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Authors: Unsworth, Kathryn (orcid: 0...  or Samaha, Georgina (orcid: 00... 

WORKSHOP: Making sense of gene and protein lists with functional enrichment analysis

This record includes training materials associated with the Australian BioCommons workshop ‘Making sense of gene and protein lists with functional enrichment analysis’. This workshop took place over two, 3 hour sessions on 20, 21 November 2024.
Event description
Omics experiments often generate...

Keywords: Bioinformatics http://edamontology.org/topic_0091, Analysis http://edamontology.org/operation_2945, Enrichment analysis http://edamontology.org/operation_3501

WORKSHOP: Making sense of gene and protein lists with functional enrichment analysis https://dresa.org.au/materials/workshop-making-sense-of-gene-and-protein-lists-with-functional-enrichment-analysis This record includes training materials associated with the Australian BioCommons workshop ‘Making sense of gene and protein lists with functional enrichment analysis’. This workshop took place over two, 3 hour sessions on 20, 21 November 2024. Event description Omics experiments often generate long lists of genes or proteins. Functional enrichment analysis identifies biological trends in the data by assessing these lists against gene ontology and pathway information. This can help interpret the experimental results in the context of larger biological systems. This workshop continues from our introductory webinar and provides a practical introduction to functional enrichment analysis. Using example data you will get hands-on with some of the most commonly used databases and tools for over representation (ORA) and gene set enrichment analysis (GSEA) and for identifying enriched biological functions in a list of genes or proteins. We’ll focus on tools available online and in R. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Lead Trainers: Dr Hossein Valipour Kahrood, Bioinformatician, Monash Genomics and Bioinformatics Platform Dr Cali Willet, Senior Research Bioinformatician, Sydney Informatics Hub, University of Sydney Facilitators: Georgina Samaha, Australian BioCommons Laura Perlaza-Jimenez, Monash Genomics and Bioinformatics Platform Infrastructure provision: Uwe Winter, Australian BioCommonsHost: Dr. Melissa Burke, Australian BioCommons Training materials Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. R notebooks (zip): R markdown and html rendered files, input files. Training materials webpage Melissa Burke (melissa@biocommons.org.au) Bioinformatics http://edamontology.org/topic_0091, Analysis http://edamontology.org/operation_2945, Enrichment analysis http://edamontology.org/operation_3501
WORKSHOP: Hello Nextflow!

This record includes training materials associated with the Australian BioCommons workshop ‘Hello Nextflow’. This workshop took place over two sessions on 24 - 25 September 2024.
Event description
The rise of big data has made it essential to be able to analyse and perform experiments on large...

Keywords: Bioinformatics, Workflows, Nextflow

WORKSHOP: Hello Nextflow! https://dresa.org.au/materials/workshop-hello-nextflow This record includes training materials associated with the Australian BioCommons workshop ‘Hello Nextflow’. This workshop took place over two sessions on 24 - 25 September 2024. Event description The rise of big data has made it essential to be able to analyse and perform experiments on large datasets in a portable and reproducible manner. Nextflow is a popular bioinformatics workflow orchestrator that makes it easy to run data-intensive computational pipelines. It enables scalable and reproducible scientific workflows using software containers on any infrastructure. It allows the adaptation of workflows written in most languages and provides the ability to customise and optimise workflows for different computational environments, types and sizes of data. This workshop will put you on the path to writing your own reproducible and scalable scientific workflows using Nextflow. You will learn how to use core Nextflow components to build, run and troubleshoot a scalable multi-step workflow. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.   Lead trainers:  Dr Chris Hakkaart, Developer Advocate, Seqera Labs. Fred Jaya, Senior Bioinformatician (Australian BioCommons), Sydney Informatics Hub, University of Sydney. Dr Georgie Samaha - Product Owner of the Australian BioCommons BioCLI Project and Bioinformatics Group Lead at the Sydney Informatics Hub, The University of Sydney. Facilitator: Dr Ziad Al Bkhetan, Australian BioCommons Infrastructure provision: Uwe Winter, Australian BioCommons Host: Dr Melissa Burke, Australian BioCommons   Training materials Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Materials shared elsewhere: The materials were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera. The workshop was enabled through the Australian BioCommons - BioCLI Platforms Project (NCRIS via Bioplatforms Australia). Training materials webpage: https://sydney-informatics-hub.github.io/hello-nextflow/   Data and documentation:  https://github.com/Sydney-Informatics-Hub/hello-nextflow Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, Nextflow
ARDC Digital Research Capabilities and Skills Framework: The Framework and Its Components

The ARDC's Digital Research Capabilities and Skills Framework, released in 2022, provides a structure for training programs to develop essential and advanced digital research skills. It aims to help researchers and professionals identify the necessary skills they need to leverage emerging...

