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Authors: Harrison, Paul (orcid: 0000...  or Pawsey Supercomputing Resea... 

WORKSHOP: Single cell RNAseq analysis in R

This record includes training materials associated with the Australian BioCommons workshop 'Single cell RNAseq analysis in R'. This workshop took place over two, 3.5 hour sessions on 26 and 27 October 2023.Event descriptionAnalysis and interpretation of single cell RNAseq (scRNAseq) data requires...

Keywords: bioinformatics, transcriptomics, single cell RNA-seq, Seurat, R statistical software

WORKSHOP: Single cell RNAseq analysis in R https://dresa.org.au/materials/workshop-single-cell-rnaseq-analysis-in-r-6a1126cf-7105-43ec-bf55-7c492f758301 This record includes training materials associated with the Australian BioCommons workshop 'Single cell RNAseq analysis in R'. This workshop took place over two, 3.5 hour sessions on 26 and 27 October 2023.Event descriptionAnalysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using Seurat - an R package for QC, analysis, and exploration of single-cell RNAseq data. We will discuss the 'why' behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data.This workshop is presented by the Australian BioCommons, Queensland Cyber Infrastructure Foundation (QCIF) and the Monash Genomics and Bioinformatics Platform with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.Lead trainers: Sarah Williams, Adele Barugahare, Paul Harrison, Laura Perlaza JimenezFacilitators: Nick Matigan, Valentine Murigneux, Magdalena (Magda) AntczakInfrastructure provision: Uwe WinterCoordinator: Melissa BurkeTraining materialsMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.Files and materials included in this record:Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.scRNAseq_Schedule (PDF): A breakdown of the topics and timings for the workshopMaterials shared elsewhere:This workshop follows the tutorial 'scRNAseq Analysis in R with Seurat'https://swbioinf.github.io/scRNAseqInR_Doco/index.htmlSlides used to introduce key topics are available via GitHubhttps://github.com/swbioinf/scRNAseqInR_Doco/tree/main/slidesThis material is based on the introductory Guided Clustering Tutorial tutorial from Seurat.It is also drawing from a similar workshop held by Monash Bioinformatics Platform Single-Cell-Workshop, with material here.   Melissa Burke (melissa@biocommons.org.au) bioinformatics, transcriptomics, single cell RNA-seq, Seurat, R statistical software
WORKSHOP: Single cell RNAseq analysis in R

This record includes training materials associated with the Australian BioCommons workshop ‘Single cell RNAseq analysis in R’. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022.

Event description

Analysis and interpretation of single cell RNAseq (scRNAseq) data...

Keywords: Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq

WORKSHOP: Single cell RNAseq analysis in R https://dresa.org.au/materials/workshop-single-cell-rnaseq-analysis-in-r-4f60b82d-2f1e-4021-9569-6955878dd945 This record includes training materials associated with the Australian BioCommons workshop ‘Single cell RNAseq analysis in R’. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022. Event description Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using Seurat - an R package for QC, analysis, and exploration of single-cell RNAseq data.  We will discuss the ‘why’ behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data. This workshop is presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.   Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. scRNAseq_Slides (PDF): Slides used to introduce topics scRNAseq_Schedule (PDF): A breakdown of the topics and timings for the workshop scRNAseq_Resources (PDF): A list of resources recommended by trainers and participants scRNAseq_QandA(PDF): Archive of questions and their answers from the workshop Slack Channel.   Materials shared elsewhere: This workshop follows the tutorial ‘scRNAseq Analysis in R with Seurat’ https://swbioinf.github.io/scRNAseqInR_Doco/index.html This material is based on the introductory Guided Clustering Tutorial tutorial from Seurat. It is also drawing from a similar workshop held by Monash Bioinformatics Platform Single-Cell-Workshop, with material here. Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq
WORKSHOP: Working with genomics sequences and features in R with Bioconductor

This record includes training materials associated with the Australian BioCommons workshop ‘Working with genomics sequences and features in R with Bioconductor’. This workshop took place on 23 September 2021.

Workshop description

Explore the many useful functions that the Bioconductor...

