These are optional lectures to introduce topics that may not be familiar to some students. If you are unfamiliar or a novice with R, Python, or the Unix/Linux command line then please go through these lessons prior to the start of the Workshop. R, Python, and the command line will be used during the practical sessions. There is no need to go through the tutorials for familiar topics.
All of these videos are in the Day 0 playlist.
Introduction to the Unix/Linux command line
Presented by Jeffrey M. Lessem, based on material from Sarah E. Medland
Many of the practical sessions will use the command line. To open a terminal and get a command line on the Workshop cluster, see the Accessing the Workshop Computing Cluster document in the technical support section of the website.
A PDF Unix cheat sheet is available, which Sarah Medland prepared for the 2019 course.
There is a video of an introduction to using the command line at the Workshop.
The abridged slides used in the video, and the original slides from Sarah Medland are available.
There are many introductions to the command line available online. Here are some which novices may find useful. Most of these generally cover the same information, so it isn't necessary to go through all of them.
- A introduction from Ubuntu, advanced to the Creating Folders and Files section.
- A tutorial document introducing some useful commands.
- A long and in depth video.
If none of these meet your needs, a web search will find numerous tutorials, guides, and videos.
Introduction to R
Presented by Elizabeth Prom-Wormley
If you are not familiar with R, then you should go through these or other introductions before starting the Workshop course.
The first video explains how to download and install R and RStudio. This step is not necessary for the Workshop, as during the course you will use the Workshop's RStudio installed on the computer cluster, however you will need to install R on your own computer for use after the course. Participants are welcome to use the Workshop's RStudio to follow these tutorials by using your Workshop credentials to login at https://workshop.colorado.edu/rstudio.
These videos refer to several sample scripts. The scripts are installed on the Workshop cluster in /faculty/elizabeth/2021. If you do not have access to the Workshop cluster, then the files can be downloaded from the 2021 Workshop file archive.
If you are familiar with R, but have never used it with twin data, then the Working with Twin Data in R video will be useful.
Downloading and Installing R and RStudio
Find, Open, and Review Files in R
Data management in R
Graphics and Basic Statistics in R
Working with Twin Data in R
Introduction to Python
Presented by Cotton Seed
Python is an extremely popular general purpose programing language which is used prominently in scientific computing and bioinformatics. It will be used at the Workshop in the Sequencing and Introduction to Hail lesson. There are many introductions, tutorials, and guides for Python availabe online. This introduction video has been prepared for the course.
We recommend following along with the video in a Jupyter notebook. We recommend using Google Colab:
https://colab.research.google.com/
You will need a Google login. The interface is slightly different than the version of Jupyter used in the video (which we will use in the Hail practical). Here is an overview of the basic features of Colab:
https://colab.research.google.com/notebooks/basic_features_overview.ipynb
The contents of the lecture has been written in a Jupyter notebook:
https://colab.research.google.com/drive/1A-SGo-vHvoZ3TnjG92L9GEmLSgcLvoBr?usp=sharing
You may find it useful to go to: View > Expand sections.
If you have questions, got to the #python-intro channel in the Boulder Workshop Slack.
