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Authors: Unsworth, Kathryn (orcid: 0...  or Morgan, Steven (orcid: 0000... 

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
WORKSHOP: Online data analysis for biologists

This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 9 September 2021.

Workshop description

Galaxy is an online platform for biological research that allows people to use computational data...

Keywords: Bioinformatics, Analysis, Workflows, Galaxy Australia

WORKSHOP: Online data analysis for biologists https://dresa.org.au/materials/workshop-online-data-analysis-for-biologists-08d66913-4ce3-4528-bdd6-0b0fcf234982 This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 9 September 2021. Workshop description Galaxy is an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. It is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It also captures run information so that workflows can be saved, repeated and shared efficiently via the web. This interactive beginners workshop will provide an introduction to the Galaxy interface, histories and available tools. The material covered in this workshop is freely available through the Galaxy Training Network. The workshop will be held via Zoom and involves a combination of presentations by the lead trainer and smaller breakout groups supported by experienced facilitators. The materials are shared under a Creative Commons 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schedule (PDF): schedule for the workshop Online_data_analysis_for_biologists_extraslides (PPTX and PDF): Slides used to introduce the data set and emphasise the importance of workflows. These slides were developed by Ms Grace Hall. Materials shared elsewhere: The tutorial used in this workshop is available via the Galaxy Training Network. Anne Fouilloux, Nadia Goué, Christopher Barnett, Michele Maroni, Olha Nahorna, Dave Clements, Saskia Hiltemann, 2021 Galaxy 101 for everyone (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html Online; accessed Fri Dec 10 2021 Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Workflows, Galaxy Australia
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
WORKSHOP: Single cell RNAseq analysis in R

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

Event description

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

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

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

This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021.

Workshop description

It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches...

Keywords: Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly

WORKSHOP: Hybrid de novo genome assembly https://dresa.org.au/materials/workshop-hybrid-de-novo-genome-assembly-714004ba-0348-47c8-a68f-038a1f8ccfb1 This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021. Workshop description It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches which enable research on organisms for which reference genomes were not previously available. These approaches combine the strengths of short (Illumina) and long (PacBio or Nanopore) read technologies, resulting in improved assembly quality. In this workshop we will learn how to create and assess genome assemblies from Illumina and Nanopore reads using data from a Bacillus Subtilis strain. We will demonstrate two hybrid-assembly methods using the tools Flye, Pilon, and Unicycler to perform assembly and subsequent error correction. You will learn how to visualise input read sets and the assemblies produced at each stage and assess the quality of the final assembly. All analyses will be performed using Galaxy Australia, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. This workshop is presented by the Australian BioCommons and Melbourne Bioinformatics with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schedule (PDF): A breakdown of the topics and timings for the workshop   Materials shared elsewhere: This workshop follows the tutorial ‘Hybrid genome assembly - Nanopore and Illumina’ developed by Melbourne Bioinformatics. https://www.melbournebioinformatics.org.au/tutorials/tutorials/hybrid_assembly/nanopore_assembly/ Melissa Burke (melissa@biocommons.org.au) Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly
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
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
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
Introduction to Unix

A hands-on workshop covering the basics of the Unix command line interface.

Knowledge of the Unix operating system is fundamental to the use of many popular bioinformatics command-line tools. Whether you choose to run your analyses locally or on a high-performance computing system, knowing...

Keywords: Unix, Command line, Command-line, CLI

Resource type: tutorial

Introduction to Unix https://dresa.org.au/materials/introduction-to-unix A hands-on workshop covering the basics of the Unix command line interface. Knowledge of the Unix operating system is fundamental to the use of many popular bioinformatics command-line tools. Whether you choose to run your analyses locally or on a high-performance computing system, knowing your way around a command-line interface is highly valuable. This workshop will introduce you to Unix concepts by way of a series of hands-on exercises. This workshop is designed for participants with little or no command-line knowledge. Tools: Standard Unix commands, FileZilla Topic overview: Section 1: Getting started Section 2: Exploring your current directory Section 3: Making and changing directories Section 4: Viewing and manipulating files Section 5: Removing files and directories Section 6: Searching files Section 7: Putting it all together Section 8: Transferring files Tutorial instructions available here: https://www.melbournebioinformatics.org.au/tutorials/tutorials/unix/unix/ For queries relating to this workshop, contact Melbourne Bioinformatics (bioinformatics-training@unimelb.edu.au). Find out when we are next running this training as an in-person workshop, by visiting the Melbourne Bioinformaitcs Eventbrite page: https://www.eventbrite.com.au/o/melbourne-bioinformatics-13058846490 For queries relating to this workshop, contact Melbourne Bioinformatics (bioinformatics-training@unimelb.edu.au). Unix, Command line, Command-line, CLI ugrad masters mbr phd ecr researcher support professional