Scientific Computing Fundamentals for CAMH Researchers
October 4th - 13th, 2016
A six-day, self-paced series of workshops on scientific computing fundamentals
taught with ♥ by CAMH researcher-nerds
(an initiative of the CAMH Scientific Computing Working Group)
Epigenetics Lab
Kimel Lab
Slaight Centre
Kimel Lab | VR Lab
Research IT
Slaight Centre
VR Lab
Kimel Lab
Bioinformatics
Epigenetics Lab
Vincent Lab
Kimel Lab
Slaight Centre
Slaight Centre
Kimel Lab
MRI Centre
Geriatric Mental Health
Sibille Lab
Kimel Lab
CAMH IT
CAMH IT
VR Lab
Research IT
Kimel Lab
Kimel Lab
Research IT
Kimel Lab
Why
Because …
… research is becoming more computational and you’ve probably never been formally trained in general computing skills.
That’s a problem.
Software is your experimental apparatus. Just like cleaning test tubes and pipetting, computing is a basic skill you need to be competent with.
These workshops will focus on some computing skills fundamentals you’ll need for getting your study data organized, doing repeatable/reproducible analysis, and making use of existing CAMH computing resources to save time.
You should attend if you are doing any sort of scientific computing work, or work that involves repetition that could be automated.
This time around, we’re using a shared dataset - spanning demographic, cognitive, imaging, and genomic data - across all workshops so we can get started faster and increase attendees’ exposure to all the great work going on around the hospital
If you have questions, send us an email at scwg@camh.ca.
Workshops
Tuesday, October 4th
Ask us Anything about Computers!
9-10am, RS 2062
Instructor: Ricardo
Helper: Sophie
Description: 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’s inside a computer (we’ll take one apart for you)
- What a hard drive is and how its different from RAM - What the differences are between Mac, Windows, and Linux
- Whatever else you’re interested in…
Prerequisites: None
You’ll need: Just you.
Programming Logic
10am-12pm, RS 2062
Instructor: Janelle
Helper: Brice
Description: Come here if you’d like to learn about programming, but have little to no prior experience. This will be an interactive workshop where you will play a game to learn new concepts.
You’ll learn:
- What is programming, anyway?
- Essential programming concepts, such as sequencing, loops, conditionals, functions, variables, and datatypes
Prerequisites: None
You’ll need: A laptop. We’ll be working with python, but you don’t need it installed.
Introduction to Linux and the Shell
1-3pm, CS 845 note CS location
Instructor: Dawn
Helper: Daniel
Description: 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 and mobaXterm.
Introduction to Python
3-5pm, CS 845 note CS location
Instructor: Dawson
Helpers: Dawn & Nikhil
Description: This basic instroduction is designed to make students familiar with programming in python.
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.
You’ll need: A laptop with python installed.
Wednesday, October 5th
Spreadsheets
9:00am-11:00am, RS 2062
Instructors: Yuliya & Navona
Helper: Marzena
Description: Everyone knows what a spreadsheet is, but most people use them terribly inefficiently.
You’ll learn:
- How to set up a spreadsheet for research logs and data
- Autofilling in sequences
- Avoiding “copy and paste” by using cell references
- What a “formula” is
- How to auto-update cells
- Helpful data cleaning tools
Prerequisites: Basic familiarity with spreadsheets (Excel/Openoffice)
You’ll need: A laptop with Excel or OpenOffice installed.
SPSS
11am-1pm, RS 2020
Note: This workshop is also offered on Thursday Oct 13th, 9-11am
Instructor: Marcos
Helper: Sarah
Description: SPSS can be very useful for simple data exploration to advanced statistics. It is widely used at CAMH and is a tool very much worth knowing.
You’ll learn:
- What is SPSS
- Types of data and how to enter them into SPSS
- Data manipulation – Creating new variables
- Data manipulation – Sorting
- Basic data analysis – Means, Frequencies and Crosstabs
Prerequisites: Some familiarity with data in general, no previous knowledge of SPSS is required
You’ll need: Just you - computer and SPSS will be provided in lab. BUT if you have a laptop with SPSS, please bring it!
