We will be adding course materials to this page during and after the summer school. For more course details now, please check individual session pages in the program.

Update: You can watch video recordings of some of the courses.

Introduction to the Linux command line

• Bash Scripting and Tools: lesson notes

High-performance computing and programming

• Introduction to high-performance computing (HPC): ZIP file with the slides and codes
• MATLAB Parallel Computing: ZIP file with slides and exercises
• Chapel parallel programming: PDF slides, notes for base language, notes for task parallelism, and notes for data parallelism
• HPC on Amazon Web Services: ZIP file with instructions

Python topics

• Jupyter Notebooks: you can either use the interactive notebook at http://bit.ly/2xcBTVU (sign-in with your GitHub acccount); or start one of the Jupyter Notebooks at the top-level portal https://syzygy.ca (select your institution to log in) and then upload and use this notebook there

Databases, visualization

• Introduction to Databases on Cedar: PDF slides
• Scientific Visualization: ZIP file with slides, scripts, and sample datasets

Bioinformatics

• Building a bioinformatics pipeline with SnakeMake: lesson notes

Machine learning

• Practical Applications of Deep Learning with MATLAB: ZIP file with slides and other files. Some of the larger files were excluded to keep the file size small. If you want these large datasets, please contact the instructor rteramot at mathworks dot com.

Security, privacy

• Best practices in data security: PDF slides
• Data privacy and REDCap platform: PDF slides