Keywords: R software, Bioconductor, Bioinformatics, Analysis, Genomics, Sequence analysis

WORKSHOP: Working with genomics sequences and features in R with Bioconductor https://dresa.org.au/materials/workshop-working-with-genomics-sequences-and-features-in-r-with-bioconductor-8399bf0d-1e9e-48f3-a840-3f70f23254bb This record includes training materials associated with the Australian BioCommons workshop ‘Working with genomics sequences and features in R with Bioconductor’. This workshop took place on 23 September 2021. Workshop description Explore the many useful functions that the Bioconductor environment offers for working with genomic data and other biological sequences.  DNA and proteins are often represented as files containing strings of nucleic acids or amino acids. They are associated with text files that provide additional contextual information such as genome annotations. This workshop provides hands-on experience with tools, software and packages available in R via Bioconductor for manipulating, exploring and extracting information from biological sequences and annotation files. We will look at tools for working with some commonly used file formats including FASTA, GFF3, GTF, methods for identifying regions of interest, and easy methods for obtaining data packages such as genome assemblies.  This workshop is presented by the Australian BioCommons and Monash Bioinformatics Platform with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schedule (PDF): schedule for the workshop providing a breakdown of topics and timings   Materials shared elsewhere: This workshop follows the tutorial ‘Working with DNA sequences and features in R with Bioconductor - version 2’ developed for Monash Bioinformatics Platform and Monash Data Fluency by Paul Harrison. https://monashdatafluency.github.io/r-bioc-2/ Melissa Burke (melissa@biocommons.org.au) R software, Bioconductor, Bioinformatics, Analysis, Genomics, Sequence analysis
Using PennyLane on Setonix

Introduction to quantum computing

Keywords: Pawsey Supercomputing Centre, Setonix, quantum, PennyLane

Using PennyLane on Setonix https://dresa.org.au/materials/using-pennylane-on-setonix Introduction to quantum computing training@pawsey.org.au Pawsey Supercomputing Centre, Setonix, quantum, PennyLane
Pawsey: AWS Quantum 101 Using Amazon Braket

Join us as AWS Quantum Specialists introduce quantum simulators and gate-based quantum computers, before turning to more advanced topics.

Keywords: Pawsey Supercomputing Centre, AWS, quantum, HPC

Pawsey: AWS Quantum 101 Using Amazon Braket https://dresa.org.au/materials/pawsey-aws-quantum-101-using-amazon-braket Join us as AWS Quantum Specialists introduce quantum simulators and gate-based quantum computers, before turning to more advanced topics. training@pawsey.org.au Pawsey Supercomputing Centre, AWS, quantum, HPC
HIP Advanced Workshop

Additional topics presented about HIP, covering memory management, kernel optimisation, IO optimisation and porting CUDA to HIP.

Keywords: HIP, Pawsey Supercomputing Centre, supercomputing

HIP Advanced Workshop https://dresa.org.au/materials/hip-advanced-workshop Additional topics presented about HIP, covering memory management, kernel optimisation, IO optimisation and porting CUDA to HIP. training@pawsey.org.au HIP, Pawsey Supercomputing Centre, supercomputing
Managing Data using Acacia @ Pawsey

Acacia is Pawsey's "warm tier" or project storage. This object store is fully integrated with Setonix, Pawsey's main supercomputer, enabling fast transfer of data for project use.

These short videos introduce this high-speed object storage for hosting research data online.

Acacia is named...

Keywords: data, data skills, Acacia, Pawsey Supercomputing Centre, object storage, File systems

Managing Data using Acacia @ Pawsey https://dresa.org.au/materials/managing-data-using-acacia-pawsey Acacia is Pawsey's "warm tier" or project storage. This object store is fully integrated with Setonix, Pawsey's main supercomputer, enabling fast transfer of data for project use. These short videos introduce this high-speed object storage for hosting research data online. Acacia is named after Australia’s national floral emblem the Golden Wattle – Acacia pycnantha. training@pawsey.org.au data, data skills, Acacia, Pawsey Supercomputing Centre, object storage, File systems ugrad masters phd ecr researcher support professional
OpenCL

Supercomputers make use of accelerators from a variety of different hardware vendors, using devices such as multi-core CPU’s, GPU’s and even FPGA’s. OpenCL is a way for your HPC application to make effective use of heterogeneous computing devices, and to avoid code refactoring for new HPC...

Keywords: supercomputing, Pawsey Supercomputing Centre, CPUs, GPUs, OpenCL, FPGAs

Resource type: activity

OpenCL https://dresa.org.au/materials/opencl Supercomputers make use of accelerators from a variety of different hardware vendors, using devices such as multi-core CPU’s, GPU’s and even FPGA’s. OpenCL is a way for your HPC application to make effective use of heterogeneous computing devices, and to avoid code refactoring for new HPC infrastructure. training@pawsey.org.au Toby Potter supercomputing, Pawsey Supercomputing Centre, CPUs, GPUs, OpenCL, FPGAs masters ecr researcher support
AMD Profiling

The AMD profiling workshop covers the AMD suite of tools for development of HPC applications on AMD GPUs.