Keywords: training material, skills framework, ARDC skills framework, ARDC capabilities framework, national skills framework, learning path, role profile, capabilities, FAIR implementation, skills, data management, research software, data governance, digital research infrastructure

ARDC Digital Research Capabilities and Skills Framework: The Framework and Its Components https://dresa.org.au/materials/ardc-digital-research-capabilities-and-skills-framework-the-framework-and-its-components The ARDC's Digital Research Capabilities and Skills Framework, released in 2022, provides a structure for training programs to develop essential and advanced digital research skills. It aims to help researchers and professionals identify the necessary skills they need to leverage emerging opportunities in data management, data analysis, data linking, AI, and machine learning. The framework aligns with technological advancements and encourages ongoing discussion and contributions to evolve the coverage of digital research skills. The framework focuses on digital research skills, excluding broader professional skills, and is intended for a wide range of stakeholders. It provides a structured approach for project teams and organisations to develop and enhance their digital research skills through six main components: a skills taxonomy, a skills glossary, a list of generalised roles, roles and skills-related profiles, learning paths, and a skills and roles matrix. The skills taxonomy classifies digital research skills into four capability families: Governance, Data, Software, and Digital Research Infrastructure Management. It provides a standard terminology for identifying and describing these skills. contact@ardc.edu.au Russell, Keith (type: Editor) Wong, Adeline (type: Editor) Lyrtzis, Ellen (type: Editor) training material, skills framework, ARDC skills framework, ARDC capabilities framework, national skills framework, learning path, role profile, capabilities, FAIR implementation, skills, data management, research software, data governance, digital research infrastructure
Ten Simple Rules for Researchers: Upskilling for a Rapidly Evolving Workforce

The following recommendations were inspired by the Australian Research Data Commons (ARDC) Digital Research Skills Summit 2023, that brought together Researchers, Learning Designers, Skills Trainers, and Librarians in productive discussions on how to run effective researcher skills training....

Keywords: Training, Training Material, Short Format Training, Digital Skills, Researcher Training, Learning

Ten Simple Rules for Researchers: Upskilling for a Rapidly Evolving Workforce https://dresa.org.au/materials/ten-simple-rules-for-researchers-upskilling-for-a-rapidly-evolving-workforce The following recommendations were inspired by the Australian Research Data Commons (ARDC) Digital Research Skills Summit 2023, that brought together Researchers, Learning Designers, Skills Trainers, and Librarians in productive discussions on how to run effective researcher skills training. These rules outline how to think about skills learning for researchers, plan training sessions, and efficiently maximize learning. We offer recommendations on how to design and develop learner-centered training programs (Rules 1 and 2), foster outreach, and connect with trainer communities (Rules 3 and 4). We then provide tips to manage and optimize training (Rules 5, 6, and 7), and conclude with valuable insights on preparing for uncertainty and the importance of post-training operations and continued learning (Rules 8, 9, and 10). contact@ardc.edu.au Training, Training Material, Short Format Training, Digital Skills, Researcher Training, Learning
WEBINAR: What exactly is bioinformatics?

This record includes training materials associated with the Australian BioCommons webinar ‘What exactly is bioinformatics?' This webinar took place on 7 August 2024.
Event description
‘Doing’ bioinformatics to extract, process, analyse, and interpret experimental results is something that all...

