[{"id":310,"title":"WEBINAR: Effective, inclusive, and scalable training in the life sciences, clinical education and beyond","url":"https://dresa.org.au/materials/webinar-effective-inclusive-and-scalable-training-in-the-life-sciences-clinical-education-and-beyond-52c113ff-573c-4ae8-a3f0-482c86f1818a.json","description":"This record includes training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Effective, inclusive, and scalable training in the life sciences, clinical education and beyond’. This webinar took place on 4 November 2022.\n\nEvent description \n\nScientists and educators working in the life sciences must continuously acquire new knowledge and skills to stay up-to-date with the latest methods, technologies and research. Short-format training, such as webinars, workshops and bootcamps, are popular ways of quickly learning about new topics and gaining new skills.\n\nAs trainers and educators, how can we ensure that short-format training is effective and inclusive for all? How can we ensure that our learners are equipped to continue learning and applying their new skills once they return to their day jobs? And how can we do this in a way that is scalable and sustainable?\n\nThe Bicycle Principles assemble education theory and community experience into a framework for improving short-format training so that it is effective, inclusive and scalable. Over 30 international experts, including colleagues from the Australian BioCommons, Melbourne Genomics and other Australian and New Zealand organisations, helped develop the principles and an associated set of recommendations.\n\nJason Williams, Assistant Director, DNA Learning Center, Cold Spring Harbor Laboratory - a leading genomics and bioinformatics educator and project lead, joins us to discuss the Principles and how they can be applied to achieve scalable and sustainable training in a range of Australian settings.\n\nThis webinar is co-hosted by Australian BioCommons and Melbourne Genomics\n\nTraining Materials\n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\t\n\tWILLIAMS-Jason_aus-biocommons_nov-2022 (PDF): A PDF copy of the slides presented during the webinar.\n\t\n\n\nMaterials shared elsewhere:\n\n \n\nA recording of this webinar is available on the Australian BioCommons YouTube Channel:\n\nhttps://youtu.be/18dub7jGeQ8","doi":"10.5281/zenodo.7281360","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":311,"title":"WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia","url":"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.json","description":"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.\n\nEvent description \n\nHave 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.\n\nUsing an established bioinformatics method, we’ll show you how to:\n\n\n\t\n\tUse the workflows creator in Galaxy Australia \n\t\n\t\n\tBuild a workflow based on a published method\n\t\n\t\n\tAnnotate workflows so that you (and others) can understand them \n\t\n\t\n\tMake workflows finable and citable (important and very easy to do!)\n\t\n\n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\t\n\tGalaxyWorkflows_Slides (PDF): A PDF copy of the slides presented during the webinar.\n\t\n\n\nMaterials shared elsewhere:\n\nA recording of this webinar is available on the Australian BioCommons YouTube Channel:\n\nhttps://youtu.be/IMkl6p7hkho","doi":"10.5281/zenodo.7251310","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":312,"title":"WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud","url":"https://dresa.org.au/materials/webinar-portable-reproducible-and-scalable-bioinformatics-workflows-using-nextflow-and-pawsey-nimbus-cloud-824bc004-4dcb-4bb5-b0dc-a207c44bbbe6.json","description":"This record includes training materials associated with the Australian BioCommons webinar ‘Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud’. This webinar took place on 20 September 2022.\n\nEvent description \n\nBioinformatics workflows can support portable, reproducible and scalable analysis of omics datasets but using workflows can be challenging for both beginners and experienced bioinformaticians. Beginners face a steep learning curve to be able to build and deploy their own bioinformatics workflows while those with more experience face challenges productionising and scaling code for custom workflows and big data. \n\nBioinformaticians across the world are using Nextflow to build and manage workflows. Many of these workflows are shared for others to use and supported by the community via nf-co.re. So far, 39 workflows for omics data are available with another 23 under development. These workflows cover common analyses such as RNAseq, mapping, variant calling, single cell transcriptomics and more and can be easily deployed by anyone, regardless of skill level.\n\nIn this webinar, Nandan Deshpande from the Sydney Informatics Hub, University of Sydney, will discuss how you can deploy freely available Nextflow (nf.co-re) bioinformatics workflows with a single command. We describe how you can quickly get started deploying these workflows using Pawsey Nimbus Cloud. For advanced users, we introduce you to Nextflow concepts to get you started with building your own workflows that will save you time and support reproducible, portable and scalable analysis.