195 materials found
Status:
active
WEBINAR: Getting started with RNAseq: Transforming raw reads into biological insights
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with RNAseq: Transforming raw reads into biological insights’. This webinar took place on 6 September 2023.
Event description
RNA sequencing (RNAseq) is a powerful technique for...
Keywords: Bioinformatics, Transcriptomics, RNA-seq, RNAseq, Gene expression
WEBINAR: Getting started with RNAseq: Transforming raw reads into biological insights
https://zenodo.org/record/8323208
https://dresa.org.au/materials/webinar-getting-started-with-rnaseq-transforming-raw-reads-into-biological-insights
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with RNAseq: Transforming raw reads into biological insights’. This webinar took place on 6 September 2023.
Event description
RNA sequencing (RNAseq) is a powerful technique for investigating gene expression in biological samples. Processing and analysing RNAseq data involves multiple steps to align raw sequence reads to a reference genome, count the number of reads mapped to each gene, and perform statistical analyses to identify differentially expressed genes and functionally annotate them. RNAseq experiments have many different applications as we apply them to a variety of research questions and organisms. This diversity of applications can make it challenging to appreciate all the design considerations, processing requirements, and limitations of RNAseq experiments as they apply to you.
In this webinar, you will gain an understanding of the key considerations for designing and performing your own successful experiments with bulk RNA. We’ll start at the lab bench with RNA extraction, quality control, and library preparation, then move to the sequencing machine where you will make essential decisions about sequencing platforms, optimal sequencing depth, and the importance of replicates. We’ll talk about bioinformatics workflows for RNAseq data processing and the computational requirements of transforming raw sequencing reads to analysis-ready count data. Finally, we’ll discuss how to apply differential expression and functional enrichment analyses to gain biological insights from differentially expressed genes.
This webinar was developed by the Sydney Informatics Hub in collaboration with the Australian BioCommons.
Training materials
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.
Getting started with RNAseq: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/tITR3WR_jWI
Melissa Burke (melissa@biocommons.org.au)
Deshpande, Nandan (orcid: 0000-0002-0324-8728)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Bioinformatics, Transcriptomics, RNA-seq, RNAseq, Gene expression
WEBINAR: Managing hands-on data analysis training with Galaxy
This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023.
Event description
Looking for flexible, scalable, real-world solutions that enable data analysis skills to...
Keywords: Bioinformatics, Galaxy, Training, Training infrastructure
WEBINAR: Managing hands-on data analysis training with Galaxy
https://zenodo.org/record/8185398
https://dresa.org.au/materials/webinar-managing-hands-on-data-analysis-training-with-galaxy
This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023.
Event description
Looking for flexible, scalable, real-world solutions that enable data analysis skills to be taught to anyone and anywhere?
Galaxy Australia, a national web service supporting 1000s of bioinformatics tools and workflows is a fantastic solution for training on bioinformatics concepts. Their "Training Infrastructure as a Service”, or TIaaS provides free compute and back-end support for data analysis training. It is paired with 100’s of easy-to-follow tutorials developed and maintained by the worldwide community on the Galaxy Training Network (GTN). TIaaS frees trainers from setting up and maintaining computational resources for their training events so that they can focus on student needs and learning outcomes
This webinar will show you how to make the most of Galaxy Australia, TIaaS and the Galaxy Training Network for bioinformatics training. We’ll highlight all the nifty features you can use to plan, manage and deliver training to any size audience efficiently.
Materials
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.
Managing data analysis training with Galaxy_slides: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/VNE0pF6Nqgw
Melissa Burke (melissa@biocommons.org.au)
Price, Gareth (orcid: 0000-0003-2439-8650)
Hiltemann, Saskia (orcid: 0000-0003-3803-468X)
Rasche, Helena (orcid: 0000-0001-9760-8992)
Bioinformatics, Galaxy, Training, Training infrastructure
WORKSHOP: Translating workflows into Nextflow with Janis
This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023.
Event description
Bioinformatics workflows are critical for reproducibly transferring methodologies...
Keywords: Bioinformatics, Workflows, Nextflow, CWL, Galaxy
WORKSHOP: Translating workflows into Nextflow with Janis
https://zenodo.org/record/8072678
https://dresa.org.au/materials/workshop-translating-workflows-into-nextflow-with-janis
This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023.
Event description
Bioinformatics workflows are critical for reproducibly transferring methodologies between research groups and for scaling between computational infrastructures. Research groups currently invest a lot of time and effort in creating and updating workflows; the ability to translate from one workflow language into another can make them easier to share, and maintain with minimal effort. For example, research groups that would like to run an existing Galaxy workflow on HPC, or extend it for their use, might find translating the workflow to Nextflow more suitable for their ongoing use-cases.
Janis is a framework that provides an abstraction layer for describing workflows, and a tool that can translate workflows between existing languages such as CWL, WDL, Galaxy and Nextflow. Janis aims to translate as much as it can, leaving the user to validate the workflow and make small manual adjustments where direct translations are not possible. Originating from the Portable Pipelines Project between Melbourne Bioinformatics, the Peter MacCallum Cancer Centre, and the Walter and Eliza Hall Institute of Medical Research, this tool is now available for everyone to use.
This workshop provides an introduction to Janis and how it can be used to translate Galaxy and CWL based tools and workflows into Nextflow. Using hands-on examples we’ll step you through the process and demonstrate how to optimise, troubleshoot and test the translated workflows.
