This one-day workshop provides an introduction to computational research, with an emphasis on leveraging open source tools to develop efficient workflows for collaborative and reproducible research.

In conjunction with the following R and Python Basics series, the goal of this workshop is to increase research integrity via exposure to basic command line tools and version control (Git), collaborative cloud tools (GitHub), programming (R or Python), and data and software management best practices.

This workshop includes modules on:

• Reproducible and Responsible Research
• Introduction to Unix Command Line,
• Introduction to Version Control with Git
• Reproducible Research for Teams with GitHub

By the end of this all-day workshop learners will be able to:

• Describe tidy data, project organization, and programming best practices;
• Explain the directory structure of their computers;
• Use command line tools to navigate across and within files and directories;
• Create, copy, edit, and delete files from the command line;
• Create new repositories and begin using Git for version control of their individual projects;
• Push local changes to a repository on GitHub, create a local copy of an existing repository from GitHub, open and merge pull requests, create branches to manage work in parallel, and create GitHub issues and notifications for project management;
• Identify where to go to learn more.

This workshop is a pre-requisite for DataLab's R Basics and Python Basics workshops.

PREREQUISITES

All UC Davis graduate students and postdocs are eligible to enroll. No prior coding experience is necessary.

All participants will need to bring a computer with internet access and a Unix shell scripting program (Terminal, Bash, etc.) and the git version control software. This software comes on default on Mac computers; Windows users should install Bash in advance of the workshop. Installation instructions can be found in the workshop reader. 

Before the workshop participants must setup a free GitHub account. Then, create an SSH key on the computer you will be using during the workshop and add it to your Github account. Instructions can be found in the GitHub help documentation. Students can request a GitHub student developer pack, which allows for unlimited free private repositories. 

If you need help troubleshooting your installations or setting up your GitHub account, come to Office Hours in advance of the workshop.

Learners are encouraged to read sections 1-4 of the command line workshop reader in advance. The remainder of the reader content will be covered live during the workshop.

Can't make it to this training? Check out our workshop schedule. Materials from prior workshops are available on DataLab's website.

Questions? Email datalab-training@ucdavis.edu.