Centre for Addiction and Mental Health (CAMH), hosted at SciNet

May 22-23, 2018

9:00 am - 4:30 pm

Instructors: Heather Gibling, Ahmed Hasan, Catalina Anghel

Helpers: Marcia Hon, Ricardo Harripaul, Arin Bakht

General Information

Data Carpentry aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain.

This is the Data Carpentry Genomics Workshop (overview page). The focus of this workshop is on working with genomics data and data management and analysis for genomics research. It covers metadata organization in spreadsheets, data organization, connecting to and using cloud computing, the command line for sequence quality control and bioinformatics workflows, and R for data analysis and visualization. The workshop does not teach any particular bioinformatics tools, but the foundational skills that will allow you to conduct any analysis and analyze the output of a genomics pipeline.

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

This Data Carpentry Genomics Workshop is generously sponsored by the Krembil Centre for Neuroinformatics.

Who: The course is aimed at learners from across the GTA medical centers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: SciNet, 661 University Ave., Suite 1140, Toronto, Ontario M5G 1M1. Get directions with OpenStreetMap or Google Maps.

When: May 22-23, 2018. 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). They are also required to abide by Data Carpentry's Code of Conduct.

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 david.rotenberg@camh.ca or catalina.anghel@alum.utoronto.ca for more information.


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

Pre-workshop Survey

Post-workshop Survey


Day 1

Before starting Pre-workshop survey
Morning Introduction to Data Carpentry and DC Genomics (Catalina)
Project organization and management (Catalina)
Logging onto the Amazon Web Services server in 5 min (Catalina)
Afternoon Introduction to the command line (Heather)


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


To participate in a Data Carpentry workshop, you will need working copies of the described software. Please make sure to install everything (or at least to download the installers) before the start of your workshop. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Please follow these Setup Instructions.

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.