This workshop event and accompanying materials were developed by the Melbourne Bioinformatics and the Peter MacCallum Cancer Centre. The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project funded by the Australian Research Data Commons and NCRIS via Bioplatforms Australia.
Materials
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.
Intro to Galaxy (PDF): Slides presented during the workshop
Intro to CWL (PDF): Slides presented during the workshop
Intro to the session & Janis (PDF): Slides presented during the workshop
Janis_Schedule (PDF): Schedule for the workshop providing a breakdown of topics and timings
Materials shared elsewhere:
This workshop follows the accompanying training materials: https://www.melbournebioinformatics.org.au/tutorials/tutorials/janis_translate/janis_translate
A recording of the workshop is available on the Australian BioCommons YouTube channel: https://youtu.be/0IiY1GEx_BY
Melissa Burke (melissa@biocommons.org.au)
Hall, Grace (orcid: 0000-0002-5105-8347)
Lupat, Richard (orcid: 0000-0002-6435-7100)
Bioinformatics, Workflows, Nextflow, CWL, Galaxy
WEBINAR:Genomic data - improving discovery and access management
This record includes training materials associated with the Australian BioCommons webinar ‘Genomic data - improving discovery and access management’. This webinar took place on 14 June 2023.
Event description
Australian human genome initiatives are generating vast amounts of human genome data...
Keywords: Bioinformatics, Data security, Genomics, Data access management
WEBINAR:Genomic data - improving discovery and access management
https://zenodo.org/record/8067584
https://dresa.org.au/materials/webinar-genomic-data-improving-discovery-and-access-management
This record includes training materials associated with the Australian BioCommons webinar ‘Genomic data - improving discovery and access management’. This webinar took place on 14 June 2023.
Event description
Australian human genome initiatives are generating vast amounts of human genome data to understand the cause of complex diseases, improve diagnosis / early disease detection and identify tailored treatment options.
To achieve this, genomic data needs to be compared between multiple individuals and cohorts, often across efforts/jurisdictions, at national or global scales, and requires the genomic data to be findable, searchable, shareable, and linkable to analytical capabilities.
The Human Genome Platform Project aims to make it as easy as possible to securely and responsibly share human genome research data nationally and internationally. The project is building a ‘services toolbox’ that combines best practice technologies in human genome data sharing.
In this webinar the project team will discuss three important aspects of human genomic data sharing
i) discovery of genomic cohorts and the GA4GH Beacon protocol that enables this functionality across multiple sites
ii) streamlining of data access request management; the Garvan will share experience using the Resource Entitlement Management System (REMS) software package.
iii) community management functionality of CILogon and
Materials
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.
Genomic data - improving discovery and access managements - slides.pdf: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/9SD6gpjDGWE
Melissa Burke (melissa@biocommons.org.au)
Holliday, Jess (orcid: 0000-0003-2855-0066)
Patterson, Andrew (orcid: 0000-0002-1163-8558)
Syed, Mustafa
Kummerfeld, Sarah (orcid: 0000-0002-0089-2358)
Bioinformatics, Data security, Genomics, Data access management
WEBINAR: Getting started with proteomics
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023.
Event description
Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is...
Keywords: Bioinformatics, Proteomics, Mass spectrometry
WEBINAR: Getting started with proteomics
https://zenodo.org/record/8019318
https://dresa.org.au/materials/webinar-getting-started-with-proteomics
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023.
Event description
Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is the most common tool for proteomics and the wide array of methods, techniques and specialised approaches available have made it a popular method for probing cells, tissue and organisms in response to various stimuli or diseases.
Each proteomics method has unique experimental design considerations and optimum workflows for data analysis meaning that there is no one-size-fits all solution. The variety of approaches available provides flexibility but can be bewildering and a barrier to getting started.
This webinar sets you up with the foundational knowledge of what to look out for when designing and understanding proteomics experiments. It outlines what you can and can’t do with proteomics, the type of data to expect as well as common data analysis approaches and quality control steps.
This webinar was developed in collaboration with the Australian Core Facilities and Australian Proteomics Communities.
Materials
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.
Getting started with proteomics_slides: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/RSrk2yqklQo
Melissa Burke (melissa@biocommons.org.au)
Padula, Matt (orcid: 0000-0002-8283-0643)
Carroll, Luke (orcid: 0000-0002-8600-4023)
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Bioinformatics, Proteomics, Mass spectrometry
WORKSHOP: Unlocking nf-core - customising workflows for your research
This record includes training materials associated with the Australian BioCommons workshop Unlocking nf-core - customising workflows for your research’. This workshop took place over two, 3 hour sessions on 18-19 May 2023.
Event description
Processing and analysing omics datasets poses many...
Keywords: Bioinformatics, Workflows, Nextflow, nf-core
WORKSHOP: Unlocking nf-core - customising workflows for your research
https://zenodo.org/record/8026170
https://dresa.org.au/materials/workshop-unlocking-nf-core-customising-workflows-for-your-research
This record includes training materials associated with the Australian BioCommons workshop Unlocking nf-core - customising workflows for your research’. This workshop took place over two, 3 hour sessions on 18-19 May 2023.