\n\nIn the latter half of the webinar, Sarah Beecroft from the Pawsey Supercomputing Research Centre will talk about their Nimbus Cloud systems. While Nextflow supports portability and can run on many computing infrastructures, we describe why we specifically love using Nimbus with Nextflow for many bioinformatics projects. We will describe some of the nf.co-re workflows that we have used on Nimbus and the research outcomes. We will also cover when not to use Nimbus and the alternatives we recommend.\n \n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\t\n\tNextflow_Nimbus_slides (PDF): A PDF copy of the slides presented during the webinar.\n\t\n\n\nMaterials shared elsewhere:\n\nA recording of this webinar is available on the Australian BioCommons YouTube Channel:\n\nhttps://youtu.be/VnLX63yXbJU","doi":"10.5281/zenodo.7095271","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":313,"title":"WORKSHOP: Single cell RNAseq analysis in R","url":"https://dresa.org.au/materials/workshop-single-cell-rnaseq-analysis-in-r-4f60b82d-2f1e-4021-9569-6955878dd945.json","description":"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.\n\nEvent description\n\n\n\t\n\tAnalysis 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. \n\t\n\t\n\tWe 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.\n\t\n\n\nThis 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.\n \n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\t\n\tscRNAseq_Slides (PDF): Slides used to introduce topics\n\t\n\t\n\tscRNAseq_Schedule (PDF): A breakdown of the topics and timings for the workshop\n\t\n\t\n\tscRNAseq_Resources (PDF): A list of resources recommended by trainers and participants\n\t\n\t\n\tscRNAseq_QandA(PDF): Archive of questions and their answers from the workshop Slack Channel.\n\t\n\n\n \n\nMaterials shared elsewhere:\n\nThis workshop follows the tutorial ‘scRNAseq Analysis in R with Seurat’\n\nhttps://swbioinf.github.io/scRNAseqInR_Doco/index.html\n\nThis material is based on the introductory Guided Clustering Tutorial tutorial from Seurat.\nIt is also drawing from a similar workshop held by Monash Bioinformatics Platform Single-Cell-Workshop, with material here.","doi":"10.5281/zenodo.7072910","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":314,"title":"WEBINAR: Getting started with whole genome mapping and variant calling on the command line","url":"https://dresa.org.au/materials/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line-2046f36b-0c7a-4523-9c21-08046900d3ff.json","description":"This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with whole genome mapping and variant calling on the command line’. This webinar took place on 24 August 2022.\n\nEvent description \n\nLife scientists are increasingly using whole genome sequencing (WGS) to ask and answer research questions across the tree of life. Before any of this work can be done, there is the essential but challenging task of processing raw sequencing data. Processing WGS data is a computationally challenging, multi-step process used to create a map of an individual’s genome and identify genetic variant sites. The tools you use in this process and overall workflow design can look very different for different researchers, it all depends on your dataset and the research questions you’re asking. Luckily, there are lots of existing WGS processing tools and pipelines out there, but knowing where to start and what your specific needs are is hard work, no matter how experienced you are. \n\nIn this webinar we will walk through the essential steps and considerations for researchers who are running and building reproducible WGS mapping and variant calling pipelines at the command line interface. We will discuss how to choose and evaluate a pipeline that is right for your dataset and research questions, and how to get access to the compute resources you need\n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\t\n\tWGS mapping and variant calling _slides (PDF): A PDF copy of the slides presented during the webinar.\n\t\n\n\n\n \n\nMaterials shared elsewhere:\n\nA recording of this webinar is available on the Australian BioCommons YouTube Channel:\n\nhttps://youtu.be/Q2EceFyizio","doi":"10.5281/zenodo.7024058","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":315,"title":"WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software","url":"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.json","description":"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.\n\nEvent description \n\nbio.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.\n\nHans 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.\n \n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\t\n\tbiotools_EDAM_slides (PDF): A PDF copy of the slides presented during the webinar.