[{"id":191,"title":"Locking the front door without leaving the windows open: positioning authentication technologies within the \"Five Safes\" framework for effective use of sensitive research data","url":"https://staging.dresa.org.au/materials/locking-the-front-door-without-leaving-the-windows-open-positioning-authentication-technologies-within-the-five-safes-framework-for-effective-use-of-sensitive-research-data.json","description":"This project explores the options for access to sensitive data sets; what authentication technologies (e.g. multi-factor authentication) are needed to access sensitive data and secure compute environments.  This project seeks to position choices around authentication technologies within the Five Safes framework for research use of sensitive data, proposed in 2003 by Felix Ritchie of the UK Office of National Statistics:\n• Safe Projects: is the proposed research use of the data appropriate? \n• Safe People: can the users be trusted to use the data in an appropriate manner? \n• Safe Settings: does the access facility limit unauthorised use?\n• Safe Data: is there a disclosure risk in the data itself?\n• Safe Outputs: are the research results non-disclosive i.e. they do not compromise privacy or breach confidentiality?","doi":"10.5281/zenodo.3547980","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":192,"title":"Show \u0026 Tell - Tackling 'no shows'","url":"https://staging.dresa.org.au/materials/show-tell-tackling-no-shows.json","description":"In this session, questions were asked on how to tackle 'no shows' for training events:\n\n- What are the motivations behind ‘no shows’?\n\n- What % of ‘no shows’ is acceptable? Any data on that?\n\n- Do we need to lay some gentle guilt trips?\n\n- Community Slides\n\n- Tackling ‘no shows’. What is your approach? What would you be willing to try?","doi":"10.5281/zenodo.4289344","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":193,"title":"European Open Science Cloud (EOSC) skills \u0026 training working group","url":"https://staging.dresa.org.au/materials/european-open-science-cloud-eosc-skills-training-working-group.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":194,"title":"ARDC Skills Impact and Strategy Community Discussion","url":"https://staging.dresa.org.au/materials/ardc-skills-impact-and-strategy-community-discussion.json","description":"The focus of this community event arose from the ARDC SKills Summit 2021, hosted in collaboration with eResearch Australasia Conference. Two key themes identified at the Summit formed the focus of this event: 1) How to convince senior management the value of digital skills training so that they don't question resourcing 2) Evaluating the long-term impact of digital skills training on researchers’ workflows and outputs.\n\nYou can watch the full video presentation on YouTube here: https://youtu.be/iSnE7OBILqs","doi":"10.5281/zenodo.5739422","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":195,"title":"Persistent Identifiers for Research: a talk to the Australasian DMP Interest Group","url":"https://staging.dresa.org.au/materials/persistent-identifiers-for-research-a-talk-to-the-australasian-dmp-interest-group.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":196,"title":"Sharing Approaches to Implementing the Data Guide at Medical Research Institutes (MRIs) Workshop","url":"https://staging.dresa.org.au/materials/sharing-approaches-to-implementing-the-data-guide-at-medical-research-institutes-mris-workshop.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":197,"title":"23 (research data) Things","url":"https://staging.dresa.org.au/materials/23-research-data-things.json","description":"23 (research data) things is a set of training materials exploring research data management. Each of the 23 things offers a variety of learning opportunities with activities at three levels of complexity:\n\n* Getting started\n* Learn more\n* Challenge me\n\nAll resources used in the program are online and free to use and reuse under a Creative Commons Attribution 4.0 International licence. You could use all of them as a self-paced course, or choose components to integrate into your own course.\n\nThe 23 things are designed to build knowledge as the program progresses, so if you’re new to the world of research data management, we suggest you start with things 1-3 and then decide where you want to go from there.\n\nThese materials supported an international community-based training program delivered in 2016 by the Australian National Data Service.\n\nThis release migrates these materials to a GitHub repository for continued maintenance. Some updates were made to material that was outdated.\n\nWe welcome contributions and suggestions via GitHub Issue or Pull Request.","doi":"10.5281/zenodo.3955524","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":198,"title":"Monash University - University of Queensland training partnership in Data science and AI","url":"https://staging.dresa.org.au/materials/monash-university-university-of-queensland-training-partnership-in-data-science-and-ai.json","description":"We describe the peer network exchange for training that has been recently created via an ARDC funded partnership between Monash University and Universities of Queensland under the umbrella of the Queensland Cyber Infrastructure Foundation (QCIF). As part of a training program in machine learning, visualisation, and computing tools, we have established a series of over 20 workshops over the year where either Monash or QCIF hosts the event for some 20-40 of their researchers and students, while some 5 places are offered to participants from the other institution. In the longer term we aim to share material developed at one institution and have trainers present it at the other. In this talk we will describe the many benefits we have found to this approach including access to a wider range of expertise in several rapidly developing fields, upskilling of trainers, faster identification of emerging training needs, and peer learning for trainers.","doi":"10.5281/zenodo.4287864","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":199,"title":"Time to fill the gaps: Building out a national training inventory","url":"https://staging.dresa.org.au/materials/time-to-fill-the-gaps-building-out-a-national-training-inventory.json","description":" \n\nThis community discussion seeks to bring together the instructors and facilitators tasked with upskilling researchers and support staff. While this collective dialogue among instructors is not new, what is new is the traction that various groups are getting.