Event description
Processing and analysing omics datasets poses many challenges to life scientists, particularly when we need to share our methods with other researchers and scale up our research. Public and reproducible bioinformatics workflows, like those developed by nf-core, are invaluable resources for the life science community.
nf-core is a community-driven effort to provide high-quality bioinformatics workflows for common analyses including, RNAseq, mapping, variant calling, and single cell transcriptomics. A big advantage of using nf-core workflows is the ability to customise and optimise them for different computational environments, types and sizes of data and research goals.
This workshop will set you up with the foundational knowledge required to run and customise nf-core workflows in a reproducible manner. On day 1 you will learn about the nf-core tools utility, and step through the code structure of nf-core workflows. Then on day 2, using the nf-core/rnaseq workflow as an example, you will explore the various ways to adjust the workflow parameters, customise processes, and configure the workflow for your computational environment.
This workshop event and accompanying materials were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet). The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project (Australian Research Data Commons and NCRIS via Bioplatforms Australia).
Materials
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.
nfcore_Schedule: Schedule for the workshop providing a breakdown of topics and timings
nfcore_Q_and_A: Archive of questions and their answers from the workshop Slack Channel.
Materials shared elsewhere:
This workshop follows the accompanying training materials that were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet).
https://sydney-informatics-hub.github.io/customising-nfcore-workshop
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Willet, Cali (orcid: 0000-0001-8449-1502)
Hakkaart, Chris (orcid: 0000-0001-5007-2684)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
Stott, Audrey (orcid: 0000-0003-0939-3173)
Ip, Alex (orcid: 0000-0001-8937-8904)
Cooke, Steele
Bioinformatics, Workflows, Nextflow, nf-core
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://www.youtube.com/playlist?list=PLmu61dgAX-aaQOCG5Jlw8oLBORJfoQC2o
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
AMD
Pawsey Supercomputing Research Centre
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://www.youtube.com/playlist?list=PLmu61dgAX-aakuGnuVPiWVaqCLgm3kdRG
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
Sameer Shende
Pawsey Supercomputing Research Centre
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://support.pawsey.org.au/documentation/display/US/Pawsey+Training+Resources
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
Pelagos
Pawsey Supercomputing Research Centre
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://www.youtube.com/playlist?list=PLmu61dgAX-aYsRsejVfwHVhpPU2381Njg
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
Pelagos
Pawsey Supercomputing Research Centre
supercomputing, C/C++, Programming
A hands on introduction to Large Language Models like Bing Chat and ChatGPT
Event run 7 June at the MQ Incubator. Event description:
A two-hour hands-on workshop giving a brief history of the last 4 months of development of "Generative AI."
These tools, these Large Language Models, offer present promise and peril -- disruption -- to ways of working and of...
Keywords: Large Language Model, ChatGPT
A hands on introduction to Large Language Models like Bing Chat and ChatGPT
https://osf.io/rd24y/
https://dresa.org.au/materials/a-hands-on-introduction-to-large-language-models-like-bing-chat-and-chatgpt
Event run 7 June at the MQ Incubator. Event description:
A two-hour hands-on workshop giving a brief history of the last 4 months of development of "Generative AI."
These tools, these Large Language Models, offer present promise and peril -- disruption -- to ways of working and of learning. Outside the "hype," these tools are "calculators for words" and allow the same manipulation and reflection of a user's words as a calculator offers for a user's numbers.
The workshop will guide users into using various free and paid tools, and the effective use of Large Language Models through chain of thought prompting.
Remember: a LLM is "Always confident and usually correct."
OSF Description (LLM generated):
This two-hour workshop provides a comprehensive introduction to the world of Large Language Models (LLMs), focusing on the recent advancements in Generative AI. Participants will gain insights into the development and functionality of prominent LLMs such as Bing Chat and ChatGPT. The workshop will delve into the concept of LLMs as "calculators for words," highlighting their potential to revolutionize ways of working and learning.
The session will explore the principles of Prompt Engineering and Transactional Prompting, demonstrating how consistent prompts can yield reliable and reproducible results. Participants will also learn about the practical applications of LLMs, including editing and proofreading papers, generating technical documentation, recipe ideation, and more.
The workshop emphasizes the importance of understanding the terms of use and the responsibilities that come with using these powerful AI tools. By the end of the session, participants will be equipped with the knowledge and skills to effectively use LLMs in various contexts, guided by the mantra that a LLM is "Always confident and usually correct."
Brian Ballsun-Stanton (brian.ballsun-stanton@mq.edu.au)
Brian Ballsun-Stanton
Large Language Model, ChatGPT
researcher
WEBINAR: Pro tips for scaling bioinformatics workflows to HPC
This record includes training materials associated with the Australian BioCommons webinar ‘Pro tips for scaling bioinformatics workflows to HPC’. This webinar took place on 31 May 2023.
Event description
High Performance Computing (HPC) infrastructures offer the computational scale and...
Keywords: Bioinformatics, Workflows, HPC, High Performance Computing
WEBINAR: Pro tips for scaling bioinformatics workflows to HPC
https://zenodo.org/record/8008227
https://dresa.org.au/materials/webinar-pro-tips-for-scaling-bioinformatics-workflows-to-hpc
This record includes training materials associated with the Australian BioCommons webinar ‘Pro tips for scaling bioinformatics workflows to HPC’. This webinar took place on 31 May 2023.
Event description
High Performance Computing (HPC) infrastructures offer the computational scale and efficiency that life scientists need to handle complex biological datasets and multi-step computational workflows. But scaling workflows to HPC from smaller, more familiar computational infrastructures brings with it new jargon, expectations, and processes to learn. To make the most of HPC resources, bioinformatics workflows need to be designed for distributed computing environments and carefully manage varying resource requirements, and data scale related to biology.
