index.Rmd

--- 
title: "Multi-omic data science with R/Bioconductor"
subtitle: "Welcome to Oulu Summer School, June 2022"
date: "`r Sys.Date()`"
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documentclass: book
bibliography: [packages.bib]
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github-repo: microbiome/course_2022_oulu
description: "Course material"
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  bookdown::gitbook
  bookdown::pdf_document2
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# Overview

<a href="https://bioconductor.org"><img src="`r rebook::BiocSticker('animated')`" width="200" alt="Bioconductor Sticker" align="right" style="margin: 0 1em 0 1em" /></a>


## Contents and learning goals

This course will teach the **basics of biomedical data analysis with
R/Bioconductor**, a popular open source environment for scientific
data analysis. The participants get an overview of the reproducible
data analysis workflow in modern multi-omics, with a focus on recent
examples from published microbiome studies. After the course you will
know how to approach new tasks in biomedical data analysis by
utilizing available documentation and R tools.

The teaching will follow open online documentation created by the
course teachers, extending the online book Orchestrating Microbiome
Analysis (https://microbiome.github.io/OMA). The openly licensed
teaching material will be available online during and after the
course, following national recommendations on open education.

The training material walks you through the standard steps of
biomedical data analysis covering data access, exploration, analysis,
visualization, reproducible reporting, and best practices in open
science.  We will teach generic data analytical skills that are
applicable to common data analysis tasks encountered in modern omics
research. The teaching format allows adaptations according to the
student's learning speed.


## Schedule and organizers

The course will be organized in a live format <a href="https://github.com/microbiome/course_2022_oulu/raw/main/flyer.pdf">(Flyer)</a>

**Venue** University of Oulu. June 20-23, 2022.

**Schedule** Contact teaching daily between 9am – 5pm, including
  lectures, demonstrations, hands-on sessions, and breaks. A 
  detailed schedule is available at the course website:
  (https://microbiome.github.io/course_2022_oulu).

**Teachers and organizers**

[Leo Lahti](https://datascience.utu.fi) is the main teacher and Associate Professor in Data Science at the University of Turku, with specialization on biomedical data analysis. Course assistants are _Tuomas Borman_ (University of Turku) is one of the main developers of the open training material covered by the course, _Jenni Hekkala_, a PhD researcher at the University of Oulu, in the group of the course coordinator Docent _Justus Reunanen_, and _Rajesh Shigdel_ who has supported the writing of the course material.

The course is jointly organized by

- Health and Biosciences Doctoral Programme University of Oulu Graduate School
- Cancer & Translational Medicine Research Unit, University of Oulu
- Department of Computing, University of Turku, Finland
- Finnish IT Center for Science (CSC) supports the course with cloud
  computing services


## How to apply

**Target audience**

The course is primarily designed for advanced MSc and PhD students,
Postdocs, and biomedical researchers who wish to learn and develop new skills in
scientific programming and biomedical data analysis. Academic students
and researchers from Finland and abroad are welcome and encouraged to
apply. The course has limited capacity of max 20 participants, and
priority will given for local students from Oulu.

**Expected background** Some earlier experience with R or another
  programming language is recommended. However, this can be
  compensated by familiarizing with the course material in advance, if
  necessary. The teaching format allows adaptations according to the
  student's learning speed.

**Application**

  * Send a brief motivation letter to Jenni Hekkala <first.last@oulu.fi>
  * Applications sent before May 20 will be given priority


**Course fee**

The course fee covers contact teaching and teaching material.

  * 285 euros with registration by May 20, 2022
  * 350 euros with registration after May 20, 2022
  * Local students are exempted from the fee


**Accommodation** 

Accommodation and travel costs are not included in the registration fee. For 
accommodation tips, see https://visitoulu.fi/en/arrival-overnight/




## 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 

**Contact** See [https://microbiome.github.io](https://microbiome.github.io)


**License and source code**

All material is released under the open [CC BY-NC-SA 3.0 License](LICENSE) and available online during and after the course, following the [recommendations on open teaching materials](https://avointiede.fi/fi/linjaukset-ja-aineistot/kotimaiset-linjaukset/oppimisen-ja-oppimateriaalien-avoimuuden-linjaus) of the national open science coordination in Finland**.

The source code of this repository is reproducible and contains
the Rmd files with executable code. All files can be rendered at one
go by running the file [main.R](main.R). You can check the file for
details on how to clone the repository and convert it into a gitbook,
although this is not necessary for the training.

- Source code (github): [miaverse teaching material](https://github.com/microbiome/course_2022_oulu)
- Course page (html): [miaverse teaching material](https://microbiome.github.io/course_2022_oulu/)