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26 materials found

Keywords: FAIR  or R software 


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
WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia

This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022.

Event description 

Have you discovered a brilliant...

Keywords: Bioinformatics, Workflows, FAIR, Galaxy Australia

WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia https://dresa.org.au/materials/webinar-here-s-one-we-prepared-earlier-re-creating-bioinformatics-methods-and-workflows-with-galaxy-australia-134a8bf5-3801-421f-a454-e0f9020f4871 This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022. Event description  Have you discovered a brilliant bioinformatics workflow but you’re not quite sure how to use it? In this webinar we will introduce the power of Galaxy for construction and (re)use of reproducible workflows, whether building workflows from scratch, recreating them from published descriptions and/or extracting from Galaxy histories. Using an established bioinformatics method, we’ll show you how to: Use the workflows creator in Galaxy Australia  Build a workflow based on a published method Annotate workflows so that you (and others) can understand them  Make workflows finable and citable (important and very easy to do!) 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. GalaxyWorkflows_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/IMkl6p7hkho Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, FAIR, Galaxy Australia
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
WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software

This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.

Event description 

bio.tools provides easy access to essential scientific...

Keywords: Bioinformatics, Research software, EDAM, Workflows, FAIR

WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software https://dresa.org.au/materials/webinar-bio-tools-making-it-easier-to-find-understand-and-cite-biological-tools-and-software-aea38c9e-0b40-4308-bafd-f7580563f520 This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022. Event description  bio.tools provides easy access to essential scientific and technical information about software, command-line tools, databases and services. It’s backed by ELIXIR, the European Infrastructure for Biological Information, and is being used in Australia to register software (e.g. Galaxy Australia, prokka). It underpins the information provided in the Australian BioCommons discovery service ToolFinder. Hans Ienasescu and Matúš Kalaš join us to explain how bio.tools uses a community driven, open science model to create this collection of resources and how it makes it easier to find, understand, utilise and cite them. They’ll delve into how bio.tools is using standard semantics (e.g. the EDAM ontology) and syntax (e.g. biotoolsSchema) to enrich the annotation and description of tools and resources. Finally, we’ll see how the community can contribute to bio.tools and take advantage of its key features to share and promote their own research software.   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. biotools_EDAM_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/K0J4_bAUG3Y Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Research software, EDAM, Workflows, FAIR
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
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
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 Your first step to FAIR

This workshop gives a brief overview of the FAIR principles, including a method to make a one-file dataset FAIR.

Keywords: training material, FAIR, data, workshop

ARDC Your first step to FAIR https://dresa.org.au/materials/ardc-your-first-step-to-fair-1ee3dc3c-23b0-4287-b96c-c120c5697932 This workshop gives a brief overview of the FAIR principles, including a method to make a one-file dataset FAIR. contact@ardc.edu.au Stokes, Liz (type: Editor) Martinez, Paula Andrea (type: Editor) Russell, Keith (type: Editor) training material, FAIR, data, workshop
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
Locking the front door without leaving the windows open: positioning authentication technologies within the "Five Safes" framework for effective use of sensitive research data

This project explores the options for access to sensitive data sets; what authentication technologies (e.g. multi-factor authentication) are needed to access sensitive data and secure compute environments.  This project seeks to position choices around authentication technologies within the Five...

Keywords: ARDC, Storage and Compute Summit, FAIR, Infrastructure, NCRIS, eResearch, training material