Introduction to REDCap
1-3pm, RS 2020
Note: This workshop is also offered on Wednesday Oct 12th, 9-11am
Instructor: Navona
Helper: Kyle
Description: REDCap is a web application for building and managing surveys and databases. It requires little programming knowledge, and it’s increasingly used at CAMH for multiple purposes.
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: Your own laptop (optional) and REDCap account (optional).
Web Development (HTML & CSS)
3-5pm, RS 2062
Instructor: Brice
Helper: Dawn
Description: We access websites in our everyday life for all types of reasons. You might even want to program you own. Come and learn what the foundation of a website is, so you can do it yourself! You’ll learn:
- Creating a static web page with HTML tags
- Integrating CSS to your HTML page
- Make a web page more appealing with CSS
- Working with “bootstrap”
What you’ll need: A laptop with Notepad++ or CoffeeCup installed.
Thursday, October 6th
Introduction to R
9:00-11:00am, RS 2062
Note: This workshop is also offered on Wednesday October 12th, 1:00pm-3:00pm
Instructors: Erin
Helper: Yuliya, David, Susana, Laura, Grace
Description: R is a free, featureful and sometimes magical language for doing statistical analysis. This workshop will introduce you to R and the Rstudio environment.
You’ll learn:
- Reading you data into and R dataframe
- Sorting/merging/filtering your data tables
- Data Cleaning
- Getting summary statistics
Prerequisites: Some familiarity with another programming language
You’ll need: A laptop with R and R studio installed. As well as packages (dplyr rms, and ggplot2)
MATLAB
11:00am-1:00pm, RS 2062
Instructor: Colin
Helper: Dawn
Description: 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 and workspace
- MATLAB variables (double, string, cell, struct)
- Basic syntax and operations (for loops, while, if, switch, try)
- How to call a function
- How to write scripts and functions
Prerequisites: Familiarity with another programming or scripting language.
You’ll need: A laptop with MATLAB installed.
MS Access
1:00pm-3:00pm, RS T321
Instructor: Tom
Helper: Jessica
Description: Many of us are using are data that is stored in Access databases but do not know how to these databases are built or how to make improvements.
You’ll learn:
- Basic architecture: table, form, query, report and why do you need them.
- How to create/modify tables. Tips and tricks.
- How to create/modify forms. Form Wizard.
- How to extract data from the database. Queries vs reports. Query Wizard, Report Wizard.
- How to make something happen when you click on a button.
- Using parameters to filter data.
- Linking tables/forms (example: multiple appointments for one person)
Prerequisites: Familiarity with spreadsheets.
What you’ll need: A laptop with MS Access 2010 or access to remote.camh.ca (optional)
SQL
3-5pm, RS T321
Instructor: Natalia & Ricardo
Helper: Dawn & Brice
Description: SQL is a langauge crucial to databases (and underlies software like Access and REDCap!). Come and get a glimpse of what SQL is and can do for you.
You’ll learn:
- how to build a database
- entering data into a database
- constructing queries for selecting, filtering, and joining tables
- calculating basic statistics.
- basic normalization principles
- Basic SQL syntax
What you’ll need: A laptop
Tuesday, October 11th
Automating in Linux
9-11am, RS 2062
Instructor: Nikhil
Helper: Dawn
Description: Doing work on lots of data by hand is boring and error prone. Learn how to use the shell 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 the Shell (e.g. cd, ls, mv, cp)
You’ll need: A laptop. If you’re using Windows, install BASH and mobaXterm.
Introduction to the SCC
11am-1pm, RS 2062
Instructor: Andy & David
Helper: Ricardo
Description: The Specialised Computing Centre (SCC) is CAMH’s own super-computer.
You can use CAMH’S SCC to speed up your processing-intensive analyses by distributing your work across many computers at once.
You’ll learn:
- How the SCC is organized into different types of nodes
- How to load software using the SCC’s modue system
- How to get your data to and from the SCC using rsync
- How to submit jobs on the SCC queue
Prerequisites: Familiarity with the Unix shell (e.g. ‘Introduction to Linux and the Shell’ and ‘Automating in Linux’ workshops)
You’ll need: An account on the SCC. We’ll provide computers, but if you’re bringing a Windows laptop, install BASH and mobaXterm.