\n\t\n\n\n \n\nMaterials shared elsewhere:\n\nA recording of this webinar is available on the Australian BioCommons YouTube Channel:\n\nhttps://youtu.be/K0J4_bAUG3Y","doi":"10.5281/zenodo.7024050","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":316,"title":"WORKSHOP: R: fundamental skills for biologists","url":"https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists-81aa00db-63ad-4962-a7ac-b885bf9f676b.json","description":"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.\n\n \n\nEvent description\n\nBiologists 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. \n\nR 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. \n\nGetting 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.\n\nTopics covered in this workshop include:\n\n\n\t\n\tSpreadsheets, organising data and first steps with R\n\t\n\t\n\tManipulating and analysing data with dplyr\n\t\n\t\n\tData visualisation\n\t\n\t\n\tSummarized experiments and getting started with Bioconductor\n\t\n\n\n \n\nThis 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.\n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\t\n\tSchedule (PDF): A breakdown of the topics and timings for the workshop\n\t\n\t\n\tRecommended resources (PDF): A list of resources recommended by trainers and participants\n\t\n\t\n\tQ_and_A(PDF): Archive of questions and their answers from the workshop Slack Channel.\n\t\n\n\nMaterials shared elsewhere:\n\n \n\nThis workshop follows the tutorial ‘Introduction to data analysis with R and Bioconductor’ which is publicly available.\n\nhttps://saskiafreytag.github.io/biocommons-r-intro/\n\nThis is derived from material produced as part of The Carpentries Incubator project\n\nhttps://carpentries-incubator.github.io/bioc-intro/","doi":"10.5281/zenodo.6766951","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":317,"title":"WEBINAR: Protection of genomic data and the Australian Privacy Act: when is genomic data 'personal information'?","url":"https://dresa.org.au/materials/webinar-protection-of-genomic-data-and-the-australian-privacy-act-when-is-genomic-data-personal-information-1f7194f9-4034-468f-8a78-614f83ef67b0.json","description":"This record includes training materials associated with the Australian BioCommons webinar ‘Protection of genomic data and the Australian Privacy Act: when is genomic data ‘personal information’?’. This webinar took place on 6 April 2022.\n\nEvent description \n\nIt is easy to assume that genomic data will be captured by legal definitions of ‘health information’ and ‘genetic information’, but the legal meaning of ‘genetic information’ need not align with scientific categories. \n\nThere are many different types of genomic data, with varied characteristics, uses and applications.  Clarifying when genomic data is covered by the Privacy Act 1988 (Cth) is an ongoing evaluative exercise but is important for at least 3 reasons: \n\n\n\tthose subject to the Privacy Act need to be able to confidently navigate their responsibilities\n\tunderstanding current controls is a prerequisite for meaningful external critique (and this is particularly important at a time when the Privacy Act is under review), and\n\twhile legislation that applies to state public sector agencies is generally distinct from the Privacy Act there are similarities that extend the relevance of the question when is genomic data ‘personal information’ under the Privacy Act?\n\n\nIn this presentation, Mark will explore the relationship between the legal concept of genetic information and the concept of genomic data relevant to health and medical research, reflect on the characteristics of each, and the possibility\n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\t\n\tTaylor_Slides (PDF): A PDF copy of the slides presented during the webinar.\n\t\n\n\nMaterials shared elsewhere:\n\nA recording of this webinar is available on the Australian BioCommons YouTube Channel:\n\nhttps://youtu.be/Iaei-9Gu-AI","doi":"10.5281/zenodo.6423621","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":318,"title":"WORKSHOP: Introduction to Metabarcoding using QIIME2","url":"https://dresa.org.au/materials/workshop-introduction-to-metabarcoding-using-qiime2-d3a7ac82-63aa-47e6-9d8e-5126419f9982.json","description":"This record includes training materials associated with the Australian BioCommons workshop ‘Introduction to Metabarcoding using QIIME2’. This workshop took place on 22 February 2022.\n\nEvent description\n\nMetabarcoding has revolutionised the study of biodiversity science. By combining DNA taxonomy with high-throughput DNA sequencing, it offers the potential to observe a larger diversity in the taxa within a single sample, rapidly expanding the scope of microbial analysis and generating high-quality biodiversity data. \n\nThis workshop will introduce the topic of metabarcoding and how you can use Qiime2 to analyse 16S data and gain simultaneous identification of all taxa within a sample. Qiime2 is a popular tool used to perform powerful microbiome analysis that can transform your raw data into publication quality visuals and statistics. In this workshop, using example 16S data from the shallow-water marine anemone E. diaphana, you will learn how to use this pipeline to run essential steps in microbial analysis including generating taxonomic assignments and phylogenic trees, and performing both alpha- and beta- diversity analysis. \n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\t\n\tSchedule (PDF): A breakdown of the topics and timings for the workshop\n\t\n\n\nMaterials shared elsewhere:\n\nThis workshop follows the tutorial ‘Introduction to metabarcoding with QIIME2’ which has been made publicly available by Melbourne Bioinformatics.