\n\nThe newly formed group of eResearch support staff gathered by the Melbourne Data Analytics Platform (MDAP) and Sydney Informatics Hub (SIH) is one such group, as is the Lightweight Working Group (LWG): Researcher digital skills training data for enabling digital infrastructure use, spearheaded by University of Melbourne’s David Flanders during the pre-Skills Summit discussions.\n\nIn this session we seek to build on the momentum, by including a hands-on working session. Participants are asked to come with information to share and questions they seek to answer. During the first half of this session, attendees will populate a public document with shareable training details. The goal is to at least double the size of the new cross-institutional national training collection started by the LWG.\n\nThe second half of this session will be to ask questions to arrive at next steps. What do we need to do to continue building out this national training inventory and who will be in charge of maintaining and distributing the archive? What platforms exist and are used to capture training data and material and make it readily maintainable and findable? Can the material be reused and how do we recognise and capture re-use? Do we know about how to apply a license to our materials for appropriate reuse or do we need guidance?\n\nWhile there will likely be more questions than these, one question has been answered. When can we move from talking to doing? That time is now.","doi":"10.5281/zenodo.4287858","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":200,"title":"Astronomy Data And Computing Services - Upskilling the Australian astronomy community","url":"https://staging.dresa.org.au/materials/astronomy-data-and-computing-services-upskilling-the-australian-astronomy-community.json","description":"The Astronomy Data And Computing Services (ADACS) initiative has been working with the Australian astronomy community for just over 3 years now. Our vision is to deliver astronomy-focused training, support and expertise to maximise the scientific return on investments in astronomical data \u0026amp; computing infrastructure.\n\nDuring these last 3 years, we have delivered dozens of face-to-face, hands-on workshops and created several hours worth of online tutorial materials. This talk will focus on our journey to deliver this computational skills training to the community, exploring how we chose different delivery pathways and content, based both on community input as well as our professional expertise and understanding of existing skill gaps. Most importantly we will discuss our plans for the future and how we are working on actively including the community in developing new training material beyond the usual skills survey.\n\nCome along to this talk if you would like to hear about a national effort to deliver computational skills training and would like to know more about potential new avenues to provide just-in-time training and how to collaborate with ADACS. ","doi":"10.5281/zenodo.4287748","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":201,"title":"Masterclass: Maximise your impact (padlet data)","url":"https://staging.dresa.org.au/materials/masterclass-maximise-your-impact-padlet-data.json","description":"Masterclass activity using Padlet. Questions asked: - How do you set the context for your learners? - What motivates or inspires your learners? - What are some tips to create and foster open communication channels? - How do you keep training interesting for yourself? - Post-pandemic will training transition to other forms (from virtual to hybrid learning)? - How do you manage diversity in subject expertise in attendees?","doi":"10.5281/zenodo.5739887","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":202,"title":"Skills initiatives at TERN","url":"https://staging.dresa.org.au/materials/skills-initiatives-at-tern.json","description":"This presentation provides insight into current training efforts at TERN around data collection, data processing and data access and analytics. Highlighting various modes of training including hands-on data collection training, tutorials on deriving data, workshops, user manuals and training at domain conferences. A list of resources and tools has also been provided for those interested in wanting to know more.\n\nYou can watch the video on YouTube here: https://youtu.be/mgGuKUGCu2g","doi":"10.5281/zenodo.5711879","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":203,"title":"Institutional Research Data Management Policies and Procedures","url":"https://staging.dresa.org.au/materials/institutional-research-data-management-policies-and-procedures.json","description":"This is a guide for those developing or updating policies and procedures related to the management of research data as an institutional asset.\nThe guide covers:\n- Why have a research data management policy or policies?\n- Possible approaches to constructing a research data policy suite\n- Examples of data management policies\n- Key topics to include in a research data policy suite\n- Checklist for a Research Data Management Policy for Australian Universities / Institutions","doi":"10.5281/zenodo.5784765","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":204,"title":"Role profiles for the Bureau's Stewardship Model","url":"https://staging.dresa.org.au/materials/role-profiles-for-the-bureau-s-stewardship-model.