Advanced SCC (Scientific Computing)
1-3pm, RS 2062
Instructor: Andy & David
Helper: Ricardo
Description: The purpose of this course is to expose students to automating process and working on the Specialized Computing Cluster. You’ll learn:
- How to run many samples in paraell using GNU Parallel
- Debugging your jobs and Interactive Nodes
- Best practices for using the cluster efficiently
Prerequisites: Familiarity with BASH scripting (e.g.’Introduction to Linux and the Shell’ and ‘Automating in Linux’ workshops) and familiarity with the SCC (e.g. Introduction to the SCC).
You’ll need: An account on the SCC, and a laptop. If it’s a Windows computer, install BASH and mobaXterm.
Managing Code, Experiments, & Data (with git’s help)
3:00-5:00pm, RS 2015
Instructors: Erin & Ricardo
Helpers: Dawson & Qing
Description: Research can get messy quickly, but there are some tried and true ways of organizing your experiments that work.
You’ll learn:
- File and directory naming conventions
- Version control with Github and GitLab (now at CAMH!)
- Backup guidelines
- Creating scripts and metadata to reproduce your work
Prerequisites: Familiarity with the Shell (e.g. cd, ls, mv, cp)
You’ll need: A laptop. If you’re using Windows, install BASH and mobaXterm.
Wednesday, October 12th
Introduction to REDCap
9-11am, RS 2020
Note: This workshop is also offered on October 5th, 1-3pm
Instructors: Steve & Kyle
Description: REDCap is a web application for building and managing surveys and databases. It requires little programming knowledge, and it’s increasingly used at CAMH for multiple purposes.
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: Your own laptop (optional) and REDCap account (optional).
Advanced REDCap
11am-1pm, RS 2062
Instructors: Natalia & Steve
Helper: Kyle
Description: You’ve built a project in REDCap, and now would like to learn more about this software.
You’ll learn:
- HTML formatting and built-in templates
- Examples of branching logic and calculating fields
- Examples of piping
- Public survey link vs. individual links
- Data Quality module
- Randomization Module
- REDCap Mobile
- And any questions you may have
Prerequisites: Some familiarity with REDCap.
You’ll need: Your own laptop (optional) and REDCap account (optional).
Introduction to R
1:00-3:00pm, RS 4100
Note: This workshop is also offered on Thusday October 6th, 9-11am.
Instructors: Erin & Yuliya
Helpers: David, Susana, Laura, Grace
Description: R is a free, featureful and sometimes magical language for doing statistical analysis. This workshop will introduce you to R and the Rstudio enviroment.
You’ll learn:
- Reading you data into and R dataframe
- Sorting/merging/filtering your data tables
- Getting summary statistics
Prerequisites: Familiarity with another programming language
You’ll need: A laptop with R and R studio installed.
Exploring Data with R
3-5pm, RS 2062
Instructors: Erin & Yuliya
Helper: David & Navona
Description: 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 visualising your data.
You’ll learn:
- Reorganize/Reshape your dataset with tidyr and dplyr
- Quickly create stats tables
- Plotting and visualization with ggplot2
Prerequisites: Basic familiarity with R (i.e. Introduction to R)
You’ll need: A laptop with R and R studio installed.
Thursday, Oct 13th
SPSS
9-11am, RS 2020
Note: This workshop is also offered on Wednesday October 11th, 11-1pm
Instructor: Marcos
Helper: Natalia
Description: SPSS can be very useful for simple data exploration to advanced statistics. It is widely used at CAMH and is a tool very much worth knowing.
You’ll learn:
- What is SPSS
- Types of data and how to enter them into SPSS
- Data manipulation – Creating new variables
- Data manipulation – Sorting
- Basic data analysis – Means, Frequencies and Crosstabs
Prerequisites: Some familiarity with data in general, no previous knowledge of SPSS is required
You’ll need: Just you - computer and SPSS will be provided in lab, BUT if you have a laptop with SPSS, please bring it!
