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Keywords: R software  or research 

ARDC Research Data Rights Management Guide

A practical guide for people and organisations working with data, about rights information and licences, and to raise awareness of the implications of not having licences on data.

Who is this for? This guide is primarily directed toward members of the research sector, particularly data rights...

Keywords: data, rights, management, licence, licensing, research, policy, guide, training material

ARDC Research Data Rights Management Guide https://dresa.org.au/materials/ardc-research-data-rights-management-guide A practical guide for people and organisations working with data, about rights information and licences, and to raise awareness of the implications of not having licences on data. Who is this for? This guide is primarily directed toward members of the research sector, particularly data rights holders users and suppliers. Some general reference is made to characteristics and management of government data, acknowledging that this kind of data can be input to the research process. Government readers should consult their agency’s data management policies, in addition to reading this guide. contact@ardc.edu.au Laughlin, Greg (type: Editor) Appleyard, Baden (type: Editor) data, rights, management, licence, licensing, research, policy, guide, training material
Tutorials to learn how to use STAN

Stan tutorials offer links to exceptional tutorial papers, videos and statistics to learn Bayesian statistical methods and applied statistics.

Keywords: Statistics, applied statistics, Bayesian statistics, R software, Python, MATLAB

Tutorials to learn how to use STAN https://dresa.org.au/materials/tutorials-to-learn-how-to-use-stan Stan tutorials offer links to exceptional tutorial papers, videos and statistics to learn Bayesian statistical methods and applied statistics. https://mc-stan.org/about/team/ Statistics, applied statistics, Bayesian statistics, R software, Python, MATLAB
Species Distribution Modelling in R

This set of scripts and videos provide an introduction to running SDMs in R and include some steps to consider that go beyond what's available in the EcoCommons SDM point-and-click tools.

Five videos include: 1. An introduction to SDM in R, 2. occurrence data, 3. environmental data, 4. fitting...

Keywords: Species Distribution Modelling, Ecology, R software, EcoCommons

Species Distribution Modelling in R https://dresa.org.au/materials/species-distribution-modelling-in-r This set of scripts and videos provide an introduction to running SDMs in R and include some steps to consider that go beyond what's available in the EcoCommons SDM point-and-click tools. Five videos include: 1. An introduction to SDM in R, 2. occurrence data, 3. environmental data, 4. fitting your model, 5. model evaluation Scripts and files are available here: https://github.com/EcoCommons-Australia/educational_material/tree/main/SDMs_in_R/Scripts Scripts for all four modules are here: https://www.ecocommons.org.au/wp-content/uploads/EcoCommons_steps_1_to_4.html https://www.ecocommons.org.au/contact/ Species Distribution Modelling, Ecology, R software, EcoCommons ugrad mbr phd
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: R: fundamental skills for biologists

This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.

 

Event description

Biologists need data analysis skills to be able to...

Keywords: Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation

WORKSHOP: R: fundamental skills for biologists https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists-81aa00db-63ad-4962-a7ac-b885bf9f676b This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.   Event description Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets.  R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes.  Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R. Topics covered in this workshop include: Spreadsheets, organising data and first steps with R Manipulating and analysing data with dplyr Data visualisation Summarized experiments and getting started with Bioconductor   This workshop is presented by the Australian BioCommons and Saskia Freytag from WEHI  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 Recommended resources (PDF): A list of resources recommended by trainers and participants Q_and_A(PDF): Archive of questions and their answers from the workshop Slack Channel. Materials shared elsewhere:   This workshop follows the tutorial ‘Introduction to data analysis with R and Bioconductor’ which is publicly available. https://saskiafreytag.github.io/biocommons-r-intro/ This is derived from material produced as part of The Carpentries Incubator project https://carpentries-incubator.github.io/bioc-intro/ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
WORKSHOP: Working with genomics sequences and features in R with Bioconductor

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

Workshop description

Explore the many useful functions that the Bioconductor...

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

WORKSHOP: Working with genomics sequences and features in R with Bioconductor https://dresa.org.au/materials/workshop-working-with-genomics-sequences-and-features-in-r-with-bioconductor-8399bf0d-1e9e-48f3-a840-3f70f23254bb This record includes training materials associated with the Australian BioCommons workshop ‘Working with genomics sequences and features in R with Bioconductor’. This workshop took place on 23 September 2021. Workshop description Explore the many useful functions that the Bioconductor environment offers for working with genomic data and other biological sequences.  DNA and proteins are often represented as files containing strings of nucleic acids or amino acids. They are associated with text files that provide additional contextual information such as genome annotations. This workshop provides hands-on experience with tools, software and packages available in R via Bioconductor for manipulating, exploring and extracting information from biological sequences and annotation files. We will look at tools for working with some commonly used file formats including FASTA, GFF3, GTF, methods for identifying regions of interest, and easy methods for obtaining data packages such as genome assemblies.  This workshop is presented by the Australian BioCommons and Monash Bioinformatics Platform with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schedule (PDF): schedule for the workshop providing a breakdown of topics and timings   Materials shared elsewhere: This workshop follows the tutorial ‘Working with DNA sequences and features in R with Bioconductor - version 2’ developed for Monash Bioinformatics Platform and Monash Data Fluency by Paul Harrison. https://monashdatafluency.github.io/r-bioc-2/ Melissa Burke (melissa@biocommons.org.au) R software, Bioconductor, Bioinformatics, Analysis, Genomics, Sequence analysis
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://dresa.org.au/materials/setting-the-scene-8a535906-352b-451e-be82-051b1db4c5de 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 research, training, skills, training material, ARDC, research data commons, digital research skills agenda
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://dresa.org.au/materials/professionalizing-training-origin-stories-for-the-modern-researcher-0198d9cf-9d8f-467e-8031-4d3a3536af63 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 research, training, skills, superheroes, formal, career, change, workshops, milestones, community, principles, bicycle principles, professionalizing, training material
Research Data Governance

This video contains key information for those who make research data-related decisions. It will help project leaders to start investigating ways to develop their own data governance policy, roles and responsibilities and procedures with the input of appropriate stakeholders.