Keywords: Bioinformatics

WEBINAR: What exactly is bioinformatics? https://dresa.org.au/materials/webinar-what-exactly-is-bioinformatics This record includes training materials associated with the Australian BioCommons webinar ‘What exactly is bioinformatics?' This webinar took place on 7 August 2024. Event description ‘Doing’ bioinformatics to extract, process, analyse, and interpret experimental results is something that all life scientists do as part of their research. But what exactly is bioinformatics? And is there a right (or a wrong) way to do it? In this webinar, Dr Georgie Samaha welcomes you to the vast world of bioinformatics. Georgie will illuminate key concepts including: What does a typical experiment look like? What kind of data will I work with? What is involved in data-preprocessing? What’s involved in data analysis? Where can I do bioinformatics? We explore common experimental use cases and share essential - but easy to overlook - practical tips for accessing data, software, and computing resources you need to get your research done. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Speaker:  Dr Georgie Samaha - Product Owner of the Australian BioCommons BioCLI Project and Bioinformatics Group Lead at the Sydney Informatics Hub, The University of Sydney.  Host: Dr Patrick Capon, Australian BioCommons Training materials 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. Samaha_2024_what_is_bioinformatics_webinar: 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/wmy2C-S-rMU  Melissa Burke (melissa@biocommons.org.au) Bioinformatics
WEBINAR: Where to go when your bioinformatics outgrows your compute

This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.

Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute...

Keywords: Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing

WEBINAR: Where to go when your bioinformatics outgrows your compute https://dresa.org.au/materials/webinar-where-to-go-when-your-bioinformatics-outgrows-your-compute-7a5a0ff8-8f4f-4fd0-af20-a88d515a6554 This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021. Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute resources. “I don’t know what compute resources I will need”, “My analysis won’t run and I don’t know why” and "Just getting it to work" are common pain points for researchers. In this webinar, you will learn how to understand the compute requirements for your bioinformatics workflows. You will also hear about ways of accessing compute that suits your needs as an Australian researcher, including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey.  We also describe bioinformatics and computing support services available to Australian researchers.  This webinar was jointly organised with the Sydney Informatics Hub at the University of Sydney. 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. Where to go when your bioinformatics outgrows your compute - slides (PDF and PPTX): Slides presented during the webinar Australian research computing resources cheat sheet (PDF): A list of resources and useful links mentioned during the webinar. Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/hNTbngSc-W0 Melissa Burke (melissa@biocommons.org.au) Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
WEBINAR: High performance bioinformatics: submitting your best NCMAS application

This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021.

Bioinformaticians are increasingly turning to specialised compute infrastructure and...

Keywords: Computational Biology, Bioinformatics, High Performance Computing, HPC, NCMAS

WEBINAR: High performance bioinformatics: submitting your best NCMAS application https://dresa.org.au/materials/webinar-high-performance-bioinformatics-submitting-your-best-ncmas-application-ee80822f-74ac-41af-a5a4-e162c10e6d78 This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021. Bioinformaticians are increasingly turning to specialised compute infrastructure and efficient, scalable workflows as their research becomes more data intensive. Australian researchers that require extensive compute resources to process large datasets can apply for access to national high performance computing facilities (e.g. Pawsey and NCI) to power their research through the National Computational Merit Allocation Scheme (NCMAS). NCMAS is a competitive, merit-based scheme and requires applicants to carefully consider how the compute infrastructure and workflows will be applied.  This webinar provides life science researchers with insights into what makes a strong NCMAS application, with a focus on the technical assessment, and how to design and present effective and efficient bioinformatic workflows for the various national compute facilities. It will be followed by a short Q&A session. 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. High performance bioinformatics: submitting your best NCMAS application - slides (PDF and PPTX): Slides presented during the webinar   Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/HeFGjguwS0Y Melissa Burke (melissa@biocommons.org.au) Computational Biology, Bioinformatics, High Performance Computing, HPC, NCMAS
WORKSHOP: RNASeq: reads to differential genes and pathways

This record includes training materials associated with the Australian BioCommons workshop 'RNASeq: reads to differential genes and pathways'. This workshop took place over two, 3 hour sessions on 11 and 12 October 2023.Event descriptionRNA sequencing (RNAseq) is a popular and powerful technique...

