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:

• JCMB 1206C: Large teaching studio containing 12 island tables, each with a screen and 6 seats. There's a front display screen next to the lectern but it's not that big and there's a pillar blocking line of sight from some angles. But that shouldn't be an issue for this size of class.
• JCMB 4325C: Medium sized teaching studio, 8 island tables, each with screen and 6 seats. There's a front projection screen, a bit bigger than 1206C. Lines of sight are good. This is a favourite out of the JCMB studios!
• JCMB 3211: Small teaching studio, 4 tables, each with screen and 6 seats. There's a good sized front screen but the room shape makes it hard to see it from some angles.

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:

• The room is wheelchair / scooter accessible.
• Accessible restrooms are available.
• JCMB 1206C: Best entrance is the JCMB North entrance. This is the one along the north side of the building rather than the main entrance. It's accessible via the footpath between the main entrance towards KB Entrance 4. So Biologists should probably find this quite easily. Once you enter the north entrance, turn right and the room is the first on the right. Accessibility note: The outer doors of the North entrance are automatic, but there are a set of manual double doors just beyond them. An alternative possible route for wheelchair users is to enter via the main entrance, then head along the long corridor that starts just beyond the post room until you get to the goods lift (on the right). Take the goods lift down to level 1, then the room is on your left. All doors on this route are either automatic are normally kept open. Note that the main passenger lifts do not go down to level 1!
• JCMB 4325C: Best to enter via the main entrance. Take the lifts or stairs up to level 4. Coming out of the lift, turn right, then right all the way down the corridor. There are some manual doors to open near the room, but they're single and reasonably light.
• JCMB 3211: Best to enter via the main entrance. The room is first on the left immediately after the first flight of stairs, so easy to find. Alternatively people can use the main passenger lifts. There are automatic doors available all the way, except for the door to the room itself.

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.

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Surveys

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

Pre-workshop Survey

Post-workshop Survey

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Schedule

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

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Syllabus

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Setup

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.