If you want to share...

Keywords: data governance, data, research, FAIR, data management, authority, share, reuse, access, provenance, policy, responsibilities, ARDC_AU, training material

Research Data Governance https://dresa.org.au/materials/research-data-governance-6ad9ab90-1a29-41db-b4aa-f1988501530d This video contains key information for those who make research data-related decisions. It will help project leaders to start investigating ways to develop their own data governance policy, roles and responsibilities and procedures with the input of appropriate stakeholders. If you want to share the video please use this: Australian Research Data Commons, 2021. Research Data Governance. [video] Available at: https://youtu.be/K_xVQRdgCIc  DOI: http://doi.org/10.5281/zenodo.5044585 [Accessed dd Month YYYY]. contact@ardc.edu.au Martinez, Paula Andrea (type: ProjectLeader) Wilkinson, Max (type: Editor) Callaghan,Shannon (type: Editor) Savill, Jo (type: Editor) Kang, Kristan (type: Editor) Levett, Kerry (type: Editor) Russell, Keith (type: Editor) Simons, Natasha (type: Editor) data governance, data, research, FAIR, data management, authority, share, reuse, access, provenance, policy, responsibilities, ARDC_AU, training material
How can software containers help your research?

This video explains software containers to a research audience. It is an introduction to why containers are beneficial for research. These benefits are standardisation, portability, reliability and reproducibility. 

Software Containers in research are a solution that addresses the challenge of a...

Keywords: containers, software, research, reproducibility, RSE, standard, agility, portable, reusable, code, application, reproducible, standardisation, package, system, cloud, server, version, reliability, program, collaborator, ARDC_AU, training material

How can software containers help your research? https://dresa.org.au/materials/how-can-software-containers-help-your-research-ca0f9d41-d83b-463b-a548-402c6c642fbf This video explains software containers to a research audience. It is an introduction to why containers are beneficial for research. These benefits are standardisation, portability, reliability and reproducibility.  Software Containers in research are a solution that addresses the challenge of a replicable computational environment and supports reproducibility of research results. Understanding the concept of software containers enables researchers to better communicate their research needs with their colleagues and other researchers using and developing containers. Watch the video here: https://www.youtube.com/watch?v=HelrQnm3v4g If you want to share this video please use this: Australian Research Data Commons, 2021. How can software containers help your research?. [video] Available at: https://www.youtube.com/watch?v=HelrQnm3v4g DOI: http://doi.org/10.5281/zenodo.5091260 [Accessed dd Month YYYY]. contact@ardc.edu.au Martinez, Paula Andrea (type: ProjectLeader) Sam Muirhead (type: Producer) The ARDC Communications Team (type: Editor) The ARDC Skills and Workforce Development Team (type: ProjectMember) The ARDC eResearch Infrastructure & Services (type: ProjectMember) The ARDC Nectar Cloud Services team (type: ProjectMember) containers, software, research, reproducibility, RSE, standard, agility, portable, reusable, code, application, reproducible, standardisation, package, system, cloud, server, version, reliability, program, collaborator, ARDC_AU, 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 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://dresa.org.au/materials/ardc-2023-skills-summit-lightning-talks-day-1-february-9-2023-c91367d6-2366-4a4e-aa05-631d1e5fd95f 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 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 Research Data Rights Management Guide 2019

A practical guide for people and organisations working with data, about rights information and licences, and to raise awareness of the implications of not having licences on data.

Who is this for? This guide is primarily directed toward members of the research sector, particularly data rights...

Keywords: data, rights, management, licence, licensing, research, policy, guide, training material

ARDC Research Data Rights Management Guide 2019 https://dresa.org.au/materials/ardc-research-data-rights-management-guide-149e27b4-fd5e-4739-8e40-be2c5ca6709c A practical guide for people and organisations working with data, about rights information and licences, and to raise awareness of the implications of not having licences on data. Who is this for? This guide is primarily directed toward members of the research sector, particularly data rights holders users and suppliers. Some general reference is made to characteristics and management of government data, acknowledging that this kind of data can be input to the research process. Government readers should consult their agency’s data management policies, in addition to reading this guide. contact@ardc.edu.au Laughlin, Greg (type: Editor) Appleyard, Baden (type: Editor) data, rights, management, licence, licensing, research, policy, guide, training material
VOSON Lab Code Blog

The VOSON Lab Code Blog is a space to share methods, tips, examples and code. Blog posts provide techniques to construct and analyse networks from various API and other online data sources, using the VOSON open-source software and other R based packages.

Keywords: visualisation, Data analysis, data collections, R software, Social network analysis, social media data, Computational Social Science, quantitative, Text Analytics

Resource type: tutorial, other

VOSON Lab Code Blog https://dresa.org.au/materials/voson-lab-code-blog The VOSON Lab Code Blog is a space to share methods, tips, examples and code. Blog posts provide techniques to construct and analyse networks from various API and other online data sources, using the VOSON open-source software and other R based packages. robert.ackland@anu.edu.au visualisation, Data analysis, data collections, R software, Social network analysis, social media data, Computational Social Science, quantitative, Text Analytics researcher support phd masters