[{"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":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":150,"title":"WORKSHOP: Online data analysis for biologists","url":"https://staging.dresa.org.au/materials/workshop-online-data-analysis-for-biologists.json","description":"This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 9 September 2021.\n\nWorkshop description\n\nGalaxy is an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience.\n\nIt is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It also captures run information so that workflows can be saved, repeated and shared efficiently via the web.\n\nThis interactive beginners workshop will provide an introduction to the Galaxy interface, histories and available tools. The material covered in this workshop is freely available through the Galaxy Training Network.\n\nThe workshop will be held via Zoom and involves a combination of presentations by the lead trainer and smaller breakout groups supported by experienced facilitators.\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\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): schedule for the workshop\n\t\n\t\n\tOnline_data_analysis_for_biologists_extraslides (PPTX and PDF): Slides used to introduce the data set and emphasise the importance of workflows. These slides were developed by Ms Grace Hall.\n\t\n\n\nMaterials shared elsewhere:\n\nThe tutorial used in this workshop is available via the Galaxy Training Network.\n\n\nAnne Fouilloux, Nadia Goué, Christopher Barnett, Michele Maroni, Olha Nahorna, Dave Clements, Saskia Hiltemann, 2021 Galaxy 101 for everyone (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html Online; accessed Fri Dec 10 2021","doi":"10.5281/zenodo.5775277","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":153,"title":"WEBINAR: Where to go when your bioinformatics outgrows your compute","url":"https://staging.dresa.org.au/materials/webinar-where-to-go-when-your-bioinformatics-outgrows-your-compute.json","description":"This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.\n\nBioinformatics analyses are often complex, requiring multiple software tools and specialised compute resources. “I don’t know what compute resources I will need”, “My analysis won’t run and I don’t know why” and \"Just getting it to work\" are common pain points for researchers. In this webinar, you will learn how to understand the compute requirements for your bioinformatics workflows. You will also hear about ways of accessing compute that suits your needs as an Australian researcher, including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey.  We also describe bioinformatics and computing support services available to Australian researchers. \n\nThis webinar was jointly organised with the Sydney Informatics Hub at the University of Sydney.\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\tWhere to go when your bioinformatics outgrows your compute - slides (PDF and PPTX): Slides presented during the webinar\n\t\n\t\n\tAustralian research computing resources cheat sheet (PDF): A list of resources and useful links mentioned during the webinar.\n\t\n\n\nMaterials shared elsewhere:\n\nA recording of the webinar is available on the Australian BioCommons YouTube Channel:\n\nhttps://youtu.be/hNTbngSc-W0","doi":"10.5281/zenodo.5240578","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]}]