Keywords: bioinformatics, transcriptomics, RNA-seq, RNAseq

WORKSHOP: RNASeq: reads to differential genes and pathways https://dresa.org.au/materials/workshop-rnaseq-reads-to-differential-genes-and-pathways This record includes training materials associated with the Australian BioCommons workshop 'RNASeq: reads to differential genes and pathways'. This workshop took place over two, 3 hour sessions on 11 and 12 October 2023.Event descriptionRNA sequencing (RNAseq) is a popular and powerful technique used to understand the activity of genes. Using differential gene profiling methods, we can use RNAseq data to gain valuable insights into gene activity and identify variability in gene expression between samples to understand the molecular pathways underpinning many different traits.  In this hands-on workshop, you will learn RNAseq fundamentals as you process, analyse, and interpret the results from a real RNAseq experiment on the command-line. In session one, you will convert raw sequence reads to analysis-ready count data with the nf-core/rnaseq workflow. In session two, you'll work interactively in RStudio to identify differentially expressed genes,perform functional enrichment analysis, and visualise and interpret your results using popular and best practice R packages.  This workshop was delivered as a part of the Australian BioCommons Bring Your Own Data Platforms Project and will provide you with an opportunity to explore services and infrastructure built specifically for life scientists working at the command line. By the end of the workshop, you will be familiar with Pawsey's Nimbus cloud platform and be able to process your own RNAseq datasets and perform differential expression analysis on the command-line. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.Lead trainers: Dr Georgina Samaha (Sydney Informatics Hub), Dr Nandan Deshpande (Sydney Informatics Hub)Facilitators: Ching-Yu Lu and Jessica Chung.Infrastructure provision: Audrey Stott (Pawsey Supercomputing Research Centre), Alex Ip (AARNet)Host: Melissa Burke, Australian BioCommons Training materialsFiles 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:This workshop follows the tutorial 'Introduction to RNAseq workshop: reads to differential gene expression' developed by the Sydney Informatics Hub.https://sydney-informatics-hub.github.io/rnaseq-workshop-2023/Additional supporting materials are available via GitHubRstudio rnaseq container: https://github.com/Sydney-Informatics-Hub/Rstudio-rnaseq-contained/tree/mainRNAseq differential expression R notebook: https://github.com/Sydney-Informatics-Hub/rna-differential-expression-Rnotebook Melissa Burke (melissa@biocommons.org.au) bioinformatics, transcriptomics, RNA-seq, RNAseq
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://dresa.org.au/materials/webinar-getting-started-with-rnaseq-transforming-raw-reads-into-biological-insights-1f7db385-e282-4332-a1c4-d1d73a769b1b 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) Bioinformatics, Transcriptomics, RNA-seq, RNAseq, Gene expression
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://dresa.org.au/materials/workshop-unlocking-nf-core-customising-workflows-for-your-research-1584ff39-e007-4422-9fd5-4e407df6b6c5 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) Bioinformatics, Workflows, Nextflow, nf-core
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://dresa.org.au/materials/webinar-pro-tips-for-scaling-bioinformatics-workflows-to-hpc-9f2a8b90-88da-433b-83b2-b1ab262dd9df 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) Bioinformatics, Workflows, HPC, High Performance Computing
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://dresa.org.au/materials/workshop-make-your-bioinformatics-workflows-findable-and-citable-74e85d1c-d869-429e-b942-8391f4bab23d 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) Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science
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...

Keywords: Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re

WORKSHOP: RNA-Seq: reads to differential genes and pathways https://dresa.org.au/materials/workshop-rna-seq-reads-to-differential-genes-and-pathways-5a384156-d3de-4d5d-9797-e689bf6592f8 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) Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re
WEBINAR: Getting started with whole genome mapping and variant calling on the command line

This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with whole genome mapping and variant calling on the command line’. This webinar took place on 24 August 2022.

Event description 

Life scientists are increasingly using whole genome...