\n\nhttps://www.melbournebioinformatics.org.au/tutorials/tutorials/qiime2/qiime2/","doi":"10.5281/zenodo.6350808","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":319,"title":"WEBINAR: Conservation genomics in the age of extinction","url":"https://dresa.org.au/materials/webinar-conservation-genomics-in-the-age-of-extinction-c7718a53-68ee-4c69-adf4-cd0550710d3f.json","description":"This record includes training materials associated with the Australian BioCommons webinar ‘Conservation genomics in the age of extinction’. This webinar took place on 8 March 2022.\n\nEvent description \n\nBiodiversity is crashing and millions of plant and animal species are at the edge of extinction. Understanding the genetic diversity of these species is an important tool for conservation biology but obtaining high quality genomes for threatened species is not always straightforward.\n\nIn this webinar Dr Carolyn Hogg speaks about the work she has been doing with the Threatened Species Initiative to build genomic resources to understand and protect Australia’s threatened species. Using examples such as the Kroombit Tinker Frog and the Greater Bilby, Carolyn describes some of the complexities and challenges of generating genomes from short reads and HiFi reads for critically endangered species. She outlines the technologies and resources being used and how these are bridging the gap between genomicists, bioinformaticians and conservation experts to help save Australian species.\n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\n\nMaterials shared elsewhere:\n\nA recording of this webinar is available on the Australian BioCommons YouTube Channel:\n\nhttps://youtu.be/Bl7CaiGQ91s\n\n ","doi":"10.5281/zenodo.6350785","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":320,"title":"WEBINAR: Establishing Gen3 to enable better human genome data sharing in Australia","url":"https://dresa.org.au/materials/webinar-establishing-gen3-to-enable-better-human-genome-data-sharing-in-australia-d8caf8c8-d447-4218-be01-95dfd0377f3e.json","description":"This record includes training materials associated with the Australian BioCommons webinar ‘Establishing Gen3 to enable better human genome data sharing in Australia’. This webinar took place on 16 February 2022.\n\nEvent description \n\nAustralian human genome initiatives are generating vast amounts of human genome data. There is a desire and need to share data with collaborators but researchers face significant infrastructural, technical and administrative barriers in achieving this. To efficiently share and distribute their genome data they need scalable services and infrastructure that: is easily administered; allows for the efficient data management; enables sharing and interoperability; and is aligned with global standards for human genome data sharing.\n\nAustralian BioCommons has brought together a team from Zero Childhood Cancer (Zero), the University of Melbourne Centre for Cancer Research (UMCCR) and Australian Access Federation to explore the use of Gen3 technology. Establishing systems for easier management and sharing of their human genome data holdings is no simple task, and the group wants to ensure that other Australian providers and Institutions can benefit from their experience and easily deploy the same solution in the future.\n\nGen3 is an open source software suite that makes use of private and public clouds to tackle the challenges of data management, interoperability, data sharing and analysis. It has been used in several very large NIH-funded projects that collectively house and describe data derived from hundreds of thousands of human samples (e.g. NCI Genomic Data Commons, BioData Catalyst, BloodPAC, BrainCommons, Kids First Data Commons).\n\nIn this webinar you’ll hear from UMCCR and Zero about their experiences and progress towards establishing Gen3 instances to better enable better human genome data sharing in Australia. They will outline the challenges and opportunities that have arisen through this Australian BioCommons project and demonstrate the capabilities of Gen3 for human genome research.\n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\t\n\tGen3_Webinar_Slides (PDF): Slides presented during the webinar\n\t\n\n\n \n\nMaterials shared elsewhere:\n\nA recording of this webinar is available on the Australian BioCommons YouTube Channel:\n\nhttps://youtu.be/1F6B03Byigk","doi":"10.5281/zenodo.6233075","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":321,"title":"WORKSHOP: Refining genome annotations with Apollo","url":"https://dresa.org.au/materials/workshop-refining-genome-annotations-with-apollo-d8f95fb3-7dc4-40e0-87d5-e7a4b2ceaf16.json","description":"This record includes training materials associated with the Australian BioCommons  workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021.