In this webinar, Dr Georgina Samaha from the Sydney Informatics Hub, Dr Matthew Downton from the National Computational Infrastructure (NCI) and Dr Sarah Beecroft from the Pawsey Supercomputing Research Centre help you navigate the world of HPC for running and developing bioinformatics workflows. They explain when you should take your workflows to HPC and highlight the architectural features you should make the most of to scale your analyses once you’re there. You’ll hear pro-tips for dealing with common pain points like software installation, optimising for parallel computing and resource management, and will find out how to get access to Australia’s National HPC infrastructures at NCI and Pawsey.
Materials
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.
Pro-tips_HPC_Slides: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/YKJDRXCmGMo
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
Downton, Matthew (orcid: 0000-0002-4693-1965)
Bioinformatics, Workflows, HPC, High Performance Computing
WEBINAR: AlphaFold: what's in it for me?
This record includes training materials associated with the Australian BioCommons webinar ‘WEBINAR: AlphaFold: what’s in it for me?’. This webinar took place on 18 April 2023.
Event description
AlphaFold has taken the scientific world by storm with the ability to accurately predict the...
Keywords: Bioinformatics, Machine Learning, Structural Biology, Proteins, Drug discovery, AlphaFold, AI, Artificial Intelligence, Deep learning
WEBINAR: AlphaFold: what's in it for me?
https://zenodo.org/record/7865494
https://dresa.org.au/materials/webinar-alphafold-what-s-in-it-for-me
This record includes training materials associated with the Australian BioCommons webinar ‘WEBINAR: AlphaFold: what’s in it for me?’. This webinar took place on 18 April 2023.
Event description
AlphaFold has taken the scientific world by storm with the ability to accurately predict the structure of any protein in minutes using artificial intelligence (AI). From drug discovery to enzymes that degrade plastics, this promises to speed up and fundamentally change the way that protein structures are used in biological research.
Beyond the hype, what does this mean for structural biology as a field (and as a career)?
Dr Craig Morton, Drug Discovery Lead at the CSIRO, is an early adopter of AlphaFold and has decades of expertise in protein structure / function, protein modelling, protein – ligand interactions and computational small molecule drug discovery, with particular interest in anti-infective agents for the treatment of bacterial and viral diseases.
Craig joins this webinar to share his perspective on the implications of AlphaFold for science and structural biology. He will give an overview of how AlphaFold works, ways to access AlphaFold, and some examples of how it can be used for protein structure/function analysis.
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.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/4ytn2_AiH8s
Melissa Burke (melissa@biocommons.org.au)
Morton, Craig (orcid: 0000-0001-5452-5193)
Bioinformatics, Machine Learning, Structural Biology, Proteins, Drug discovery, AlphaFold, AI, Artificial Intelligence, Deep learning
WEBINAR AND PANEL DISCUSSION: Sustainability of biodata resources
This record includes training materials associated with the Australian BioCommons webinar and panel discussion ‘Sustainability of biodata resources’. This event took place on 8 March 2023.
Event description
Environmental, agricultural and biomedical research is dependent on the availability of...
Keywords: Bioinformatics, Open science, Services and resources, Tools, Databases, Global Biodata Coalition
WEBINAR AND PANEL DISCUSSION: Sustainability of biodata resources
https://zenodo.org/record/7816268
https://dresa.org.au/materials/webinar-and-panel-discussion-sustainability-of-biodata-resources
This record includes training materials associated with the Australian BioCommons webinar and panel discussion ‘Sustainability of biodata resources’. This event took place on 8 March 2023.
Event description
Environmental, agricultural and biomedical research is dependent on the availability of high quality data that is made available through biodata resources and databases hosted locally, nationally and internationally. The reality is that funding for development, maintenance and sustainability of biodata resources is often short-term and piecemeal leaving the resources that life scientists depend on in a precarious position. The Global Biodata Coalition was formed in response to this challenge to provide a forum for research funders and others around the globe to better coordinate and share approaches for the efficient management and growth of biodata resources worldwide.
In this extended webinar we discuss the theme of development and sustainability of biodata resources with a panel of guests. We’ll hear about the goals and activities of the Global Biodata Coalition and the challenges faced by well established and highly curated Australian and international data resources (Stemformatics, Community for Antimicrobial Drug Discovery (CO-ADD) Database and InnateDB) in sustaining these resources.
The presentations and panel discussion will be followed by questions from the audience.
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.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/T5Z5prXkvEA
Melissa Burke (melissa@biocommons.org.au)
Cochrane, Guy (orcid: 0000-0001-7954-7057)
Wells, Christine (orcid: 0000-0003-3133-3628)
Zuegg, Johannes (orcid: 0000-0001-6240-6020)
Lynn, David (orcid: 0000-0003-4664-1404)
Bioinformatics, Open science, Services and resources, Tools, Databases, Global Biodata Coalition
WORKSHOP: Make your bioinformatics workflows findable and citable
This record includes training materials associated with the Australian BioCommons workshop ‘Make your bioinformatics workflows findable and citable’. This workshop took place on 21 March 2023.
Event description
Computational workflows are invaluable resources for research communities. They help...
