Everything you’ve always wanted to know about computers but were too afraid to ask!

This an informal, friendly Q&A session for any and all novice questions about computers and computing.

You’ll learn:

• What the different parts of a computer are
• The difference between software and hardware
• What a server is and how it’s different from a desktop or laptop

Prerequisites: None

You’ll need: Just you.

Computers aren’t scary (yet) and knowing how to use them will make doing science better/easier/quicker.

You’ll learn:

• About Unix/Linux
• What a terminal/shell is.
• Managing (making, moving, editing) files and folders
• Remote access (SSH/FTP)
• Where to find help online/etc.
• Some super useful Linux commands

Prerequisites: None

You’ll need: A laptop. If you’re using Windows, install BASH.

Everyone knows how to use a spreadsheet, but most people use them terribly inefficiently.

You’ll learn:

• Navigating a spreadsheet
• Autofilling in sequences, and advanced cut and paste
• Avoiding “copy and paste” by using cell references
• What a “formula” is
• Important formulas to make auto-updating cells

Prerequisites: Basic familiarity with spreadsheets (Excel/Openoffice)

You’ll need: A laptop with Excel or Openoffice installed.

Doing work on lots of data by hand is boring and error prone. Learn how to write shell scripts to automate your work.

You’ll learn:

• Running commands on many files (globbing, looping, if statements)
• Reading and writing to files & sorting/filtering data in files
• Writing scripts, chaining tools together (pipes, redirection)

Prerequisites: Familiarity with Linux (e.g. cd, ls, mv, cp)

You’ll need: A laptop. If you’re using Windows, install BASH and mobaXterm.

R is a free, featureful and sometimes magical language for doing statistical analysis. This workshop won’t cover much stats (see Part II for that).

You’ll learn:

• loading libraries/installing packages
• basic syntax, commands, and scripting practices
• reading/sorting/merging/filtering tabular data (e.g. CSV files)
• basic summary statistics

Prerequisites: Familiarity with another programming language

You’ll need: A laptop with R and Rstudio installed.

TBA

Git/Github are ugly but necessary tools to help you (and others) manage changes to scripts and data, and publish your code.

You’ll learn:

• Put documents/code in a git repository
• Push and pull code changes to github
• Merge in changes from other users
• Manage code changes on branches, send pull requests

Prerequisites: Preferably some version control experience.

You’ll need: Laptop with git installed.

REDCap is a web application for building and managing surveys and databases, and requires little programming knowledge.

You’ll learn:

• How to design a study in REDCap
• Sending surveys to participants
• Setting up basic branching and display logic
• Exporting data and generating reports
• Using internal applications to review data quality

Prerequisites: None

You’ll need: (Optional) your own laptop.

This short module is designed to give students familiar with programming a basic introduction to the python language.

You’ll learn:

• Data types (e.g. lists and dictionaries)
• String manipulation
• Reading and writing to files
• Modules and packages
• Basic plotting with matplotlib

Prerequisites: Familiarity with another programming language (e.g. MATLAB, R).

What you’ll need: A laptop with a Python distribution installed.

Python is useful to MRI data. It’s flexible. And it’s free!

You’ll learn:

• Use the interactive Python terminal
• Import your NIFTI data
• Interact with it and visualize it
• Use common command-line python tools to analyze your NIFTI data

Prerequisites: Familiarity with Python.

You’ll need: A laptop with Python installed.

MATLAB is a scripting and programming language paired with an interactive environment that focuses on manipulation, analysis, and visualization of numerical data.

You’ll learn:

• Using the graphical MATLAB environment
• Basic syntax and operations
• Manipulating vectors, matrices, and tabular data
• Writing scripts and functions
• Basics of built-in commands for plotting and statistics

Prerequisites: Familiarity with another programming or scripting language.

You’ll need: A laptop with MATLAB.

You know the basic functionality of R, but the hardest part is getting your data in order.

In this workshop you’ll learn some fundamental ways of organizing and manipulating datasets, as well as modelling/visualising your data.

You’ll learn:

• Melting/casting dataframes
• Transforming your data
• Linear modelling
• Plotting and visualization with ggplot2

Prerequisites: Basic familiarity with R

You’ll need: A laptop with R and Rstudio installed.

The Specialised Computing Centre (SCC) is CAMH’s own super-computer.

You can use this to speed up your processing-intensive analyses by distributing your work across many computers at once.

You’ll learn:

• How the SCC is organized
• Suitable tasks for the SCC
• How to run many tasks in parallel

Prerequisites: Familiarity with the Unix shell

You’ll need: Computers provided. If bringing a Windows laptop, install BASH and mobaXterm.

The purpose of this course is to expose students to automating process and working on the Specialized Computing Cluster. Topics will be:

You’ll learn:

• Advanced bash loops – automating processing
• Parallelization using GNU Parallel
• Using the Debugging and Interactive Nodes
• I/O
• Using the RAMDISK

Prerequisites: Familiarity with BASH scripting.

You’ll need: A laptop. If it’s a Windows computer, install BASH and mobaXterm.