\n\nWorkshop description \n\nGenome annotation is crucial to defining the function of genomic sequences. This process typically involves a round of automated annotation followed by manual curation. Manual curation allows you to visualise your annotations so you can understand what your organism looks like, and then to manually refine these annotations along with any additional data you might have. This process is typically performed collaboratively as part of a team effort.\n\nApollo is a popular tool for facilitating real-time collaborative, manual curation and genome annotation editing. In this workshop we will learn how to use Apollo to refine genome annotations using example data from an E. coli strain. We’ll focus on the basics like getting data into Apollo, viewing evidence tracks, editing and adding structural and functional annotation, visualising the results and collaborating on genome annotations.\n\nThis workshop made use of a training instance of  the new Australian Apollo Service. This service enables Australian-based research groups and consortia to access Apollo and host genome assembly and supporting evidence files for free. This service has been made possible by The Australian BioCommons and partners at QCIF and Pawsey. To learn more about the Australian Apollo Service you can watch the Australian Apollo Launch Webinar.\n\nThis workshop was presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) .\n\nThe Australian Apollo Service is operated by QCIF and underpinned by computational resources provided by the Pawsey Supercomputing Research Centre and receives NCRIS funding through Bioplatforms Australia and the Australian Research Data Commons as well as Queensland Government RICF funding.\n\nThe training materials presented in this workshop were developed by Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet for the Galaxy Training Network. Helena and Anthony are part of the Gallantries project which is supported by Erasmus  Programme of the European Union.\n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\n\n\n\t\n\tSchedule (PDF): A breakdown of the topics and timings for the workshop\n\t\n\t\n\t2021 Apollo Training Intro (PPTX and PDF): Slides used to introduce the Australian Apollo Service\n\t\n\t\n\tAugustus.gff3 (gff3): E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia.\n\t\n\t\n\tBlastp_vs_swissprot.gff3: E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia.\n\t\n\n\nMaterials shared elsewhere:\n\nThis workshop is based on the tutorial ‘Refining genome annotations with Apollo’ which was developed for the Galaxy Training Network.\n\nAnthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet, Erasmus  Programme, 2021 Refining Genome Annotations with Apollo (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/tutorial.html Online; accessed Wed Dec 15 2021\n\nSee also:\n\nBatut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012","doi":"10.5281/zenodo.5781812","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":322,"title":"WORKSHOP: Hybrid de novo genome assembly","url":"https://dresa.org.au/materials/workshop-hybrid-de-novo-genome-assembly-714004ba-0348-47c8-a68f-038a1f8ccfb1.json","description":"This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021.\n\nWorkshop description\n\nIt’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.\n\nIn 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.\n\nAll 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.\n\nThis workshop is presented by the Australian BioCommons and Melbourne Bioinformatics with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.\n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\t\n\tSchedule (PDF): A breakdown of the topics and timings for the workshop\n\t\n\n\n \n\nMaterials shared elsewhere:\n\nThis workshop follows the tutorial ‘Hybrid genome assembly - Nanopore and Illumina’ developed by Melbourne Bioinformatics.\nhttps://www.melbournebioinformatics.org.au/tutorials/tutorials/hybrid_assembly/nanopore_assembly/","doi":"10.5281/zenodo.5781781","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":323,"title":"WORKSHOP: Working with genomics sequences and features in R with Bioconductor","url":"https://dresa.org.au/materials/workshop-working-with-genomics-sequences-and-features-in-r-with-bioconductor-8399bf0d-1e9e-48f3-a840-3f70f23254bb.json","description":"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.\n\nWorkshop description\n\nExplore the many useful functions that the Bioconductor environment offers for working with genomic data and other biological sequences. \n\nDNA 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.\n\nThis 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. \n\nThis 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.\n\nMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.\n\nFiles and materials included in this record:\n\n\n\t\n\tEvent metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.\n\t\n\t\n\tIndex 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.