Keywords: Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science
WORKSHOP: Make your bioinformatics workflows findable and citable
https://zenodo.org/record/7787488
https://dresa.org.au/materials/workshop-make-your-bioinformatics-workflows-findable-and-citable
This record includes training materials associated with the Australian BioCommons workshop ‘Make your bioinformatics workflows findable and citable’. This workshop took place on 21 March 2023.
Event description
Computational workflows are invaluable resources for research communities. They help us standardise common analyses, collaborate with other researchers, and support reproducibility. Bioinformatics workflow developers invest significant time and expertise to create, share, and maintain these resources for the benefit of the wider community and being able to easily find and access workflows is an essential factor in their uptake by the community.
Increasingly, the research community is turning to workflow registries to find and access public workflows that can be applied to their research. Workflow registries support workflow findability and citation by providing a central repository and allowing users to search for and discover them easily.
This workshop will introduce you to workflow registries and support attendees to register their workflows on the popular workflow registry, WorkflowHub. We’ll kick off the workshop with an introduction to the concepts underlying workflow findability, how it can benefit workflow developers, and how you can make the most of workflow registries to share your computational workflows with the research community. You will then have the opportunity to register your own workflows in WorkflowHub with support from our trainers.
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.
2023-03-21_Workflows_slides (PDF): A copy of the slides presented during the workshop
Materials shared elsewhere:
A recording of the first part of this workshop is available on the Australian BioCommons YouTube Channel: https://youtu.be/2kGKxaPuQN8
Melissa Burke (melissa@biocommons.org.au)
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science
ARDC 2023 Skills Summit - Frameworks Panel Discussion (Day 2 - February 10, 2023)
Presentations to the ARDC Skills Summit 2023 (Panel Talks Day 2 - February 10th, 2023)
Dr Peter Derbyshire - Unpacking the ATSE report - Our STEM skilled future and the need for a national skills taxonomy
Anthony Beitz - Applying Skills Framework for the Information Age (SFIA) within DSTG
Kate...
Keywords: training material, research, training, skills, framework, sfia, eresearch, skills frameworks, skills taxonomies, skills classifications, skill shortages, transferrable skills, applying SFIA, training gaps, workforce requirements, job requirements, DReSA, digital literacy, applying skills frameworks, Australian Skills Classification framework, ASC
ARDC 2023 Skills Summit - Frameworks Panel Discussion (Day 2 - February 10, 2023)
https://zenodo.org/record/7711287
https://dresa.org.au/materials/ardc-2023-skills-summit-frameworks-panel-discussion-day-2-february-10-2023
Presentations to the ARDC Skills Summit 2023 (Panel Talks Day 2 - February 10th, 2023)
Dr Peter Derbyshire - Unpacking the ATSE report - Our STEM skilled future and the need for a national skills taxonomy
Anthony Beitz - Applying Skills Framework for the Information Age (SFIA) within DSTG
Kate Morrison - A national skills taxonomy - Australian Skills Classification (ASC)
Kathryn Unsworth - ARDC Digital Research Capabilities & Skills Framework
Peter Embelton - Enhancing skills uplift for researchers through the alignment and implementation of skills frameworks
These presentations cover skills frameworks/taxonomies/classifications, skill shortages, transferrable skills, applying SFIA (Skills Framework for the Information Age), Australian Skills Classification framework, training gaps, workforce/job requirements, Digital Research Skills Australasia (DReSA), digital literacy and applying skills frameworks.
contact@ardc.edu.au
Derbyshire, Peter
Beitz, Anthony (orcid: 0000-0002-2071-2852)
Morrison, Kate
Unsworth, Kathryn (orcid: 0000-0002-5407-9987)
Embelton, Peter
training material, research, training, skills, framework, sfia, eresearch, skills frameworks, skills taxonomies, skills classifications, skill shortages, transferrable skills, applying SFIA, training gaps, workforce requirements, job requirements, DReSA, digital literacy, applying skills frameworks, Australian Skills Classification framework, ASC
ARDC 2023 Skills Summit Lightning Talks (Day 1 - February 9, 2023)
Presentations to the ARDC Skills Summit 2023 (Lightning Talks Day 1 - February 9th, 2023)
Dr Pablo Franco - Assessing the effectiveness of training: Teaching digital skills to researchers
Aidan Wilson - Scaling training operations & succession planning
Dr Paula Martinez - Building...
Keywords: training material, research, training, Kirkpatrick framework, RezBaz, impact, skills, impact assessment, training at scale, succession planning, automated training organisation systems, trainer workforce, research software community, participation models, community building, visible research software interest group, carpentries, social infrastructure
ARDC 2023 Skills Summit Lightning Talks (Day 1 - February 9, 2023)
https://zenodo.org/record/7710856
https://dresa.org.au/materials/ardc-2023-skills-summit-lightning-talks-day-1-february-9-2023
Presentations to the ARDC Skills Summit 2023 (Lightning Talks Day 1 - February 9th, 2023)
Dr Pablo Franco - Assessing the effectiveness of training: Teaching digital skills to researchers
Aidan Wilson - Scaling training operations & succession planning
Dr Paula Martinez - Building community
Dr Mark Crowe - Bringing training to research communities - ResBaz
Liz Stokes - The Carpentries Partnership
These presentations cover theoretical frameworks for assessing training, The Kirkpatrick Model of Training Evaluation, outreach, RezBaz, impact assessment, training at scale, succession planning, automated training organisation systems, trainer workforce, research software community, participation models, community building ideas, visible research software interest group, The Carpentries and social infrastructure.
