[{"id":218,"title":"WEBINAR: Protection of genomic data and the Australian Privacy Act: when is genomic data 'personal information'?","url":"https://staging.dresa.org.au/materials/webinar-protection-of-genomic-data-and-the-australian-privacy-act-when-is-genomic-data-personal-information.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":217,"title":"WEBINAR: Conservation genomics in the age of extinction","url":"https://staging.dresa.org.au/materials/webinar-conservation-genomics-in-the-age-of-extinction.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":215,"title":"WEBINAR: Establishing Gen3 to enable better human genome data sharing in Australia","url":"https://staging.dresa.org.au/materials/webinar-establishing-gen3-to-enable-better-human-genome-data-sharing-in-australia.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":147,"title":"WORKSHOP: Refining genome annotations with Apollo","url":"https://staging.dresa.org.au/materials/workshop-refining-genome-annotations-with-apollo.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":148,"title":"WORKSHOP: Hybrid de novo genome assembly","url":"https://staging.dresa.org.au/materials/workshop-hybrid-de-novo-genome-assembly.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":149,"title":"WORKSHOP: Working with genomics sequences and features in R with Bioconductor","url":"https://staging.dresa.org.au/materials/workshop-working-with-genomics-sequences-and-features-in-r-with-bioconductor.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":151,"title":"WEBINAR: Launching the new Apollo Service: collaborative genome annotation for Australian researchers","url":"https://staging.dresa.org.au/materials/webinar-launching-the-new-apollo-service-collaborative-genome-annotation-for-australian-researchers.json","description":"This record includes training materials associated with the Australian BioCommons webinar ‘Launching the new Apollo Service: collaborative genome annotation for Australian researchers’. This webinar/workshop took place on 29 September 2021.\n\nEvent description \n\nGenome annotation is crucial to defining the function of genomic sequences. Apollo is a popular tool for facilitating real-time collaborative curation and genome annotation editing. The technical obstacles faced by Australian researchers wanting to access and maintain this software have now been solved. \n\nThe new Australian Apollo Service can host your genome assembly and supporting evidence files, taking care of all the system administration so you and your team can focus on the annotation curation itself. The Australian BioCommons and partners at QCIF and Pawsey are now offering the Apollo Service free to use for Australian-based research groups and research consortia.\n\nAs part of this launch, you’ll hear what’s possible from some of the early adopters who helped guide the development of the service. These Australian researchers will highlight the benefits that Apollo is bringing to their genome annotation and curation workflows.\n\nJoin us to find out how you can get access to the Australian Apollo Service.\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\tDegnan Lab - Apollo Launch Webinar (PDF): Slides presented by Professors Sandie and Bernie Degnan\n\t\n\t\n\tNelson - Apollo Launch Webinar (PDF): Slides presented by Dr Tiffanie Nelson\n\t\n\t\n\tVoelker - Apollo Launch Webinar (PDF): Slides presented by Julia Voelker\n\t\n\t\n\tRane - Apollo Launch Webinar (PDF): Slides presented by Dr Rahul Rane.\n\t\n\n\nMaterials shared elsewhere:\n\nA recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/o8jhRra-x4Y\n\n ","doi":"10.5281/zenodo.5775233","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":158,"title":"WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset","url":"https://staging.dresa.org.au/materials/webinar-detection-of-and-phasing-of-hybrid-accessions-in-a-target-capture-dataset.json","description":"This record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021.\n\nHybridisation plays an important role in evolution, leading to the exchange of genes between species and, in some cases, generate new lineages. The use of molecular methods has revealed the frequency and importance of reticulation events is higher than previously thought and this insight continues with the ongoing development of phylogenomic methods that allow novel insights into the role and extent of hybridisation. Hybrids notoriously provide challenges for the reconstruction of evolutionary relationships, as they contain conflicting genetic information from their divergent parental lineages. However, this also provides the opportunity to gain insights into the origin of hybrids (including autopolyploids).\n\nThis webinar explores some of the challenges and opportunities that occur when hybrids are included in a target capture sequence dataset. In particular, it describes the impact of hybrid accessions on sequence assembly and phylogenetic analysis and further explores how the information of the conflicting phylogenetic signal can be used to detect and resolve hybrid accessions. The webinar showcases a novel bioinformatic workflow, HybPhaser, that can be used to detect and phase hybrids in target capture datasets and will provide the theoretical background and concepts behind the workflow.\n\nThis webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focuses on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference.\n\nThe materials are shared under a Creative Commons 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\tNauheimer_hybphaser_slides (PDF): Slides presented during the webinar\n\t\n\n\nMaterials shared elsewhere:\nA recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/japXwTAhA5U","doi":"10.5281/zenodo.5105013","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":159,"title":"WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation","url":"https://staging.dresa.org.au/materials/webinar-conflict-in-multi-gene-datasets-why-it-happens-and-what-to-do-about-it-deep-coalescence-paralogy-and-reticulation.json","description":"This record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021.\n\nMulti-gene datasets used in phylogenetic analyses, such as those produced by the sequence capture or target enrichment used in the Genomics for Australian Plants: Australian Angiosperm Tree of Life project, often show discordance between individual gene trees and between gene and species trees. This webinar explores three different forms of discordance: deep coalescence, paralogy, and reticulation. In each case, it considers underlying biological processes, how discordance presents in the data, and what bioinformatic or phylogenetic approaches and tools are available to address these challenges. It covers Yang and Smith paralogy resolution and general information on options for phylogenetic analysis.\n\nThis webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focused on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference.\n\nThe materials are shared under a Creative Commons 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\tSchmidt-Lebuhn - paralogy lineage sorting reticulation - slides (PDF): Slides presented during the webinar\n\t\n\n\n \n\nMaterials shared elsewhere:\n\nA recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/1bw81q898z8","doi":"10.5281/zenodo.5104998","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]}]