Locking the front door without leaving the windows open: positioning authentication technologies within the "Five Safes" framework for effective use of sensitive research data https://dresa.org.au/materials/locking-the-front-door-without-leaving-the-windows-open-positioning-authentication-technologies-within-the-five-safes-framework-for-effective-use-of-sensitive-research-data-b83124f8-2add-41c6-b194-d5dd50d098f6 This project explores the options for access to sensitive data sets; what authentication technologies (e.g. multi-factor authentication) are needed to access sensitive data and secure compute environments.  This project seeks to position choices around authentication technologies within the Five Safes framework for research use of sensitive data, proposed in 2003 by Felix Ritchie of the UK Office of National Statistics: • Safe Projects: is the proposed research use of the data appropriate?  • Safe People: can the users be trusted to use the data in an appropriate manner?  • Safe Settings: does the access facility limit unauthorised use? • Safe Data: is there a disclosure risk in the data itself? • Safe Outputs: are the research results non-disclosive i.e. they do not compromise privacy or breach confidentiality? contact@ardc.edu.au ARDC, Storage and Compute Summit, FAIR, Infrastructure, NCRIS, eResearch, training material
ARDC FAIR Data 101 self-guided

FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles

The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course.

The course structure was based on 'FAIR Data in the...

Keywords: training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management

ARDC FAIR Data 101 self-guided https://dresa.org.au/materials/ardc-fair-data-101-self-guided-2d794a84-f0ff-4e11-a39c-fa8ea481e097 FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course. The course structure was based on 'FAIR Data in the Scholarly Communications Lifecycle', run by Natasha Simons at the FORCE11 Scholarly Communications Institute. These training materials are hosted on GitHub. contact@ardc.edu.au training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management
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 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
WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia

This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022.

Event description 

Have you discovered a...

Keywords: Bioinformatics, Workflows, FAIR, Galaxy Australia

WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia https://dresa.org.au/materials/webinar-here-s-one-we-prepared-earlier-re-creating-bioinformatics-methods-and-workflows-with-galaxy-australia This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022. **Event description**  Have you discovered a brilliant bioinformatics workflow but you’re not quite sure how to use it? In this webinar we will introduce the power of Galaxy for construction and (re)use of reproducible workflows, whether building workflows from scratch, recreating them from published descriptions and/or extracting from Galaxy histories. Using an established bioinformatics method, we’ll show you how to: * Use the workflows creator in Galaxy Australia  * Build a workflow based on a published method * Annotate workflows so that you (and others) can understand them  * Make workflows finable and citable (important and very easy to do!) 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. * GalaxyWorkflows_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/IMkl6p7hkho Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, FAIR, Galaxy Australia
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
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 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
WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software

This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.

Event description

bio.tools provides easy access to essential...

Keywords: Bioinformatics, Research software, EDAM, Workflows, FAIR

WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software https://dresa.org.au/materials/webinar-bio-tools-making-it-easier-to-find-understand-and-cite-biological-tools-and-software-9180e32a-f4f5-4993-a90a-a9bfcfafd4f3 This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022. **Event description** bio.tools provides easy access to essential scientific and technical information about software, command-line tools, databases and services. It’s backed by ELIXIR, the European Infrastructure for Biological Information, and is being used in Australia to register software (e.g. Galaxy Australia, prokka). It underpins the information provided in the Australian BioCommons discovery service ToolFinder. Hans Ienasescu and Matúš Kalaš join us to explain how bio.tools uses a community driven, open science model to create this collection of resources and how it makes it easier to find, understand, utilise and cite them. They’ll delve into how bio.tools is using standard semantics (e.g. the EDAM ontology) and syntax (e.g. biotoolsSchema) to enrich the annotation and description of tools and resources. Finally, we’ll see how the community can contribute to bio.tools and take advantage of its key features to share and promote their own research software.   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. * biotools_EDAM_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/K0J4_bAUG3Y Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Research software, EDAM, Workflows, FAIR
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 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
WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software

This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.

Event description

bio.tools provides easy access to essential...