contact@ardc.edu.au
Franco, Pablo (orcid: 0000-0003-2608-2035)
Wilson, Aidan (orcid: 0000-0001-9858-5470)
Martinez, Paula (orcid: 0000-0002-8990-1985)
Crowe, Mark (orcid: 0000-0002-9514-2487)
Stokes, Liz (orcid: 0000-0002-2973-5647)
training material, research, training, Kirkpatrick framework, RezBaz, impact, skills, impact assessment, training at scale, succession planning, automated training organisation systems, trainer workforce, research software community, participation models, community building, visible research software interest group, carpentries, social infrastructure
Professionalizing Training - Origin Stories for the Modern Researcher
Keynote Presentation for the ARDC Skills Summit 2023
This keynote presentation provides a brief outline of Jason William’s experience and an overview of the training initiatives he has been involved in. His presentation looks at what makes a good researcher and provokes thinking about modern...
Keywords: research, training, skills, superheroes, formal, career, change, workshops, milestones, community, principles, bicycle principles, professionalizing, training material
Professionalizing Training - Origin Stories for the Modern Researcher
https://zenodo.org/record/7710785
https://dresa.org.au/materials/professionalizing-training-origin-stories-for-the-modern-researcher
Keynote Presentation for the ARDC Skills Summit 2023
This keynote presentation provides a brief outline of Jason William’s experience and an overview of the training initiatives he has been involved in. His presentation looks at what makes a good researcher and provokes thinking about modern researchers and the need for them to get serious bout career-spanning training. Jason also provides an overview of the Bike Principles and focuses on the first Bike Principles recommendation - Professionalize the training of short-format training instructors and instructional designers.
contact@ardc.edu.au
Williams, Jason (orcid: 0000-0003-3049-2010)
research, training, skills, superheroes, formal, career, change, workshops, milestones, community, principles, bicycle principles, professionalizing, training material
ARDC 2023 Skills Summit Lightning Talks (Day 2 - February 10, 2023)
Presentations to the ARDC Skills Summit 2023 (Lightning Talks Day 2 - February 10th, 2023)
Dr Nisha Ghatak - From local to the global: NeSI's efforts in building digital skills capabilities across Aotearoa
Dr Melissa Burke - No one has time for training. Is doing less the answer?
Dr Giorgia Mori...
Keywords: training material, digital skills capability, digital skills partnerships, The Carpentries, bioinformatics training, cooperative training approaches, industry partnered training, learner pathways, user guidance, new training approaches, innovative training approaches
ARDC 2023 Skills Summit Lightning Talks (Day 2 - February 10, 2023)
https://zenodo.org/record/7711377
https://dresa.org.au/materials/ardc-2023-skills-summit-lightning-talks-day-2-february-10-2023
Presentations to the ARDC Skills Summit 2023 (Lightning Talks Day 2 - February 10th, 2023)
Dr Nisha Ghatak - From local to the global: NeSI's efforts in building digital skills capabilities across Aotearoa
Dr Melissa Burke - No one has time for training. Is doing less the answer?
Dr Giorgia Mori - Industry training collaborations. Is this the future?
Ann Backhaus - Skills pathways for developing the research workforce - status quo or let's get creative?
These presentations cover a national perspective of New Zealand's digital skills capability and partnerships, The Carpentries, bioinformatics training, innovative and cooperative training approaches, industry-partnered training, learner pathways, and the importance of user guidance.
contact@ardc.edu.au
Ghatak, Nisha (orcid: 0000-0002-1213-2196)
Burke, Melissa (orcid: 0000-0002-5571-8664)
Mori, Giorgia (orcid: 0000-0003-3469-5632)
Backhaus, Ann (orcid: 0000-0002-9023-055X)
training material, digital skills capability, digital skills partnerships, The Carpentries, bioinformatics training, cooperative training approaches, industry partnered training, learner pathways, user guidance, new training approaches, innovative training approaches
Setting The Scene
Opening Address for the ARDC Skills Summit 2023
This presentation provides a welcome to the ARDC Skills Summit 2023, and includes an outline of the importance of digital research skills to data-enriched research, the value of skills training and highly skilled research workforce to the broader...
Keywords: research, training, skills, training material, ARDC, research data commons, digital research skills agenda
Setting The Scene
https://zenodo.org/record/7710621
https://dresa.org.au/materials/setting-the-scene
Opening Address for the ARDC Skills Summit 2023
This presentation provides a welcome to the ARDC Skills Summit 2023, and includes an outline of the importance of digital research skills to data-enriched research, the value of skills training and highly skilled research workforce to the broader economy, and an overview of related ARDC activity.
contact@ardc.edu.au
Russell, Keith (orcid: 0000-0001-5390-2719)
research, training, skills, training material, ARDC, research data commons, digital research skills agenda
Introduction to REDCap at Griffith University
This site is designed as a companion to Griffith Library’s Research Data Capture workshops. It can also be treated as a standalone, self-paced tutorial for learning to use REDCap (Research Electronic Data Capture) a secure web application for building and managing online surveys and databases.
