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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.

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 to perform complex tasks.

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.

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 for scheduling and execution. 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.

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 your goals. 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 of running and viewing different types of parallel programs/concepts on an HPC cluster.

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.

Intermediate Python: Python on the Cluster

This hands-on workshop (two sessions, both three hours) will give students an insight into running Python code on high-performance computing clusters. Includes setting up jobs for batch submission, loading dependent Python packages, and interactive use on the cluster. Students should have some experience with the shell (e.g., HPC Shell Basics workshop), experience submitting jobs (e.g., HPC Essentials workshop), and at least one introductory Python course.

Building and Managing Reproducible Pipelines as a Non-Root User in HPC with Apptainer

This workshop introduces Apptainer, a powerful containerization tool designed for high-performance computing (HPC) environments. Participants will learn how to build, manage, and deploy pipelines efficiently as non-root users, leveraging the flexibility and security of containerized workflows in resource-constrained environments. Topics will include container creation, pipeline integration, and best practices for seamless execution in HPC systems. For Alliance HPC users, this workshop will demonstrate how to build a Conda environment within an Apptainer container.

Cloud Introduction

You may have already heard about "Cloud" or "Cloud computing" or have seen this term everywhere. However, what is its nature? What's the difference from the traditional computing model? How to access and use a cloud, in particular for research purposes?

The Cloud Intro will clarify all of the above, starting with an overview of cloud computing including the evolution of HPC/ARC computer technologies, public & private clouds, and the cloud deployed by Digital Research Alliance of Canada (Alliance), followed by an introduction to the national cloud sites, compute resources and different types of cloud storage such as volume, shared filesystem, and object storage. Finally, you will be guided on how to apply for/access those cloud resources as a prerequisite for the Cloud Hands-on and Cloud Advanced sessions.

Cloud Hands-on

In this session, you will be guided step by step on how to use the Alliance cloud system including launching your own instances or virtual machines, setting up the environment such as network, authentication, storage volumes, etc. You will also be shown how to conveniently access various research computing software repositories on the basis of CVMFS that is a potent & convenient research software distribution system used around the world.

Attendees are strongly recommended to take the Cloud Intro session and to register for an account with before attending the session. Attendees who do not have an account can use pre-set guest user credentials.

Cloud Advanced/Containerization

This session aims to accommodate different topics of advanced cloud technologies and applications. Containerization is a hot topic in cloud computing and this session will present a broad overview of containerization and related technologies. This session is intended to lead into future sessions that will go deeper into each specific containerization subject.

We will start by answering the question "What is a container?" followed by the benefits of using containers, and a comparison between containers and virtual machines. Docker, as the most popular containerization tool, will be introduced, with a discussion of concepts and basic operations, and how to interact with image repositories. Two other tools for implementing containerization in specific scenarios (Singularity and Kubernetes) will also be briefly introduced. Time permitting, we will demonstrate examples of using Singularity and Kubernetes.

Introduction to OpenRefine

This session will introduce participants to OpenRefine, a powerful, free and open source tool to work with large datasets. We will quickly work through how to use OpenRefine to effectively clean and format tabular data while automatically tracking any changes.

This session is suitable for beginners with no prior knowledge of OpenRefine. There are no prerequisite coding skills. While the examples and data used will be aimed at the humanities and social sciences, the session is open to anyone and everyone interested in learning about OpenRefine.

Introduction to R

This session will introduce participants to R. In this session, participants will learn the basics of coding in R, and will become familiar with using RStudio. We will cover creating objects, importing and working with data, using the basic libraries, and performing simple operations.

This session is suitable for beginners with no prior knowledge of R. No prior coding skills are required. While the examples and data used will be aimed at the humanities and social sciences community, the session is open to anyone and everyone interested in learning about R.

Globus

Got research data to store, move and share? Globus can help! Globus is a data transfer service for fast, secure and reliable data transfers and sharing. The service automatically tunes transfer settings, restarts interrupted transfers and checks file integrity. This informational and hands-on session will guide you in securely transferring data between individual computers, data storage resources and national computing systems using the Globus web interface. You will also learn how to use Globus to share files or folders. Globus integration with U of A storage resources is coming soon. There will be time available for answering questions and providing instructions so that all can use the service—no prior knowledge or experience with Globus required.

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.

Linux Security: Access Control Basics

This workshop provides an introduction to Linux security principles and practices, focusing on key areas to help you secure your systems. You'll learn about essential topics like firewalls, the Linux permission model, and mandatory access control, as well as how to monitor your systems and ensure compliance.

Research Computing Network

This workshop will introduce you to the Research Computing Network, a digital community of practice platform where ¾ÅÐãÖ±²¥ faculty, staff and student researchers can connect with peers, discuss topics related to advanced research computing and share resources, tips, and tricks.

RAC Best Practices

The Resource Allocation Competition (RAC) from the Digital Research Alliance of Canada is a way to access computing and storage resources beyond what is available by non-competitive means. This can range from hundreds of cores or several GPUs and some extra terabytes of storage to thousands of cores and hundreds of terabytes of storage. This annual competition is open for applications each October. This session will quickly cover the most important things to consider when applying to maximize success and then open the floor to questions.