ELIXIR Data Carpentry Workshop

Trainer Christof De Bo, Janick Mathys and Rekin's Janky
BITS Courses TRAINING AT VIB

Goal

The fast generation of large amounts of data is fundamentally changing the way how research is done today. Many domains of research are challenged with managing, analyzing and sharing genomics data. This is not just a challenge, it is an opportunity to implement this workshop for researchers to learn basic handling of genomics concepts, skills and tools. This workshop is aimed at researchers in the life sciences at all career stages and is designed for learners with little to no prior knowledge of Linux and command line tools, programming in R or biological networks in Cytoscape.

Summary

The main ambition or this workshop is that researchers get more familiar with genomics data and handle it in a more efficient way. The following topics will be covered during the workshop:

  • Introduction to Linux and the command line:
    The first session will introduce you to the use of Linux and the command line for managing and analyzing genomics data
  • Data manipulation in R:
    This session gives an introduction to the use of the R packages plyr and ggplot2 for data manipulation and subsequent graphing
  • Initiation Cytoscape:
    In this tutorial, you will be introduced to the basics of Cytoscape (how to make a network, change the visualisation parameters such as the layout,...), and to more advanced functionalities such as data integration and data analysis using Cytoscape plugins

Prerequisites

None

Schedule

Available on the TRAINING AT VIB website (see link above).

Training material

Will be made available during the workshop.

Links

Linux Mint
The purpose of Linux Mint is to produce a modern, elegant and comfortable operating system which is both powerful and easy to use. Linux Mint is the most popular desktop Linux distribution and the 3rd most widely used home operating system behind Microsoft Windows and Apple Mac OS X
https://www.linuxmint.com

R Studio
People all over the world are turning to R, an open source statistical language, to make sense of data. Inspired by the innovations of R users in science, education, and industry, RStudio develops free and open tools for R
https://www.rstudio.com

Cytoscape
Cytoscape is a free, Open Source bioinformatics environment for integration, visualisation, and query of biological networks
http://www.ncbi.nlm.nih.gov/pubmed/14597658?dopt=Abstract
http://www.ncbi.nlm.nih.gov/pubmed/17947979
http://www.cytoscape.org

Other links:
http://www.elixir-belgium.org
http://www.datacarpentry.org

Scientific topics Data visualisation, Genomics
Target audience Life Science Researchers, PhD students, post-docs