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":205,"title":"Data Policy","url":"https://staging.dresa.org.au/materials/data-policy.json","description":"Increasing the availability of research data for reuse is in part being driven by research data policies. While the number of research funders, journals and institutions with some form of research data policy is growing, the landscape is complex and therefore the implementation and implications of policies for researchers can be unclear, confusing and sometimes even contradictory. The RDA Data Policy Standardisation and Implementation IG was established to help address these challenges.\n\nInitially the Group focussed on Developing a Research Data Policy Framework for All Journals and Publishers and with journal adoptions of the framework growing, the Group is now focussing on alignment between publishers and funders. This session provided an overview of the joint session held at RDA P17 of the Research Funders and Stakeholders on Open Research and Data Management and Practices IG, the Data Policy Standardisation and Implementation IG and the FAIRsharing WG.\n\nThe focus of this RDA VP17 session was to provide an overview of a joint project to examine funder-publisher policy alignment and provide recommendations on how to improve alignment.","doi":"10.5281/zenodo.4922756","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":167,"title":"OECD Report - Building digital workforce capacity and skills for data-intensive science (2020)","url":"https://staging.dresa.org.au/materials/oecd-report-building-digital-workforce-capacity-and-skills-for-data-intensive-science-2020.json","description":" \n\nAs a lead contributor to the OECD's Building Digital Workforce Capacity and Skills for Data-Intensive Science (2020) report, Dr Michelle Barker outlines in this presentation the goal of the report, i.e. to make recommendations to policy makers on how to facilitate the digital workforce capacity needed for data-intensive science, based on analysis of best practice.\n\nThe presentation highlights:\n\n- Digital workforce capacity and COVID19: the importance of digital skills, the need for shared access to open data, software and code, and the shortfall in skills to enable a comprehensive response to such emergencies\n\n- The ongoing need for a digital skilled workforce for data-intensive science\n\n- Five focus areas in the report include:\n\n1. Enablers for digital workforce capacity development\n\n2. Defining needs: digital skills, frameworks and roles\n\n3. Provision of training\n\n4. Community development\n\n5. Career paths and reward structures - Recommendations for actors incl. universities, national or regional governments","doi":"10.5281/zenodo.4289356","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":162,"title":"ARDC Your first step to FAIR","url":"https://staging.dresa.org.au/materials/ardc-your-first-step-to-fair.json","description":"This workshop gives a brief overview of the FAIR principles, including a method to make a one-file dataset FAIR.","doi":"10.5281/zenodo.5009206","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":163,"title":"Training resources for sharing and reuse","url":"https://staging.dresa.org.au/materials/training-resources-for-sharing-and-reuse.json","description":"This presentation outlines the work completed during a consultancy for ARDC by Dr Paula Martinez to develop new and publish existing national skills materials for reuse by the sector. She was responsible for the work package targeted to co-develop national skills materials with a strong emphasis on sharing and reuse. This was a very collaborative project with the opportunity to work with different target audiences, topics and support expertise. To accommodate for a short timeline. We defined the scope to six topics. 1) Containers in Research 2) Data Governance 3) Software citation and Licensing 4) FAIR Data 101 5) Metadata for Training Materials 6) Machine Learning Resources.\n\nYou can watch the video on YouTube here: https://youtu.be/10Yv_BFa-mw","doi":"10.5281/zenodo.5711887","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":164,"title":"DReSA: Project team reflections","url":"https://staging.dresa.org.au/materials/dresa-project-team-reflections.json","description":"This presentation provides thoughts and reflections from the Digital Research Skills Australaisa (DReSA) project team on DReSA. Team members highlight their perspectives on value propositions and benefits for their respective institutiosn/organisations and nationally, as well as individual reflections on collaboration and working together on the project so far.\n\nYou can watch the video on YouTube here: https://youtu.be/qqH92itI8SI \n\n ","doi":"10.5281/zenodo.5712129","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":165,"title":"ARDC FAIR Data 101 self-guided","url":"https://staging.dresa.org.au/materials/ardc-fair-data-101-self-guided.json","description":"FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles\n\nThe FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course.\n\nThe course structure was based on 'FAIR Data in the Scholarly Communications Lifecycle', run by Natasha Simons at the FORCE11 Scholarly Communications Institute. These training materials are hosted on GitHub.","doi":"10.5281/zenodo.5094034","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":166,"title":"Skills training \u0026 materials - developing sharing guidelines and agreements","url":"https://staging.dresa.org.au/materials/skills-training-materials-developing-sharing-guidelines-and-agreements.json","description":"Anyone who has developed training content - specifically hands-on, short format, data science training - will know that it is expensive and time consuming. As a rule of thumb, one can expect to spend 15-20 hours of development time per hour of delivery time.\n\nEven once the main work is done, there are still ongoing maintenance demands, from correcting the inevitable typos and adapting to software version updates, to major rewrites as best practice techniques evolve. Few Australians training organisations have a funding mandate for developing training material for general use.