Introduction to bioinformatics

DNF Coding Club Session #01 (06/11/2019)

Welcome

As you might know, some people in our department are encouraging the use of new technologies for data analysis, visualisation and database scraping. With the support of the PIs, we are happy to announce the start of the DNF coding sessions (i.e. “DNF coding club”) that will provide the basics on daily research technologies such as bash, R, Jupyter and Shiny.

The first coding session will take place in the APP room on Wednesday, November 6 from 13:30 to 18:00. The schedule is the following:

1. A quick intro to tools for reproducible research: git, bash, docker and jupyter.
2. A quick intro to R tools for data manipulation and visualization: dplyr and ggplot2.
3. Open discussion to prepare for coding topics next session and introduction to a custom-made application for batch image analysis.
4. Closure with food for brain: pizza.

Every module will take approximately 1h30, with intermittent breaks of 15 min.

The session is open to anyone with or without prior technical knowledge. These activities are designed to get familiar and used to these skills in a friendly and interactive environment. Only requirement is to bring your own laptop with wifi connection.

Server Connection

http://130.223.196.101:8080

Github

https://github.com/

https://github.com/DNF-UNIL/Introduction_to_bioinformatics

Bash

https://explainshell.com/

Download image script

#/bin/bash

for i in {0..100}
do

echo $i
wget https://spainweather.es/webcams/malaga/current.jpg
sleep 3

done

Jupyter Notebooks

https://jupyter.org/

Binder

https://mybinder.org/

Docker

https://www.docker.com/

https://hub.docker.com/

R

by L. Telley

https://juba.github.io/tidyverse/02-prise_en_main.html

EBImage

It is necessary to first install this dependency in the terminal

sudo apt-get update
sudo apt-get install libfftw3-3 libfftw3-dev libtiff5-dev
sudo conda install -c eumetsat fftw3

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("EBImage")

Shiny

by Adrian

https://github.com/DNF-UNIL/Introduction_to_bioinformatics/blob/master/presentations/2019.11.06_shiny_introduction.pptx

How to install Docker

https://docs.docker.com/install/linux/docker-ce/ubuntu/

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -

sudo add-apt-repository \
   "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
   $(lsb_release -cs) \
   stable"
   
sudo apt-get update
sudo apt-get install docker-ce docker-ce-cli containerd.io

DNF Coding Club Session #02 (04/12/2019)

Welcome

The next coding session will take place in the Petit Auditoire on Wednesday December 4 from 13:00 to 17:30. In this session, we have the additional contribution of Tilmann and Romain.

The schedule will be the following:

Theory:

• Summary of the session
• Showcase of Arduino Projects

Practise:

• Basics on bash and terminal
• Basics of programming with R in Jupyter Notebooks
• Machine Learning for pattern recognition (automatic cell extraction)

Closure:

• Apero and social dynamics

The session is open to anyone regardless of prior technical knowledge. These activities are designed to become familiar and used to these skills in a friendly and interactive environment. Only requirement is to bring your own laptop with wifi connection.