Keywords: Genome mapping, Variant calling, Bioinformatics, Workflows

WEBINAR: Getting started with whole genome mapping and variant calling on the command line https://dresa.org.au/materials/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line-2046f36b-0c7a-4523-9c21-08046900d3ff This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with whole genome mapping and variant calling on the command line’. This webinar took place on 24 August 2022. Event description  Life scientists are increasingly using whole genome sequencing (WGS) to ask and answer research questions across the tree of life. Before any of this work can be done, there is the essential but challenging task of processing raw sequencing data. Processing WGS data is a computationally challenging, multi-step process used to create a map of an individual’s genome and identify genetic variant sites. The tools you use in this process and overall workflow design can look very different for different researchers, it all depends on your dataset and the research questions you’re asking. Luckily, there are lots of existing WGS processing tools and pipelines out there, but knowing where to start and what your specific needs are is hard work, no matter how experienced you are.  In this webinar we will walk through the essential steps and considerations for researchers who are running and building reproducible WGS mapping and variant calling pipelines at the command line interface. We will discuss how to choose and evaluate a pipeline that is right for your dataset and research questions, and how to get access to the compute resources you need 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. WGS mapping and variant calling _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/Q2EceFyizio Melissa Burke (melissa@biocommons.org.au) Genome mapping, Variant calling, Bioinformatics, Workflows
DReSA: Project team reflections

This presentation provides thoughts and reflections from the Digital Research Skills Australaisa (DReSA) project team on DReSA. Team members highlight their perspectives on value propositions and benefits for their respective institutiosn/organisations and nationally, as well as individual...

Keywords: training events, training material, training repository, skilled workforce, digital research skills, digital research training, digital research, trainers, FAIR training

DReSA: Project team reflections https://dresa.org.au/materials/dresa-project-team-reflections-9dcb8538-6b7c-4822-b0ee-fbe57085dc70 This presentation provides thoughts and reflections from the Digital Research Skills Australaisa (DReSA) project team on DReSA. Team members highlight their perspectives on value propositions and benefits for their respective institutiosn/organisations and nationally, as well as individual reflections on collaboration and working together on the project so far. You can watch the video on YouTube here: https://youtu.be/qqH92itI8SI   contact@ardc.edu.au training events, training material, training repository, skilled workforce, digital research skills, digital research training, digital research, trainers, FAIR training
ARDC Skills Landscape

The Australian Research Data Commons is driving transformational change in the research data ecosystem, enabling researchers to conduct world class data-intensive research. One interconnected component of this ecosystem is skills development/uplift, which is critical to the Commons and its...

Keywords: skills, data skills, eresearch skills, community, skilled workforce, FAIR, research data management, data stewardship, data governance, data use, data generation, training material

ARDC Skills Landscape https://dresa.org.au/materials/ardc-skills-landscape-56b224ca-9e30-4771-8615-d028c7be86a6 The Australian Research Data Commons is driving transformational change in the research data ecosystem, enabling researchers to conduct world class data-intensive research. One interconnected component of this ecosystem is skills development/uplift, which is critical to the Commons and its purpose of providing Australian researchers with a competitive advantage through data.   In this presentation, Kathryn Unsworth introduces the ARDC Skills Landscape. The Landscape is a first step in developing a national skills framework to enable a coordinated and cohesive approach to skills development across the Australian eResearch sector. It is also a first step towards helping to analyse current approaches in data training to identify: - Siloed skills initiatives, and finding ways to build partnerships and improve collaboration - Skills deficits, and working to address the gaps in data skills - Areas of skills development for investment by skills stakeholders like universities, research organisations, skills and training service providers, ARDC, etc.   contact@ardc.edu.au skills, data skills, eresearch skills, community, skilled workforce, FAIR, research data management, data stewardship, data governance, data use, data generation, training material
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://dresa.org.au/materials/ardc-2023-skills-summit-frameworks-panel-discussion-day-2-february-10-2023-c00730b5-3444-4ccd-8f8f-9ae8ec3dfbe6 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 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 Training Materials Metadata Checklist v1.1

The ARDC Training Materials Metadata Checklist aims to support learning designers, training materials creators, trainers and national training infrastructure providers to capture key information and apply appropriate mechanisms to enable sharing and reuse of their training materials

Keywords: checklist, Training material, FAIR, standard, requirements, metadata

ARDC Training Materials Metadata Checklist v1.1 https://dresa.org.au/materials/ardc-training-materials-metadata-checklist-v1-1 The ARDC Training Materials Metadata Checklist aims to support learning designers, training materials creators, trainers and national training infrastructure providers to capture key information and apply appropriate mechanisms to enable sharing and reuse of their training materials contact@ardc.edu.au checklist, Training material, FAIR, standard, requirements, metadata
Show & Tell - Tackling 'no shows'

In this session, questions were asked on how to tackle 'no shows' for training events:

  • What are the motivations behind ‘no shows’?

