Scientific Computing Fundamentals for CAMH Researchers
February 9-10, 2017
Doctor’s Association Building, 101 Stokes Street (QS)
Two days of self-paced workshops on scientific computing fundamentals
taught with ♥ by CAMH researcher-nerds
(an initiative of the CAMH Scientific Computing Working Group)
Sibille Lab
Kimel Lab
Kimel Lab
Bioinformatics
Vincent Lab
Slaight Centre
Research IT
MRI Centre
Geriatrics
Mueller Pharmacogenetics Lab
Sibille Lab
Kimel Lab
CAMH IT
CAMH IT
Research IT
Temerty Centre
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
Thursday, February 9th
Database Creation - REDCap
9:00am - 11:00am
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 set up a study in REDCap
- Writing display logic
- Writing formulas for all sorts of calculations
- Setting up multiple arms, visits, and timepoints
- Incorporating html tags
- Cool tricks to customize your study
Prerequisites: None
Database Management - REDCap
11:00am - 1:00pm
Instructor: Steve
Helper: Sophie
Description: You’ve built a project in REDCap, and now would like to learn more about this software.
You’ll learn:
- Customized Data Export with Reports tool
- User Rights, multi-site access and DAGs
- Randomization module
- Data quality module
- Data resolution workflow
- Project audit with Logging tool
Prerequisites: Database Creation - REDCap
Data Collection - REDCap Surveys
1:00pm - 3:00pm
Instructor: Natalia
Helper: Mawahib
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:
- Survey Design.
- Inviting Participants by email.
- Types of surveys: anonymous and non-anonymous.
- Public link and individual links.
- Survey Queue and Autocontinue option.
- Survey notifications
- Automatic survey invitations vs manual
- Data Import Tool
- REDCap Mobile
Prerequisites: Database Creation - REDCap
Data Collection - Using Excel
3:00pm - 5:00pm
Instructor: Yuliya & Arin
Helper: Victoria
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)
Friday, February 10th
Database Creation - MS Access
9:00am - 11:00am
Instructor: Ricardo & Tom
Description: Many of us are using 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.
Data Analysis - SPSS
11:00am - 1:00pm
Instructor: Marcia
Helper: Erin
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!
Data Cleaning - R
1:00pm - 3:00pm
Instructor: Erin
Helper:Leon
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
Data Analysis and Reporting - R
3:00pm - 5:00pm
Instructor: Erin
Helper: Leon
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)
Register
Workshop Schedule and Registration
The SCWG workshop series is FREE for all CAMH students, staff, and trainees. It is also open to other members of the community that might find the courses useful.
All courses are being held in the TD Learning Centre in the Doctor’s Association Building at 101 Stokes Street, G1105.
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.
R
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.
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.
-
University of Toronto Scientific Coders
Meets weekly to run workshops and co-working sessions.
-
SciNet is U of T’s supercomputing organization. Don’t let that intimidate you, though; they run amazing introductory courses on Linux, R, Python, and HPC.
-
SickKids: Bioinformatics Tools & Tricks: Hands-On Tutorials for Biologists