Scientific Computing Fundamentals for CAMH Researchers
Are you looking for our October 2016 series of workshops? Click here
A six-day, self-paced series of workshops on scientific computing fundamentals taught with ♥ by CAMH researcher-nerds (we’re part of the CAMH Scientific Computing Working Group).
Epigenetics Lab
Kimel Lab
Kimel Lab | VR Lab
Kimel Lab
Vincent Lab
Kimel Lab
Slaight Centre
De Luca Lab
Slaight Centre
Kimel Lab
Sibille Lab
Kimel Lab
CAMH IT
CAMH IT
Research IT
Kimel Lab
Kimel Lab
Research IT
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. If you have questions, send email.
Workshops
Tuesday, May 17th
Ask us Anything about Computers!
9-10am, RS 2062
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.
Introduction to Programming
10am-12pm, RS 2062
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, RS 4100
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 R
3-5pm, RS 4100
Note: This workshops is also offered on Tuesday May 24th, 10am-12pm
R is a free, featureful and sometimes magical language for doing statistical analysis. This workshop will introduce you to R and the Rstudio environment (see Part II for that).
You’ll learn:
- Reading you data into and R dataframe
- Sorting/merging/filtering your data tables
- Getting summary statistics
Prerequisites: Some familiarity with another programming language
You’ll need: A laptop with R and R studio installed.
Wednesday, May 18th
Managing Code, Experiments, & Data
10am-12pm, RS 2015
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 and backup
- 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.
Automating in Linux
1-3pm, RS 4100
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.
Organizing your Files with GitHub
3-5pm, RS 2062
Git/Github are ugly but necessary tools to help you (and others) work. Git is the ultimate “undo” button for your scripts and data, and also it lets you publish your code online and work with others.
You’ll learn:
- Track documents/code changes with git and github
- Merge in changes from other users
- Discuss issues on GitHub
- Manage code changes on branches, send pull requests
Prerequisites: Preferably some familiarity with the Shell and version control experience (git, subversion, etc..).
You’ll need: Laptop with git and the shell installed.
Thursday, May 19th
Spreadsheets
10am-12pm, RS 2062
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.
SPSS
1-3pm, RS 2020 (please note same time as Web Design)
Note: This workshops is also offered on Friday May 27th, 1-3pm
SPSS can be very useful for simple data exploration to advanced statistics. It is widely used at CAMH and is a tool 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!
Web Design
1-3pm, CS 845 (please note same time as SPSS)
MS Access
3pm-5pm, RS 2020
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)
Tuesday, May 24th
Introduction to R
10am-12pm, RS 2062
Note: This workshops is also offered on Tuesday May 17th, 3-5pm.
R is a free, featureful and sometimes magical language for doing statistical analysis. This workshop will introduce you to R and the Rstudio enviroment (see Part II for that).
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.
Advanced R
1-3pm, RS 2062
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 to reorganize your dataset
- Transforming your variables
- Linear modelling - 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.
Introduction to REDCap
3-5pm, RS 2062
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: Your own laptop (optional) and REDCap account (optional).
Wednesday, May 25th
Introduction to Python
9-11am, CS 734 note CS location
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.
You’ll need: A laptop with python installed.
Introduction to the SCC
11am-12pm, CS 734 note CS location
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 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
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.
MATLAB
3-5pm, RS 2062
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.
Thursday, May 26th
Writing Papers with RStudio
9-10:30am, RS 2062
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
- Managing your bibliography and citations
- Creating a paper ready for journal submission
Prerequisites: Some R and Rstudio. Bonus points for familiarity with Git.
You’ll need: A laptop with R and Rstudio installed.
How to (ethically) use Photoshop for Figures
10:30am-12pm, RS 2062
Using some microscopy image data as an example, we’ll cover the all the steps in creating a figure for publication and address some of the ethical considerations when presenting your data.
You’ll learn:
- Setting up 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 (optional)
Python for MRI
1-3pm, RS 2062
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.
Advanced REDCap
3-5pm, RS 2062
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).
Friday, May 27th: Repeat SPSS workshop by popular demand!
SPSS
1-3pm, RS 2020
Note: This workshops is also offered on Thursday May 19th, 1-3pm
SPSS can be very useful for simple data exploration to advanced statistics. It is widely used at CAMH and is a tool 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!
Register
Workshop Schedule and Registration
Are you looking for our October 2016 series of workshops? Click here
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
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:
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**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.
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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.
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University of Toronto Scientific Coders
Meets weekly to run workshops and co-working sessions.
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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