Statistics with R
11-1pm, RS T321
Instructors: Erin & Yuliya
Helper: Laura & Navona
Description: You know the basic functionality of R, now let’s actually run some statistical tests.
You’ll learn:
- Transforming variables to normality
- Linear modeling and regression
- Building tables and figures to publish your results
Prerequisites: Some knowledge of statistics. Basic familiarity with R (i.e. Introduction to R)
You’ll need: A laptop with R and Rstudio installed. R packages dplyr, tidyr, cars and rms.
Writing Papers with RStudio
1:00-3:00pm, RS T321
Instructors: Erin & Leon
Helper: Ricardo & Grace
Description:Keeping your figures and data tables in sync with your paper text, and sharing it for editing can be a pain. There is another way.
You’ll learn:
- Markdown, the plain-text format for writing documents
- Creating figures, tables, and stats that update automatically
- Keeping all things things organized
Prerequisites: Some R and Rstudio. Bonus points for familiarity with Git. Keeping your figures and data tables in sync with your paper text, and sharing it for editing can be a pain. There is another way.
You’ll need: A laptop with R and Rstudio installed.
Creating a Scientific poster using Photoshop
3-5pm, RS T321
Instructor: Steve
Helper: TBA
Description:You’re probably used to creating posters in MS PowerPoint, which is all well and good. If you’d like to take your posters to the next level, however, you’ll need something with a little more power under the hood. With its powerful image and text-editing capabilities, and fine control over layers and groups, Photoshop is an excellent option!
You’ll learn:
- Setting up and laying out your document
- Importing images and keeping your layers organized
- Aligning and re-sizing images
- Adding text and shape layers
- Masking vs cropping
- Ethical file management, and use of layer effects and filters
Prerequisites: A basic familiarity with Photoshop may be useful, but not required.
You’ll need: Your own laptop with Photoshop installed.
Register
Workshop Schedule and Registration
The SCWG workshop series is FREE for all CAMH students, staff, and trainees (please sign up with a CAMH email address, so that we know who you are!).
All others are welcome to join us for $20 per course. Questions? Email us at scwg@camh.ca
Preparation
Install the following bits of software before you come to the workshops. For more detailed installation instructions go here.
Send us email if you are having trouble.
Linux/Shell (windows users only)
- Git for Windows which includes a BASH shell
- mobaXterm for remote access
R
Python
MATLAB
- MATLAB trial version
- mobaXterm for remote access (Windows only)
Version Control with Git
Optionally:
- Source Tree (Mac and Windows only)
- SmartGit (all platforms)
REDCap
MS Access
- remote.camh.ca for basic remote access (you’ll need to install Citrix Receiver)
Spreadsheets
- Excel via remote.camh.ca (you’ll need to install Citrix Receiver). Or download OpenOffice for free.
SCC
Photoshop
- A free 30-day trial can be downloaded from Adobe, and a full license can be bought for (a very reasonable) $9.99 USD a month. Note that while the basic principles of this course could be applied to free alternatives such as GIMP, direct translation between programs is difficult as there are many minor differences (which add up) between the programs.
More Help
What more help/instruction? There are lots of things going on at CAMH and U of T that you can get involved in:
-
**Weekly Office Hours - CS 163, Tuesday 1-2pm
All staff, students and trainees welcome to drop in. This is an informal space to ask your knowledgeable colleagues about any computing issue, programming/scripting question, or analysis design.
-
Peers Teaching Peers - CS 163 Tue 12-1pm, Lunch provided!
Weekly presentations by students and staff. The purpose of PTP is simply to get others thinking about how they may implement a method they are not familiar with and/or to build a working relationship with someone to help you with that method.
-
University of Toronto Scientific Coders
Meets weekly to run workshops and co-working sessions.
-
SciNet is U of T’s super computing organization. Don’t let that intimidate you though; they run amazing introductory courses on linux, R, Python, and HPC.
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SickKids: Bioinformatics Tools & Tricks: Hands-On Tutorials for Biologists