\n\t\n\n\n\n\t\n\tSchedule (PDF): schedule for the workshop providing a breakdown of topics and timings\n\t\n\n\n \n\nMaterials shared elsewhere:\n\nThis 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.\n\nhttps://monashdatafluency.github.io/r-bioc-2/","doi":"10.5281/zenodo.5781776","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":270,"title":"NCI training strategy and impact story to address pressing needs from user community","url":"https://dresa.org.au/materials/nci-training-strategy-and-impact-story-to-address-pressing-needs-from-user-community-70a328d3-a1e1-45ce-bac0-d8b896db4ca0.json","description":"This presentation looks at how NCI provides training opportunities, supporting users to develop their digital skills with the aim of underpinning the integrity of research. NCI's new training strategy is outlined along with how training is evaluated and impact is measured. Through extensive internal polling the training team have identified a number of gaps. Based on the gaps an end-to-end learning journey has been created. The presentation also provides an overview of immediate, middle term and community impacts of training at NCI.\n\nYou can watch the video on YouTube here:https://youtu.be/LVn5TZFufjI","doi":"10.5281/zenodo.5739725","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":271,"title":"Sharing Approaches to Implementing the Data Guide at Medical Research Institutes (MRIs) Workshop","url":"https://dresa.org.au/materials/sharing-approaches-to-implementing-the-data-guide-at-medical-research-institutes-mris-workshop-66fd5cb3-e161-44e2-aa96-514f195ab54d.json","description":"Co-authored by the Australian Research Council (ARC), the National Health and Medical Research Council (NHMRC) and Universities Australia (UA), the Management of Data and Information in Research Guide contains guidance for institutions and researchers on how they can implement the new Code as it relates to the subject of research data.\n\nThis workshop included presentations and breakout discussions considering MRI approaches to data management practices in light of the Code and Guide. \n\nThis workshop was delivered as part of the Management of Data and Information in Research Guide Event.  The aims of the Event were to enable research offices within universities and Medical Research Institutes (MRIs) to have a clear and consistent understanding of the data management requirements and responsibilities as outlined in the Code and the Data Guide.","doi":"10.5281/zenodo.4291067","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":269,"title":"Role profiles for the Bureau's Stewardship Model","url":"https://dresa.org.au/materials/role-profiles-for-the-bureau-s-stewardship-model-19ee77b4-d15e-42da-96b4-9e3056d1b3e7.json","description":"This presentation provides an overview of the approach being taken in the creation of a Data Stewardship framework that looks at the tools, guidance, skills and clarity of data stewardship roles at the Bureau of Meteorology. A major focus of the framework is the creation of role profiles which provide the role description, assignment and key responsibilities.\n\nYou can watch the YouTube video here: https://youtu.be/RLf6B-NIffU","doi":"10.5281/zenodo.5711869","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":272,"title":"Setting The Scene","url":"https://dresa.org.au/materials/setting-the-scene-8a535906-352b-451e-be82-051b1db4c5de.json","description":"Opening Address for the ARDC Skills Summit 2023\n\nThis 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.","doi":"10.5281/zenodo.7710621","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":273,"title":"Evaluating training at Pawsey: Motivated, confident \u0026 \"changed\"","url":"https://dresa.org.au/materials/evaluating-training-at-pawsey-motivated-confident-changed-a2435a20-bfa5-457d-afa3-08193a199f24.json","description":"This presentation outlines the digital reserach skills training evaluation methods used at Pawsey. Using the Kirpatrick Training Evaluation model in designing their training evaluation survey, Pawsey measure learning motivation (How did the participant respond to the training?), improved confidence of the learner (Did participants understand the training?) and were there any behavioual changes (How participants applied their new knowledge in practice?).\n\nYou can watch the video of the presentation on YouTube here: https://youtu.be/IOKVrBumEBQ","doi":"10.5281/zenodo.5739608","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":275,"title":"An open source textbook for research software engineering","url":"https://dresa.org.au/materials/an-open-source-textbook-for-research-software-engineering-f275be2a-698e-4e8a-94a4-5b701b26eef8.json","description":"Over the past year, a group of Carpentries instructors have been working on an open source textbook called Research Software Engineering with Python. The book is a ready-to-go university semester course aimed at helping learners go from writing code for themselves, to creating tools that help their entire field advance. A physical version of the book will be published with Taylor \u0026amp; Francis in early 2021. During the review phase of the publication process, we are seeking feedback on the content and scope of the book from the digital skills training community.","doi":"10.5281/zenodo.4287860","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":276,"title":"ARDC digital research capabilities and skills framework","url":"https://dresa.org.au/materials/ardc-digital-research-capabilities-and-skills-framework-3b376311-87dd-470f-bb8d-e99459434c97.json","description":"This informational flyer outlines the value of skills frameworks and describes at a high level the various elements of the ARDC's Capabilities and Skills Framework.