Research Computing Bootcamps

Introduction to the Digital Research Alliance of Canada and Bootcamp overview

This workshop is a high-level overview of Digital Research Alliance of Canada resources available to researchers, the workshops in the bootcamp series and how the bootcamps set researchers up to use local and national resources. Not sure which Bootcamp sessions to take? Wondering how your particular research project fits into the Alliance? This is an open space to ask these and similar questions.

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HPC: Shell Basics

This workshop will introduce you to the basic interface, or command line environment used on High-Performance Computing (HPC) systems: the Linux Shell. You will learn how to log in to a remote HPC machine, use common commands to move through directories, view files, transfer files on and off the system and connect commands together to perform complex tasks.

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HPC: Scripting Basics

In this direct follow-up to HPC: Shell Basics, you will be introduced to the fundamentals of Linux shell scripting. You will learn how to create and execute shell scripts, how to write loops and how to generalize your scripts by allowing them to take inputs directly from the command line. This workshop will not cover the mechanics of submitting work to the HPC Clusters via scripts but is instead an optional preparatory workshop for HPC: Essentials, which covers this.

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HPC: Essentials

This is the second workshop in the series designed to move researchers from no previous experience using high performance computing (HPC) clusters towards a position of confidence and competence. This workshop focuses on the mechanics of submitting programs (aka “jobs”) to the clusters so that they can be scheduled and run. Led by Kamil Marcinkowski, scheduling team lead for the Digital Research Alliance of Canada, this workshop will contain extra emphasis on interacting with the scheduler to ensure that your work is getting done rather than sitting in the queue. This workshop provides that background in a friendly, jargon-minimized, hands-on environment.

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HPC: Parallelism

Are you having a hard time understanding parallel computing and High Performance Computing (HPC)? Specifically, all the terms such as: thread, process, job, vector processor, core, CUDA, MPI and many more. This session will provide you with a map to understand parallel computing, a description of the terms and concepts and how they relate to each other. Like any good map, it will let you know which concepts and terms you need to know in greater detail, and how they relate to what you are trying to do. With this map in hand, you will be in a better position to decide when and how to take advantage of the parallel computing architectures that are available to you. This workshop will include a simple and practical live demonstration running and viewing different types of parallel programs/concepts on an HPC cluster.

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HPC: Interactive Tuning + Debugging

Your research has gone beyond the capabilities of your laptop, and you're now getting started with the cluster. Now what? How do you figure out what resources your jobs need on the cluster? What do you do when things go wrong? This workshop will share secrets of interactive cluster usage so you can schedule work efficiently, learn how to fix problems when things go wrong and use the system for interactive code development. High performance computing (HPC) clusters are composed of Linux machines, understanding and controlling work on a cluster is an extension of the skills in doing the same on a Linux machine. You will learn how to debug by telling how many resources: memory, open files, how much disk IO, Iops and how much network traffic a program uses.

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Research Computing Network

This workshop will introduce you to the Research Computing Network, a digital communities of interest platform where University of Alberta faculty, staff and student researchers can connect with peers, discuss topics related to advanced research computing and share resources, tips and tricks.

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Linux Security Basics

This presentation offers a broad overview of Linux security principles and best practices. We'll cover topics ranging from system management and disaster recovery to network security, vulnerability management, and incident response. Get an introduction to the key tools and techniques used to protect Linux systems from a variety of threats.

This session is suitable for anyone seeking a general understanding of Linux security and is intended to be the first of an ongoing series on security with more detailed content to follow.

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Bioinformatics Pipeline for scRNA-seq: From Raw Data to Insights

This two-session workshop provides a comprehensive introduction to the bioinformatics pipeline for single-cell RNA sequencing (scRNA-seq), with a focus on data processing, quality control (QC), and analysis. While the primary emphasis is on computational workflows, key wet-lab concepts relevant to data quality and preprocessing will also be covered.

Session 1: Understanding scRNA-seq and Data Preprocessing

- Overview of scRNA-seq experimental workflow: sample preparation, sequencing technologies, and critical wet-lab QC steps.
- Introduction to bioinformatics tools for preprocessing: handling raw sequencing data, demultiplexing, and quality control.
- Hands-on session using tools like Cell Ranger, FastQC, and MultiQC to assess sequencing quality and detect common issues.

Session 2: Data Processing, Analysis, and Visualization

- Processing single-cell data with Seurat (R) or Scanpy (Python): normalization, filtering, and feature selection.
- Dimensionality reduction, clustering, and cell type annotation.
- Differential expression analysis and integration of multiple datasets.
- Best practices for visualizing results and reporting findings.

Who should attend?This workshop is ideal for researchers, bioinformaticians, and students who want a hands-on introduction to scRNA-seq data processing and analysis, with insights into wet-lab considerations for data quality. No prior experience in scRNA-seq analysis is required, but basic knowledge of Linux command line, HPC, R or Python is beneficial.

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