JCMB, University of Edinburgh

12 November (JCMB 1206C); 13 November (JCMB 4325C); 19 November (JCMB 3211); 20 November (JCMB 4325C)

14:00 - 17:00

Instructors: Evgenij Belikov, David McKain, Mike Wallis, Angela Chitzanidi

Helpers: Edward Wallace, Lora Boteva, Al Ivens, Yen Peng Chew,

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Introduction to Unix Shell and Eddie. This workshop will focus on the unix command line shell and how to run programs on Eddie, the university's computing cluster.

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

This workshop is focused on researchers at the University of Edinburgh's School of Biological Sciences, but is open to others within the university. It is appropriate for beginners, those who want to refresh their skills, or for those who wish to learn how to run pipelines (e.g. genomics) on the university's powerful central compute clusters.

Where: James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD . Get directions with OpenStreetMap or Google Maps.

This is held in 3 different rooms within the JCMB:

When: 12 November (JCMB 1206C); 13 November (JCMB 4325C); 19 November (JCMB 3211); 20 November (JCMB 4325C). Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email Edward.Wallace@ed.ac.uk for more information.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


12 November

JCMB 1206C, 14:00 - 17:00

The Unix Shell part 1

13 November

JCMB 4325C, 14:00 - 17:00

The Unix Shell part 2

19 November

JCMB 3211, 14:00 - 17:00

Introduction to Eddie part 1

20 November

JCMB 4325C, 14:00 - 17:00

Introduction to Eddie part 2

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


The Unix Shell part 1

The Unix Shell part 2


To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

  1. If you are using a latop download the MobaXterm personal edition for Windows installer.
  2. Run the installer.

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.