\n\n\n\tCapabilities and Skills Landscape\n\tGlossary - Framework terminology\n\tData and Digital Research roles\n\tSkills/Role profiles\n\tLearning paths\n\tSkills/Data roles matrix","doi":"10.5281/zenodo.6558642","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":274,"title":"Successful data training stories from NCI","url":"https://dresa.org.au/materials/successful-data-training-stories-from-nci-33f110e3-0c06-492e-9cc5-fa0f886ca1b8.json","description":"NCI Australia manages a multi-petabyte sized data repository, collocated with its HPC systems and data services, which allows high performance access to many scientific research datasets across many earth science domains.\nAn important aspect is to provide training materials that proactively engages with the research community to improve their understanding of the data available, and to share knowledge and best practices in the use of tools and other software. We have developed multiple levels of training modules (introductory, intermediate and advanced) to cater for users with different levels of experience and interest. We have also tailored courses for each scientific domain, so that the use-cases and software will be most relevant to their interests and needs.\nFor our training, we combine brief lectures followed by hands-on training examples on how to use datasets, using working examples of well-known tools and software that people can use as a template and modify to fit their needs. For example, we take representative use-cases from some scientific activities, from our collaborations and from user support issues, and convert to Jupyter notebook examples so that people can repeat the workfIow and reproduce the results. We also use the training as an opportunity to raise awareness of growing issues in resource management. Some examples include a familiarity of the FAIR data principles, licensing, citation, data management and trusted digital repositories. This approach to both our online training materials and workshops has been well-received by PhD students, early careers, and cross disciplinary users.","doi":"10.5281/zenodo.4287750","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":277,"title":"Data Management at CLEX","url":"https://dresa.org.au/materials/data-management-at-clex-4351940a-b868-4c6d-879b-2cae212ff172.json","description":"In this presentation, Paula Petrelli outlines the opportunities and challenges of data management for climate science, and how she implemented DMPOnline to facilitate better workflows for publishing research data. This talk was presented to the Australasian Data Management Plans Interest Group on 19 August 2021. The group is hosted by Liz Stokes and meets every two months to discuss data management planning infrastructure.","doi":"10.5281/zenodo.5403344","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":278,"title":"Accelerating skills development in Data science and AI at scale","url":"https://dresa.org.au/materials/accelerating-skills-development-in-data-science-and-ai-at-scale-2d8a65fa-f96e-44ad-a026-cfae3f38d128.json","description":"At the Monash Data Science and AI  platform, we believe that upskilling our research community and building a workforce with data science skills are key to accelerating the application of data science in research. To achieve this, we create and leverage new and existing training capabilities within and outside Monash University. In this talk, we will discuss the principles and purpose of establishing collaborative models to accelerate skills development at scale. We will talk about our approach to identifying gaps in the existing skills and training available in data science, key areas of interest as identified by the research community and various sources of training available in the marketplace. We will provide insights into the collaborations we currently have and intend to develop in the future within the university and also nationally.\n\nThe talk will also cover our approach as outlined below\n•        Combined survey of gaps in skills and trainings for Data science and AI\n•        Provide seats to partners\n•        Share associate instructors/helpers/volunteers\n•        Develop combined training materials\n•        Publish a repository of open source trainings\n•        Train the trainer activities\n•        Establish a network of volunteers to deliver trainings at their local regions\n\nIndustry plays a significant role in making some invaluable training available to the research community either through self learning platforms like AWS Machine Learning University or Instructor led courses like NVIDIA Deep Learning Institute. We will discuss how we leverage our partnerships with Industry to bring these trainings to our research community.