> Overview<a href="index.html#overview" class="anchor-section" aria-label="Anchor link to header"></a></h1>
@@ -160,9 +159,9 @@ <h2><span class="header-section-number">1.1</span> Contents and learning goals<a
 <p><strong>Teaching material</strong>: We will follow open online documentation created by the course teachers, primarily the <a href="https://microbiome.github.io/OMA">Orchestrating Microbiome Analysis</a> (OMA) book. The training material walks you through the standard steps of omics data analysis covering data access, exploration, analysis, visualization, and reproducible workflows. Preparatory material and video clips, and online support are available before the course. All teaching materials are shared openly.</p>
 </div>
 <div class="g-col-3">
-<div class="float">
-<img src="fig.png" fig-align="center" width="300" alt="Figure source: Moreno-Indias et al. (2021) Frontiers in Microbiology 12:11." />
-<div class="figcaption">Figure source: Moreno-Indias <em>et al</em>. (2021) <em>Frontiers in Microbiology</em> 12:11.</div>
+<div class="figure">
+<img src="fig.png" fig-align="center" width="300" alt="" />
+<p class="caption">Figure source: Moreno-Indias <em>et al</em>. (2021) <em>Frontiers in Microbiology</em> 12:11.</p>
 </div>
 </div>
 </div>
@@ -191,7 +190,7 @@ <h2><span class="header-section-number">1.4</span> Before the course<a href="ind
 <div id="teachers-and-organizers" class="section level2 hasAnchor" number="1.5">
 <h2><span class="header-section-number">1.5</span> Teachers and organizers<a href="index.html#teachers-and-organizers" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p><strong>Teachers</strong>: <a href="https://datascience.utu.fi">Leo Lahti</a> is the main teacher and Professor in Data Science at the University of Turku, and a certified <a href="https://carpentries.org">Carpentries</a> Instructor. PhD researcher <em>Tuomas Borman</em> is a co-teacher and main developer of the data science framework used in the course. <em>Anna Kaisanlahti</em> (Oulu) is a course assistant, and Docent <em>Justus Reunanen</em> is the course coordinator. The course is organized by <a href="https://www.oulu.fi/en/research/graduate-school/organisation-and-contact-information-uniogs/health-and-biosciences-doctoral-programme">Health and Biosciences Doctoral Programme (HBS-DP)</a> University of Oulu Graduate School, Research Unit of Translational Medicine, University of Oulu. We thank the <a href="https://csc.fi/">Finnish IT Center for Science (CSC)</a> supports the course by providing cloud computing services.</p>
-<p>This is a Bioconductor course <span class="citation">Drnevich et al. (<a href="#ref-Soneson2024">2024</a>)</span> and we follow the best practices recommended by <a href="https://carpentries.org">Software carpentries</a>.</p>
+<p>This is a Bioconductor course <span class="citation">Drnevich et al. (<a href="#ref-Soneson2024" role="doc-biblioref">2024</a>)</span> and we follow the best practices recommended by <a href="https://carpentries.org">Software carpentries</a>.</p>
 </div>
 <div id="code-of-conduct" class="section level2 hasAnchor" number="1.6">
 <h2><span class="header-section-number">1.6</span> Code of Conduct<a href="index.html#code-of-conduct" class="anchor-section" aria-label="Anchor link to header"></a></h2>
@@ -206,15 +205,15 @@ <h2><span class="header-section-number">1.6</span> Code of Conduct<a href="index
 </div>
 <div id="acknowledgments" class="section level2 hasAnchor" number="1.7">
 <h2><span class="header-section-number">1.7</span> Acknowledgments<a href="index.html#acknowledgments" class="anchor-section" aria-label="Anchor link to header"></a></h2>
-<p><strong>Citation</strong>: We thank all <a href="https://microbiome.github.io">developers and contributors</a> who have contributed open resources that supported the development of the training material. Kindly cite the course material as <span class="citation">Tuomas Borman and Leo Lahti (<a href="#ref-miacourse">2024</a>)</span>.</p>
+<p><strong>Citation</strong>: We thank all <a href="https://microbiome.github.io">developers and contributors</a> who have contributed open resources that supported the development of the training material. Kindly cite the course material as <span class="citation">Tuomas Borman and Leo Lahti (<a href="#ref-miacourse" role="doc-biblioref">2024</a>)</span>. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 952914 (FindingPheno).</p>
 <p><strong>Contact</strong>: Refer to <a href="https://microbiome.github.io">https://microbiome.github.io</a>.</p>
 <p><strong>License and source code</strong>:</p>
 <p>All material is released under the open <a href="LICENSE">CC BY-NC-SA 3.0 License</a> and available online during and after the course, following the <a href="https://avointiede.fi/fi/linjaukset-ja-aineistot/kotimaiset-linjaukset/oppimisen-ja-oppimateriaalien-avoimuuden-linjaus">recommendations on open teaching materials</a> of the national open science coordination in Finland.</p>
 
 </div>
 </div>
 <h3>References</h3>
-<div id="refs" class="references csl-bib-body hanging-indent" entry-spacing="0">
+<div id="refs" class="references csl-bib-body hanging-indent">
 <div id="ref-Soneson2024" class="csl-entry">
 Drnevich, Jenny, Frederick J. Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C. Culhane, Sean Davis, Maria A. Doyle, et al. 2024. <span>“<span class="nocase">Learning and teaching biological data science in the Bioconductor community</span>.”</span> <a href="https://arxiv.org/abs/2410.01351">https://arxiv.org/abs/2410.01351</a>.
 </div>

diff --git a/docs/index.md b/docs/index.md
@@ -1,7 +1,7 @@
 --- 
 title: "Microbiome Data Science & Multi-Omics with R/Bioconductor"
 subtitle: "Oulu, December 2024"
-date: "2024-11-14"
+date: "2025-01-03"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [packages.bib]
@@ -90,7 +90,7 @@ More details on its enforcement are available [here](https://bioconductor.github
 
 ## Acknowledgments
 
-**Citation**: We thank all [developers and contributors](https://microbiome.github.io) who have contributed open resources that supported the development of the training material. Kindly cite the course material as @miacourse.
+**Citation**: We thank all [developers and contributors](https://microbiome.github.io) who have contributed open resources that supported the development of the training material. Kindly cite the course material as @miacourse. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 952914 (FindingPheno).
 
 **Contact**: Refer to [https://microbiome.github.io](https://microbiome.github.io).
 

diff --git a/docs/program.html b/docs/program.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>2 Program | Microbiome Data Science &amp; Multi-Omics with R/Bioconductor</title>
   <meta name="description" content="Course material" />
-  <meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />
 
   <meta property="og:title" content="2 Program | Microbiome Data Science &amp; Multi-Omics with R/Bioconductor" />
   <meta property="og:type" content="book" />
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-11-14" />
+<meta name="date" content="2025-01-03" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -63,7 +63,6 @@
 div.csl-bib-body { }
 div.csl-entry {
   clear: both;
-  margin-bottom: 0em;
 }
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