Friday, 9 June

Domain-Specific Applications and Workflows

Today's tutorials will occur along four tracks running concurrently, each devoted to computational methods associated with different research domain. Each tab below corresponds to one of the tracks. The tutorials associated with each track are listed on the relevant tab.

Bioinformatics

Using Nextflow on Oscar | 9:30 - 12:30 EDT

Description coming soon!

video

Introduction to Biomarker Discovery | 1:30 - 4:30 EDT

Biomarker discovery is one of the most important tasks in both the clinic and in biomedical data science. However, clinicians and bioinformaticians often have different views about what makes a biomarker useful and how to interpret biomarker data. This session will focus on basic methods of biomarker discovery and assessment and will include discussions on linear and logistic regression, exploratory analysis, omics data analysis, and machine learning for biomarker discovery.

repo | video

Health Informatics

Health Data and Computing Basics | 9:00 - 12:00 EDT

This hybrid session will cover basic processing and analysis of an openly-available health dataset using Unix commands, SQL, Julia, and Python.

Instructions | video

Neuroimaging

XNAT: Data Management | 9:30 - 11:00 EDT *Hybrid*

Join us for a hands-on workshop where we will provide a comprehensive overview of the XNAT neuroimaging data platform, in addition to showcasing the latest features in our data processing tools. During the workshop, we will guide you step-by-step through our documentation, while offering our best practices and demonstrating a live demo of our data processing pipeline alongside a new utility script for running on Oscar.

Whether you’re new to XNAT or an experienced user, this workshop is designed to help you stay up-to-date with our most recent changes to xnat-tools, which are now available to your lab. You’ll walk away with a deeper understanding of our xnat2bids pipeline and be ready to implement it in your lab’s workflow.

Neuroimaging Tools on Oscar | 11:00 - 12:30 EDT *Hybrid*

Join us for a hands-on workshop showcasing the various neuroimaging tools available on our high-performance cluster, Oscar. We will showcase a few of our BIDS Apps, such as fmriprep and mriqc, that carry out preprocessing and quality control checks on neuroimaging data. In addition, a few of our experienced users will be there to showcase their own workflows and tools on Oscar. They will walk you through their step-by-step processes and share their best practices, providing valuable insights into real-world applications of neuroimaging data processing.

Working With NGS Counts

Introduction to RNAseq Experimental Analysis and Design | 9:30 - 11:00 EDT *Hybrid*

Description coming soon!

Introduction to Single Cell RNA-seq with Seurat | 11:00 - 12:30 EDT *Hybrid*

We will cover the standard Seurat pre-processing pipeline for single cell RNA-seq. We will discuss working with Seurat objects, data QC and filtering, normalization, merging and integrating multiple data sets, data vizualisation, and differential expression testing.

Annotation Resources for Downstream Analyses using Bioconductor | 1:30 - 3:00 EDT *Hybrid*

This session is devoted to annotation resources and downstream analyses of NGS data using R and Bioconductor. We will cover different annotation file formats, public resources for annotation data, and leveraging those resources for downstream analyses in R.

video (all sessions)