  • What % of ‘no shows’ is acceptable? Any data on that?

  • Do we need to lay some gentle guilt trips?

  • Community Slides

  • Tackling ‘no shows’. What is your...

Keywords: training attendance, no shows, skills training, training material

Show & Tell - Tackling 'no shows' https://dresa.org.au/materials/show-tell-tackling-no-shows-9f0d32c0-b2af-4624-9df1-d4e087da81b6 In this session, questions were asked on how to tackle 'no shows' for training events: - What are the motivations behind ‘no shows’? - What % of ‘no shows’ is acceptable? Any data on that? - Do we need to lay some gentle guilt trips? - Community Slides - Tackling ‘no shows’. What is your approach? What would you be willing to try? contact@ardc.edu.au training attendance, no shows, skills training, training material
National skills ecosystem - call to action

In this Community Action session working groups will be formed based on the challenges/opportunities that were prioritised in Community Action session #4.

  • Skilled trainers / facilitators

  • National training registry

  • National training event calendar

  • Jointly developed training

  • Research...

Keywords: national skills initiatives, data skills, training, skills community, training material

National skills ecosystem - call to action https://dresa.org.au/materials/national-skills-ecosystem-call-to-action-ffd9b4ed-b557-496b-ac35-72467c03c71b In this Community Action session working groups will be formed based on the challenges/opportunities that were prioritised in Community Action session #4. - Skilled trainers / facilitators - National training registry - National training event calendar - Jointly developed training - Research support professionals: career/progression contact@ardc.edu.au national skills initiatives, data skills, training, skills community, training material
ARDC Skills Impact and Strategy Community Discussion

The focus of this community event arose from the ARDC SKills Summit 2021, hosted in collaboration with eResearch Australasia Conference. Two key themes identified at the Summit formed the focus of this event: 1) How to convince senior management the value of digital skills training so that they...

Keywords: training impact, evaluation, skills training, resourcing, value proposition, training material

ARDC Skills Impact and Strategy Community Discussion https://dresa.org.au/materials/ardc-skills-impact-and-strategy-community-discussion-e9d63cee-0d9c-4f8d-9c0f-58afe99b649b The focus of this community event arose from the ARDC SKills Summit 2021, hosted in collaboration with eResearch Australasia Conference. Two key themes identified at the Summit formed the focus of this event: 1) How to convince senior management the value of digital skills training so that they don't question resourcing 2) Evaluating the long-term impact of digital skills training on researchers’ workflows and outputs. You can watch the full video presentation on YouTube here: https://youtu.be/iSnE7OBILqs contact@ardc.edu.au training impact, evaluation, skills training, resourcing, value proposition, training material
Decoding Bioinformatics: A Primer For Life Scientists

Bioinformatics is a vital component of biological and medical research, supporting data-driven discoveries, genomic medicine, and the development of innovative therapeutics. As the life sciences becomes increasingly data-driven, ‘doing’ bioinformatics to extract, process, analyse, and interpret...

Keywords: Bioinformatics, bioinformatics training, training material

Decoding Bioinformatics: A Primer For Life Scientists https://dresa.org.au/materials/decoding-bioinformatics-a-primer-for-life-scientists Bioinformatics is a vital component of biological and medical research, supporting data-driven discoveries, genomic medicine, and the development of innovative therapeutics. As the life sciences becomes increasingly data-driven, ‘doing’ bioinformatics to extract, process, analyse, and interpret this data has become an essential skill for molecular life scientists. In this masterclass, we delve into the vast world of bioinformatics, illuminating key concepts and experimental design considerations. We explore common experimental applications and essential but easy to overlook practical considerations like how to access the database, software, and computing resources you need. *The Sydney Informatics Hub is a Core Research Facility at The University of Sydney, enabling excellence in research* [https://sydney.edu.au/informatics-hub](https://sydney.edu.au/informatics-hub) sih.training@sydney.edu.au Bioinformatics, bioinformatics training, training material