Data and Compute Setup
This workshop runs on your own laptop — there is no shared cloud compute environment to log into. The setup below mirrors the pre-work form; please work through it before the workshop begins, as we will start where the pre-work leaves off. If you run into any issues, email training@bioinformatics.ca and we will help you troubleshoot.
Laptop requirements
You will need a laptop for this course. We prefer that students bring their own so that you are set up and ready to handle your own data after the workshop. If your laptop does not meet the minimum requirements listed below, contact training@bioinformatics.ca to arrange a loaner.
Minimum requirements: 1024×768 screen resolution, 1.5 GHz CPU, 2 GB RAM, 10 GB free disk space, and a recent version of Windows, macOS, or Linux. Most computers purchased in the past 3–4 years meet these requirements.
Software installations
Please install the following on the computer you will be working on (not your phone) before the workshop:
- A modern web browser — Firefox, Safari, or Chrome. Do not use Internet Explorer.
- A PDF viewer — Adobe Acrobat, Preview, or any equivalent. Reading PDFs in your browser is also fine.
- Slack (desktop app) — install from https://slack.com/. Please install the desktop client on your workshop computer, not your phone.
- R (latest version) — download and install from https://cran.r-project.org/. (~3 minutes)
- RStudio (recommended) — download and install from https://posit.co/download/rstudio-desktop/. (~10 minutes; optional but strongly recommended.)
R packages
Once R is installed, open R (or RStudio) and run the following commands to install the packages used in the labs:
install.packages(c("stringr", "ggplot2", "ggrepel", "gprofiler2"))
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("DESeq2")
BiocManager::install("fgsea")If any package fails to install, email training@bioinformatics.ca with the error message and we will help you troubleshoot before the workshop.
Slack setup
Communication during the workshop happens on Slack. Use the invitation link provided in your registration email to join the Bioinformatics.ca Slack workspace, then use the left sidebar to join the #pna_calsask-2605 channel. If you have trouble joining, contact training@bioinformatics.ca.
A few Slack features come up often during the workshop:
- Pinned messages — important links (workshop website, lab data, etc.) are pinned to the channel. Click the pin icon near the top of the channel to view them.
- Save for later — to bookmark a message for yourself, hover over it and click the bookmark icon. Saved messages appear in the Later folder in your sidebar (visible only to you).
- Reply in thread — when answering an instructor or another student, hover over the message and click Reply in thread, so the discussion stays attached to its original message rather than scrolling away in the main channel.