Keywords: REDCap, survey instruments
Resource type: tutorial
Introduction to REDCap at Griffith University
https://griffithunilibrary.github.io/redcap-intro/
https://dresa.org.au/materials/introduction-to-redcap-at-griffith-university
This site is designed as a companion to Griffith Library’s Research Data Capture workshops. It can also be treated as a standalone, self-paced tutorial for learning to use REDCap (Research Electronic Data Capture) a secure web application for building and managing online surveys and databases.
y.banens@griffith.edu.au
Yuri Banens
REDCap, survey instruments
mbr
phd
ecr
researcher
support
Introduction to text mining and analysis
In this self-paced workshop you will learn steps to:
- Build data sets: find where and how to gather textual data for your corpus or data set.
- Prepare data for analysis: explore useful processes and tools to prepare and clean textual data for analysis
- Analyse data: identify different...
Keywords: textual training materials
Resource type: tutorial
Introduction to text mining and analysis
https://griffithunilibrary.github.io/intro-text-mining-analysis/
https://dresa.org.au/materials/introduction-to-text-mining-and-analysis
In this self-paced workshop you will learn steps to:
- Build data sets: find where and how to gather textual data for your corpus or data set.
- Prepare data for analysis: explore useful processes and tools to prepare and clean textual data for analysis
- Analyse data: identify different types of analysis used to interrogate content and uncover new insights
s.stapleton@griffith.edu.au; y.banens@griffith.edu.au;
Yuri Banens
Sharron Stapleton
Ben McRae
textual training materials
mbr
phd
ecr
researcher
support
Introducing Computational Thinking
This workshop is for researchers at all career stages who want to understand the uses and the building blocks of computational thinking. This skill is useful for all kinds of problem solving, whether in real life or in computing.
The workshop will not teach computer programming per se. Instead...
Keywords: computational skills, data skills
Resource type: tutorial
Introducing Computational Thinking
https://griffithunilibrary.github.io/intro-computational-thinking/
https://dresa.org.au/materials/introducing-computational-thinking
This workshop is for researchers at all career stages who want to understand the uses and the building blocks of computational thinking. This skill is useful for all kinds of problem solving, whether in real life or in computing.
The workshop will not teach computer programming per se. Instead it will cover the thought processes involved should you want to learn to program.
s.stapleton@griffith.edu.au
Belinda Weaver
computational skills, data skills
Advanced Data Wrangling with OpenRefine
This online self-paced workshop teaches advanced data wrangling skills including combining datasets, geolocating data, and “what if” exploration using OpenRefine.
Keywords: data skills, data
Resource type: tutorial
Advanced Data Wrangling with OpenRefine
https://griffithunilibrary.github.io/advanced-data-wrangle-2/
https://dresa.org.au/materials/advanced-data-wrangling-with-openrefine
This online self-paced workshop teaches advanced data wrangling skills including combining datasets, geolocating data, and “what if” exploration using OpenRefine.
s.stapleton@griffith.edu.au
Sharron Stapleton
data skills, data
mbr
phd
ecr
researcher
support
professional
Introduction to Data Cleaning with OpenRefine
Learn basic data cleaning techniques in this self-paced online workshop using open data from data.qld.gov.au and open source tool OpenRefine openrefine.org. Learn techniques to prepare messy tabular data for comupational analysis. Of most relevance to HASS disciplines, working with textual data...
Keywords: data skills, Data analysis
Resource type: tutorial
Introduction to Data Cleaning with OpenRefine
https://griffithunilibrary.github.io/data-cleaning-intro/
https://dresa.org.au/materials/introduction-to-data-cleaning-with-openrefine
Learn basic data cleaning techniques in this self-paced online workshop using open data from data.qld.gov.au and open source tool OpenRefine openrefine.org. Learn techniques to prepare messy tabular data for comupational analysis. Of most relevance to HASS disciplines, working with textual data in a structured or semi-structured format.
s.stapleton@griffith.edu.au;
Sharron Stapleton
data skills, Data analysis
mbr
phd
ecr
researcher
support
professional
Digital research skills trainer certification guide
This guide to certification is for those who currently design, develop and deliver training as full-time trainers or where training is part of their role, and for those who are considering becoming a skills trainer.
Keywords: digital research skills training, trainer certification, training material
Digital research skills trainer certification guide
https://zenodo.org/record/7587668
https://dresa.org.au/materials/digital-research-skills-trainer-certification-guide
This guide to certification is for those who currently design, develop and deliver training as full-time trainers or where training is part of their role, and for those who are considering becoming a skills trainer.
contact@ardc.edu.au
ARDC
digital research skills training, trainer certification, training material
Guide to designing digital research skills training materials: presentations and videos
The Australian Research Data Commons (ARDC) Guide to Designing Digital Research Skills Training Materials: Presentations and Videos aims to support training materials creators, trainers and national training infrastructure providers in the design and delivery of presentations and videos while...
Keywords: digital research skills training, learning design, training presentations, training videos, training material
Guide to designing digital research skills training materials: presentations and videos
https://zenodo.org/record/7587657
https://dresa.org.au/materials/guide-to-designing-digital-research-skills-training-materials-presentations-and-videos
The Australian Research Data Commons (ARDC) Guide to Designing Digital Research Skills Training Materials: Presentations and Videos aims to support training materials creators, trainers and national training infrastructure providers in the design and delivery of presentations and videos while also encouraging the sharing and reuse of their training materials. It aims to facilitate the design, development and delivery of digital research and data skills videos and presentations in alignment with best practices for learning and training.