\n\nFinally, we will discuss how we map our training to the ARDC skills roadmap and how the ARDC platforms project “Environments to accelerate Machine Learning based Discovery” has enabled collaboration between Monash University and University of Queensland to develop and deliver training together.","doi":"10.5281/zenodo.4287746","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":280,"title":"Professionalizing Training - Origin Stories for the Modern Researcher","url":"https://dresa.org.au/materials/professionalizing-training-origin-stories-for-the-modern-researcher-0198d9cf-9d8f-467e-8031-4d3a3536af63.json","description":"Keynote Presentation for the ARDC Skills Summit 2023\n\nThis 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.","doi":"10.5281/zenodo.7710785","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":281,"title":"Persistent Identifiers for Research: a talk to the Australasian DMP Interest Group","url":"https://dresa.org.au/materials/persistent-identifiers-for-research-a-talk-to-the-australasian-dmp-interest-group-672051fa-f5f8-4939-838f-c4bd79fb2b33.json","description":"ARDC's Data Management Planning Interest Group hosted a meetup on persistent identifiers and data management planning infrastructure on 17 June 2021. These slides accompanied Siobhann McCafferty's talk on PIDs infrastructure, RAiD and the Instruments for Identifiers Australasia Interest Group (I4IOZ).","doi":"10.5281/zenodo.5002519","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":282,"title":"Intersect: Training portfolio","url":"https://dresa.org.au/materials/intersect-training-portfolio-8c82060d-5eea-4091-af7b-396c9c073dab.json","description":"This presentation explores Intersect's training evaluation model. Short term evaluation for immediate satisfaction and value of the training. Long term evaluation methods with a specific survey design to determine behavioural change and impact over time of the training on researchers' workflows, use of support services post training and looking for links between digital tools/technologies training and research outputs and grants.\n\nYou can watch the full video on YouTube here: https://youtu.be/J3tCC-t_eO4","doi":"10.5281/zenodo.5739603","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":285,"title":"Research Data Governance","url":"https://dresa.org.au/materials/research-data-governance-6ad9ab90-1a29-41db-b4aa-f1988501530d.json","description":"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.\n\nIf you want to share the video please use this:\n\nAustralian 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].","doi":"10.5281/zenodo.5044585","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":283,"title":"European Open Science Cloud (EOSC) skills \u0026 training working group","url":"https://dresa.org.au/materials/european-open-science-cloud-eosc-skills-training-working-group-e41d62e6-55ee-4e0c-9897-bfd1068799c8.json","description":"European Open Science Cloud (EOSC) skills \u0026amp; training working group","doi":"10.5281/zenodo.4289348","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":284,"title":"Data Fluency: a community of practice supporting a digitally skilled workforce","url":"https://dresa.org.au/materials/data-fluency-a-community-of-practice-supporting-a-digitally-skilled-workforce-b911a1a8-0331-496e-95a6-0015a12acc34.json","description":"This presentation showcases the impact of the Monash Data Fluency Community of Practice upon digitally skilled Graduate Research students involved as learners and instructors in the program. The strong focus on building community to complement training, has fostered an environment of learning, networking and sharing of expertise. Hear what the Graduate research students have to say about the value of skills training and how it has impacted their research; how the community has enabled them to network with a broad range of researchers and affiliate partner groups they would not ordinarily be in contact with; how their research journey has been enhanced by working as part of a multi-disciplinary team, as well as sharpening their teaching skills.\nThe rapid refocus from face - face to online delivery, as a result of the pandemic, highlights the importance of the multi-faceted online approach including workshops, drop-in sessions, SLACK chat and online learning resources. As a result of the shift to online, the range of strategic external partner/affiliate groups has extended and demand for workshops and drop-ins has increased.  Learn how the instructors have altered their pedagogical approach to engage workshop and drop-in participants; how they have overcome some of the challenges of facilitating in an online environment; and how this is preparing them to become part of a digitally skilled workforce.","doi":"10.5281/zenodo.4287752","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]}]