\n\nInstead most of us build training for our own communities in response to demand from those communities, allocating our limited resources to the areas of perceived highest demand. Notwithstanding this local focus, most training organisations operate in similar research environments with similar community demands, so there are real opportunities for benefit from collaboration between those organisations. In this session we will discuss how such collaboration could occur and whether a standardised national agreement around sharing of training material is an achievable outcome.\n\nThis session will not discuss co-delivery opportunities, institution-specific content such as HPC training and data management, or consolidation of existing similar workshops into a single course. These are important topics, but we don’t have time to do them justice today.","doi":"10.5281/zenodo.4287848","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":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":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":152,"title":"WEBINAR: KBase - A knowledge base for systems biology","url":"https://staging.dresa.org.au/materials/webinar-kbase-a-knowledge-base-for-systems-biology.json","description":"This record includes training materials associated with the Australian BioCommons webinar ‘KBase - A knowledge base for systems biology’. This webinar took place on 22 September 2021.\n\nEvent description \n\nDeveloped for bench biologists and bioinformaticians, The Department of Energy Systems Biology Knowledgebase (KBase) is a free, open source, software and data science platform designed to meet the grand challenge of systems biology: predicting and designing biological function.\n\nThis webinar will provide an overview of the KBase mission and user community, as well as a tour of the online platform and basic functionality. You’ll learn how KBase can support your research: Upload data, run analysis tools (Apps), share your analysis with collaborators, and publish your data and reproducible workflows. We’ll highlight a brand new feature that enables users to link environment and measurement data to sequencing data. You’ll also find out how KBase supports findable, accessible, interoperable, and reusable (FAIR) research by providing open, reproducible, shareable bioinformatics workflows.\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\tQ\u0026amp;A for Australian BioCommons KBase Webinar [PDF]: Document containing answers to questions asked during the webinar and links to additional resources\n\t\n\t\n\tIntroduction to KBase: Australian BioCommons Webinar [PDF]: Slides presented 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/tJ94i9gOJfU\n\nThe slides are also available as Google slides: \n\nhttps://tinyurl.com/KBase-webinar-slides","doi":"10.5281/zenodo.5717580","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":[]},{"id":154,"title":"WEBINAR: High performance bioinformatics: submitting your best NCMAS application","url":"https://staging.dresa.org.au/materials/webinar-high-performance-bioinformatics-submitting-your-best-ncmas-application.json","description":"This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021.\n\nBioinformaticians are increasingly turning to specialised compute infrastructure and efficient, scalable workflows as their research becomes more data intensive. Australian researchers that require extensive compute resources to process large datasets can apply for access to national high performance computing facilities (e.g. Pawsey and NCI) to power their research through the National Computational Merit Allocation Scheme (NCMAS). NCMAS is a competitive, merit-based scheme and requires applicants to carefully consider how the compute infrastructure and workflows will be applied. \n\nThis webinar provides life science researchers with insights into what makes a strong NCMAS application, with a focus on the technical assessment, and how to design and present effective and efficient bioinformatic workflows for the various national compute facilities. It will be followed by a short Q\u0026amp;A session.\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\tHigh performance bioinformatics: submitting your best NCMAS application - slides (PDF and PPTX): 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:\n\nhttps://youtu.be/HeFGjguwS0Y","doi":"10.5281/zenodo.5239883","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]},{"id":155,"title":"WEBINAR: Getting started with R","url":"https://staging.dresa.org.au/materials/webinar-getting-started-with-r.json","description":"This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with R’. This webinar took place on 16 August 2021.\n\nData analysis skills are now central to most biological experiments. While Excel can cover some of your data analysis needs, it is not always the best choice, particularly for large and complex datasets.\n\nR is an open-source software and programming language that enables data exploration, statistical analysis visualisation and more. While it is the tool of choice for data analysis, getting started can be a little daunting for those without a background in statistics.\n\nIn this webinar Saskia Freytag, an R user with over a decade of experience and member of the Bioconductor Community Advisory Board, will walk you through their hints and tips for getting started with R and data analysis. She’ll cover topics like R Studio and why you need it, where to get help, basic data manipulation, visualisations and extending R with libraries. The webinar will be followed by a short Q\u0026amp;A session\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\tGetting started with R - slides (PDF): Slides used in the presentation\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/JS7yZw7bnX8","doi":"10.5281/zenodo.5214277","remote_updated_date":null,"remote_created_date":null,"scientific_topics":[],"operations":[]}]