Keywords: Bioinformatics, Research software, EDAM, Workflows, FAIR

WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software https://dresa.org.au/materials/webinar-bio-tools-making-it-easier-to-find-understand-and-cite-biological-tools-and-software This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022. **Event description** bio.tools provides easy access to essential scientific and technical information about software, command-line tools, databases and services. It’s backed by ELIXIR, the European Infrastructure for Biological Information, and is being used in Australia to register software (e.g. Galaxy Australia, prokka). It underpins the information provided in the Australian BioCommons discovery service ToolFinder. Hans Ienasescu and Matúš Kalaš join us to explain how bio.tools uses a community driven, open science model to create this collection of resources and how it makes it easier to find, understand, utilise and cite them. They’ll delve into how bio.tools is using standard semantics (e.g. the EDAM ontology) and syntax (e.g. biotoolsSchema) to enrich the annotation and description of tools and resources. Finally, we’ll see how the community can contribute to bio.tools and take advantage of its key features to share and promote their own research software.   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. - biotools_EDAM_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/K0J4_bAUG3Y Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Research software, EDAM, Workflows, FAIR
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 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
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-cab2ebba-4e56-418d-b52f-197619e542f8 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
ARDC Your first step to FAIR

This workshop gives a brief overview of the FAIR principles, including a method to make a one-file dataset FAIR.

Keywords: training material, FAIR, data, workshop

ARDC Your first step to FAIR https://dresa.org.au/materials/ardc-your-first-step-to-fair This workshop gives a brief overview of the FAIR principles, including a method to make a one-file dataset FAIR. contact@ardc.edu.au Stokes, Liz (type: Editor) Martinez, Paula Andrea (type: Editor) Russell, Keith (type: Editor) training material, FAIR, data, workshop
Locking the front door without leaving the windows open: positioning authentication technologies within the "Five Safes" framework for effective use of sensitive research data

This project explores the options for access to sensitive data sets; what authentication technologies (e.g. multi-factor authentication) are needed to access sensitive data and secure compute environments.  This project seeks to position choices around authentication technologies within the Five...

Keywords: ARDC, Storage and Compute Summit, FAIR, Infrastructure, NCRIS, eResearch, training material

Locking the front door without leaving the windows open: positioning authentication technologies within the "Five Safes" framework for effective use of sensitive research data https://dresa.org.au/materials/locking-the-front-door-without-leaving-the-windows-open-positioning-authentication-technologies-within-the-five-safes-framework-for-effective-use-of-sensitive-research-data This project explores the options for access to sensitive data sets; what authentication technologies (e.g. multi-factor authentication) are needed to access sensitive data and secure compute environments.  This project seeks to position choices around authentication technologies within the Five Safes framework for research use of sensitive data, proposed in 2003 by Felix Ritchie of the UK Office of National Statistics: • Safe Projects: is the proposed research use of the data appropriate?  • Safe People: can the users be trusted to use the data in an appropriate manner?  • Safe Settings: does the access facility limit unauthorised use? • Safe Data: is there a disclosure risk in the data itself? • Safe Outputs: are the research results non-disclosive i.e. they do not compromise privacy or breach confidentiality? contact@ardc.edu.au ARDC, Storage and Compute Summit, FAIR, Infrastructure, NCRIS, eResearch, training material
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 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 FAIR Data 101 self-guided

FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles

The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course.

The course structure was based on 'FAIR Data in the...

Keywords: training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management

ARDC FAIR Data 101 self-guided https://dresa.org.au/materials/ardc-fair-data-101-self-guided-bba41a59-8479-4f4f-b9ee-337b9eb294bf FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course. The course structure was based on 'FAIR Data in the Scholarly Communications Lifecycle', run by Natasha Simons at the FORCE11 Scholarly Communications Institute. These training materials are hosted on GitHub. contact@ardc.edu.au training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management
ARDC FAIR Data 101 self-guided

FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles

The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course.

Keywords: training material, FAIR data, research data, data management, FAIR

Resource type: presentation, quiz, activity

ARDC FAIR Data 101 self-guided https://dresa.org.au/materials/ardc-fair-data-101-self-guided FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course. ARDC Contact us: https://ardc.edu.au/contact-us/ training material, FAIR data, research data, data management, FAIR phd ecr researcher support