This tool is informed by the Universal Design for Learning framework, which aims to eliminate barriers in the design of learning materials and make content accessible to all.
contact@ardc.edu.au
ARDC
digital research skills training, learning design, training presentations, training videos, training material
Guide to designing digital research skills training materials: textual materials
The Australian Research Data Commons (ARDC) Guide to Designing Digital Research Skills Training Materials: Textual Materials aims to support training materials creators, trainers and national training infrastructure providers in the creation of textual guides while also encouraging the sharing...
Keywords: digital research skills training, learning design, textual training materials, training material
Guide to designing digital research skills training materials: textual materials
https://zenodo.org/record/7587651
https://dresa.org.au/materials/guide-to-designing-digital-research-skills-training-materials-textual-materials
The Australian Research Data Commons (ARDC) Guide to Designing Digital Research Skills Training Materials: Textual Materials aims to support training materials creators, trainers and national training infrastructure providers in the creation of textual guides while also encouraging the sharing and reuse of their training materials. It aims to facilitate the design, development and delivery of textual guides on digital research and data skills in alignment with best practices in learning and training.
This tool is informed by the Universal Design for Learning principles which aims to eliminate barriers in the design of learning materials to make content accessible to all.
contact@ardc.edu.au
ARDC
digital research skills training, learning design, textual training materials, training material
WORKSHOP: RNA-Seq: reads to differential genes and pathways
This record includes training materials associated with the Australian BioCommons workshop ‘RNA-Seq: reads to differential genes and pathways’. This workshop took place over two, 3.5 hour sessions on 27 and 28 September 2022.
Event description
RNA sequencing (RNA-seq) is a common method...
Keywords: Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re
WORKSHOP: RNA-Seq: reads to differential genes and pathways
https://zenodo.org/record/7439804
https://dresa.org.au/materials/workshop-rna-seq-reads-to-differential-genes-and-pathways
This record includes training materials associated with the Australian BioCommons workshop ‘RNA-Seq: reads to differential genes and pathways’. This workshop took place over two, 3.5 hour sessions on 27 and 28 September 2022.
**Event description**
RNA sequencing (RNA-seq) is a common method used to understand the differences in gene expression and molecular pathways between two or more groups. This workshop introduces the fundamental concepts of RNA sequencing experiments and will allow you to try out the analysis using data from a study of Williams-Beuren Syndrome, a rare disease.
In the first part of the workshop you will learn how to convert sequence reads into analysis ready count data. To do this we will use nf-core/rnaseq - a portable, scalable, reproducible and publicly available workflow on Pawsey Nimbus Cloud. In the second part of the workshop you will use the count data you created to identify differential genes and pathways using R/Rstudio. By the end of the workshop, you should be able to perform your own RNA-seq analysis for differential gene expression and pathway analysis!
This workshop is presented by the Australian BioCommons and Sydney Informatics Hub 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.
* RNAseq reads to differential genes and pathways - Additional Resources (PDF): Additional resources compiled by the Sydney Informatics Hub
* rnaseq_DE_analysis_Day2.html: HTML version of code used on day 2 of the workshop
* rnaseq_DE_analysis_Day2.Rmd: R Markdown version of code used on day 2 of the workshop
* RNAseq reads to differential genes and pathways_Q_and_A (PDF): Archive of questions and their answers from the workshop Slack Channel.
**Materials shared elsewhere:**
This workshop follows the tutorial ‘RNA-seq: reads to differential gene expression workshop series’ developed by the Sydney Informatics Hub.
https://sydney-informatics-hub.github.io/training.RNAseq.series-quarto/
Melissa Burke (melissa@biocommons.org.au)
Deshpande, Nandan (orcid: 0000-0002-0324-8728)
Chew, Tracy (orcid: 0000-0001-9529-7705)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re
Exploring Chi-Square and Correlation in SPSS
This hands-on training is designed to familiarize you further with the SPSS data analysis environment. In this session, we will traverse into the realm of inferential statistics, beginning with linear correlation and reliability. We will present a brief conceptual overview and the SPSS procedures...
Keywords: Data Analysis, SPSS
Exploring Chi-Square and Correlation in SPSS
https://intersect.org.au/training/course/spss102
https://dresa.org.au/materials/exploring-chi-square-and-correlation-in-spss-d38c2067-302a-4194-80a2-71f2311f8756
This hands-on training is designed to familiarize you further with the SPSS data analysis environment. In this session, we will traverse into the realm of inferential statistics, beginning with linear correlation and reliability. We will present a brief conceptual overview and the SPSS procedures for computing Pearson's r and Spearman's Rho, followed by a short session on reliability . In the remainder of the session, we will explore the Chi-Square Goodness-of-Fit test and Chi-Square Test of Association for analysing categorical data.
#### You'll learn:
- Perform Pearson’s Correlation (r) Test
- Perform Spearman’s Rho Correlation (⍴) Test
- Carry out basic reliability analysis on survey items
- Perform Chi-Square Goodness-of-Fit test
- Perform Chi-Square Test of Association
#### Prerequisites:
In order to participate, attendees must have a licensed copy of SPSS installed on their computer. Speak to your local university IT or Research Office for assistance in obtaining a license and installing the software.
This workshop is recommended for researchers and postgraduate students who have previously attended the Intersect’s [Data Entry and Processing in SPSS](https://intersect.org.au/training/course/spss101/) workshop.
**For more information, please click [here](https://intersect.org.au/training/course/spss102).**
training@intersect.org.au
Data Analysis, SPSS