| June,2024 |
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| 3 Jun 9:00 am 12:00 pmRunning programs on the supercomputers is done via the BASH shell. This course is two three hour live demos on using bash. No prior familiarity with bash is assumed. In addition to the basics of getting around, globbing, regular expressions, redirection, pipes, and scripting will be covered. A series of exercises are required to be done in order to complete the course. Level: Introductory Length: Two 3-Hour Sessions Format: Lecture + Hands-on Prerequisites: None (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 3 Jun 9:00 am 12:00 pmThis course provides you with essential knowledge and skills to effectively prepare data for analysis. Starting with an overview of the Data Analytics pipeline and processes, the course explores various statistical and visualization techniques used in Exploratory and Descriptive Analytics to understand historical data. You will then delve into the art of Data Preparation, gaining expertise in data cleaning, handling missing values, detecting, and handling outliers, as well as transforming and engineering features. By the end of the course, you will be equipped with the necessary tools to ensure data quality and integrity, enabling you to make informed decisions and derive valuable insights from their data. Level: Introductory Length: 3 Hours Format: Lecture + Hands-on Prerequisites: Basic Python (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 3 Jun 1:30 pm 4:30 pmBe aware. Stay secure. Join us to learn more about the tools you can use to prevent the theft of your data and possibly of your identity. Other topics of discussion will include common hacking attempts, how to recognize them, and how to avoid having your data compromised, stolen, or destroyed. We will also talk about data encryption and provide tips for when travelling with electronic devices. Level: Introductory Length: 3 hours Format: Lecture Prerequisites: None (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 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 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 |
| 6 Jun 1:30 pm 2:50 pmThis session will provide participants with information, guidance, and resources for supporting research through the development and implementation of data management plans (DMPs). Level: Introductory Length: 1.5 Hours Format: Lecture Prerequisites: None General topics covered will include the importance and benefits of DMPs, their content, and impending DMP requirements relating to the Tri-Agency research data management (RDM) policy. Specific focus will be given to the Digital Research Alliance of Canada DMP Assistant platform that is hosted nationally at the University of Alberta Library, along with a new DMP template developed by the Alliance’s DMP Expert Group (DMPEG). This new template is targeted specifically to support researchers in meeting DMP requirements at the funding opportunity application stage. Additional information relating to an accompanying assessment rubric that is currently in development will be shared. Time will be reserved for questions and discussion. (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 6 Jun 1:30 pm 4:30 pmThis half-day session offers a brief introduction to R, with a focus on data analysis and statistics. We will discuss the following topics: the R interface, primitive data types, lists, vectors, matrices, and data frames - a crucial data type in data analysis and the trademark of the R language. Advanced topics to be covered include: basics statistics and function creation; *apply family functions; and the basics of scripting. Level: Introductory Length: 3 Hours Format: Lecture + Hands-on Prerequisite: Some programming experience in another programming language (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
| 6 Jun 3:00 pm 4:20 pmThe reproducibility of research is essential to the scientific community, as it ensures the accuracy and reliability of research findings that are used to build upon existing knowledge. However, reproducibility is often hindered by the lack of access to research data, documentation, and code. This workshop will provide an overview of the concepts of open science, reproducibility, and the FAIR principles of research data, as well as explore how to deposit and share data in Borealis, the Canadian Dataverse Repository, a bilingual, multidisciplinary, secure, Canadian research data repository, supported by academic libraries and research institutions across Canada. Level: Introductory; Length: 1.5 Hours; Format: Lecture; Prerequisites: None (part of the 2024 Compute Ontario Summer School) Virtual | COSS2024 |
