| June,2024 |
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| 4 Jun 9:00 am 12:00 pmThis workshop is a primer for those largely new to supercomputing, i.e., to computing on shared, remote resources. It is intended to demystify the somewhat intimidating term "High-Performance Computing" (HPC), and to serve as a foundation upon which to build over the coming days. Topics will include motivation for HPC, available resources, essential issues, and a high level overview of parallel programming models commonly used on these systems. Level: Introductory Length: 3 Hours Format: Lecture + Hands-on Prerequisites: Basic Linux e.g. "Introduction to Linux Shell" (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 4 Jun 9:00 am 12:00 pmRNA-Seq refers to high throughput sequencing methods that probes the entire transcriptomic landscape of a given tissue or sample of interest. The data acquired from such experiments can be used to explore the overall RNA profile of a sample as well as comparing samples under various conditions. While extremely powerful, RNA-Seq is susceptible to numerous experimental pitfalls and requires intimate knowledge of the experimental procedures and data analysis methods. When conducted properly RNA-Seq can reveal information about gene/transcript expression, splicing and the effects of mutations. In this session we will take a thorough look at a comprehensive RNA-Seq pipeline, from sample processing methods to final differential expression analysis. Relevant R / BioConductor packages will be introduced. We will have the opportunity to investigate numerous quality control metrics, perform genomic alignment, differential expression and pathway enrichment analysis. We will cover several “gotcha”s and common mistakes in experimental design and data analysis. Basic familiarity with R and Linux command line will be beneficial but not required. All necessary commands and parameters will be explained during the class. Participants will be offered hands-on practice in which they will use RStudio to run R/BioConductor scripts for data analysis as well as the Integrative Genomic Viewer (IGV) software to visualize genomic data on their laptops Level: Intermediate Length: 3 Hours Format: Lecture + Hands-on Prerequisites: Basic R and Linux beneficial but not required (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 4 Jun 1:30 pm 4:30 pmUsing version control for your scripts, codes, documents, papers, and even data, allows you to track changes, keep backups, and facilitate collaboration. This introductory workshop will teach you the basics of version control with the popular distributed version control software GIT. This workshop assumes that students have an understanding of basic Linux shell commands. Level: Introductory Length: 3 Hours Format: Lecture + Hands-on Prerequisites: Basic Linux (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 4 Jun 1:30 pm 4:30 pmLong-read sequencing technologies enable the sequencing of DNA fragments 10KB and longer. This read length greatly improves sequence mappability and assembly, providing an advantage over short-read sequences that are difficult to map uniquely to repetitive and GC-rich regions. Long-read sequencing has applications in a number of fields including genome assembly, diagnosis of genetic diseases, and metagenomics. In this workshop, we will focus on PacBio HiFi sequences and introduce you to tools for haplotyping, calling and visualizing structural variants and repeat expansions, visualizing read methylation, and detecting novel isoforms from PacBio Iso-Seq data. Participants will be offered hands-on practice in which they will use RStudio to run R/BioConductor scripts for data analysis as well as the Integrative Genomic Viewer (IGV) software to visualize genomic data on their laptops Level: Intermediate Length: 3 Hours Format: Lecture + Hands-on Prerequisites: Basic R (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 5 Jun 9:00 am 10:20 amThe role of good research data management practices in supporting research reproducibility is becoming increasingly well known. The literature is replete, however, with examples of poor methodology, lack of transparency, mistakes, and misconduct leading to bad science and an inability to reproduce results. This introductory session will provide real-world, illustrative examples of each of these, along with practical suggestions on how to avoid them. Level: Introductory Length: 1.5 Hours Format: Lecture Prerequisites: None (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 5 Jun 9:00 am 12:00 pmThis course is designed to provide you with a solid foundation in Python programming language. Through a comprehensive curriculum and hands-on coding exercises, participants will learn the fundamentals of Python syntax, data types, functions, and file handling. By the end of the course, you will have gained the essential skills to write Python programs, solve problems, and build the foundation for more advanced Python development. Whether you are a beginner or have some programming experience, this course will equip you with the necessary tools to start your journey in Python programming. Level: Introductory Length: Two 3-Hour Sessions Format: Lecture + Hands-on Prerequisites: None (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 5 Jun 10:30 am 11:50 amGoogle's 2017 research paper "Attention Is All You Need" described the transformer, a new machine learning technique. From that paper the modern Large Language Model was born, and we're now living in the thick of a new era brought on by companies like OpenAI, Mistral and Anthropic. But where does this cutting-edge technology come from? What are its roots? What are its problems? This talk explores the history of procedural generation in text and games, from the I-Ching to tranformer-based language models and beyond. The talk will emphasize current state of the art in text-based language models, and include demonstrations on how to run language models locally on your own hardware. Level: Introductory Length: 1.5 Hours Format: Lecture Prerequisites: None (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 5 Jun 1:30 pm 2:50 pmIn this workshop, we will explore the potential uses of generative artificial intelligence tools in research data management (RDM) with a focus on specific use cases. For example, can AI tools be used to write Data Management Plans, summarize funder requirements, assist with data analysis, or suggest file naming conventions and folder structures? This workshop will be interactive, and participants will be welcome to practice using AI tools along with the presenters using real-world data and prompts. We will also discuss the ethical considerations, including benefits and risks, of using AI tools in research and whether it is possible to use AI for RDM practices in an ethical manner. Level: Introductory Length: 1.5 Hours Format: Lecture + Hands-on Prerequisites: None (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 5 Jun 1:30 pm 4:30 pmThis course is designed to provide you with a solid foundation in Python programming language. Through a comprehensive curriculum and hands-on coding exercises, participants will learn the fundamentals of Python syntax, data types, functions, and file handling. By the end of the course, you will have gained the essential skills to write Python programs, solve problems, and build the foundation for more advanced Python development. Whether you are a beginner or have some programming experience, this course will equip you with the necessary tools to start your journey in Python programming. Level: Introductory Length: Two 3-Hour Sessions Format: Lecture + Hands-on Prerequisites: None (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 5 Jun 3:00 pm 4:20 pmThis session provides an overview of the Research Data Management (RDM) Services offered by the Digital Research Alliance of Canada, including the DMP Assistant, a national, bilingual platform for the creation and management of data management plans (DMPs), the Federated Research Data Repository (FRDR), a bilingual publishing platform for sharing and preserving Canadian research data, and Lunaris, Canada’s national discovery service for multidisciplinary data from over 90 academic, government, and research repositories across the country. This session will introduce participants to these platforms and provide an overview of how they support the research lifecycle. Attendees will gain valuable insights into the benefits of these tools and how they can help researchers to streamline their data management workflows. Level: Introductory Length: 1.5 Hours Format: Lecture Prerequisites: None (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