You will learn how to use the rocprof profiler and trace visualization tool that has long been available as part of the ROCm software suite.

You will also learn how to use the new...

Keywords: supercomputing, performance, GPUs, CPUs, AMD, HPC, ROCm

Resource type: activity

AMD Profiling https://dresa.org.au/materials/amd-profiling The AMD profiling workshop covers the AMD suite of tools for development of HPC applications on AMD GPUs. You will learn how to use the rocprof profiler and trace visualization tool that has long been available as part of the ROCm software suite. You will also learn how to use the new Omnitools - Omnitrace and Omniperf - that were introduced at the end of 2022. Omnitrace is a powerful tracing profiler for both CPU and GPU. It can collect data from a much wider range of sources and includes hardware counters and sampling approaches. Omniperf is a performance analysis tool that can help you pinpoint how your application is performing with a visual view of the memory hierarchy on the GPU as well as reporting the percentage of peak for many different measurements. training@pawsey.org.au supercomputing, performance, GPUs, CPUs, AMD, HPC, ROCm
Evaluate Application Performance using TAU and E4S

In this workshop, you learn about the Extreme-scale Scientific Software Stack and the TAU Performance System® and its interfaces to other tools and libraries. The workshop includes sample codes that illustrate the different instrumentation and measurement choices.

Topics covered include...

Keywords: supercomputing, TAU, E4S, Performance, ROCm, OpenMP

Resource type: activity

Evaluate Application Performance using TAU and E4S https://dresa.org.au/materials/evaluate-application-performance-using-tau-and-e4s In this workshop, you learn about the Extreme-scale Scientific Software Stack and the TAU Performance System® and its interfaces to other tools and libraries. The workshop includes sample codes that illustrate the different instrumentation and measurement choices. Topics covered include generating performance profiles and traces with memory utilization and headroom, I/O, and interfaces to ROCm, including ROCProfiler and ROCTracer with support for collecting hardware performance data. The workshop also covers instrumentation of OpenMP programs using OpenMP Tools Interface (OMPT), including support for target offload and measurement of a program’s memory footprint. During the session, there are hands-on activities on scalable tracing using OTF2 and visualization using the Vampir trace analysis tool. Performance data analysis using ParaProf and PerfExplorer are demonstrated using the performance data management framework (TAUdb) that includes TAU’s performance database. training@pawsey.org.au supercomputing, TAU, E4S, Performance, ROCm, OpenMP
HIP Workshop

The Heterogeneous Interface for Portability (HIP) provides a programming framework for harnessing the compute capabilities of multicore processors, such as the MI250X GPU’s on Setonix.

In this course we focus on the essentials of developing HIP applications with a focus on...

Keywords: HIP, supercomputing, Programming, GPUs, MPI, debugging

Resource type: full-course

HIP Workshop https://dresa.org.au/materials/hip-workshop The Heterogeneous Interface for Portability (HIP) provides a programming framework for harnessing the compute capabilities of multicore processors, such as the MI250X GPU’s on Setonix. In this course we focus on the essentials of developing HIP applications with a focus on supercomputing. Agenda - Introduction to HIP and high level features - How to build and run applications on Setonix with HIP and MPI - A complete line-by-line walkthrough of a HIP-enabled application - Tools and techniques for debugging and measuring the performance of HIP applications training@pawsey.org.au HIP, supercomputing, Programming, GPUs, MPI, debugging
C/C++ Refresher

The C++ programming language and its C subset is used extensively in research environments. In particular it is the language utilised in the parallel programming frameworks CUDA, HIP, and OpenCL.

This workshop is designed to equip participants with “Survival C++”, an understanding of the basic...

Keywords: supercomputing, C/C++, Programming

Resource type: activity

C/C++ Refresher https://dresa.org.au/materials/c-c-refresher The C++ programming language and its C subset is used extensively in research environments. In particular it is the language utilised in the parallel programming frameworks CUDA, HIP, and OpenCL. This workshop is designed to equip participants with “Survival C++”, an understanding of the basic syntax, how information is encoded in binary format, and how to compile and debug C++ software. training@pawsey.org.au supercomputing, C/C++, Programming