Content provider: Australian BioCommons or QCIF
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WEBINAR: Getting started with containers
12 May 2021
WEBINAR: Getting started with containers https://www.biocommons.org.au/events/containers-for-beginners https://dresa.org.au/events/webinar-getting-started-with-containers What are containers? Who uses them? When, and why? You'll hear an expert's overview of using containers on supercomputers and the Cloud, and learn from real life examples of simple, domain-agnostic use. Absolute beginners are welcome to come along and ask the questions you’ve been too embarrassed to ask! This webinar is a collaboration between Pawsey Supercomputing Centre and Australian BioCommons to celebrate Data Science Week. **Presenter:** Dr Sarah Beecroft, HPC Research Fellow, Pawsey Supercomputing Centre **Date/time:** 12 May 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST [**Register here**](https://unimelb.zoom.us/webinar/register/WN_s5vlb2ZqRJGdcN6mGHFsGw) 2021-05-12 12:00:00 UTC 2021-05-12 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] [] 500 webinar open_to_all BioinformaticsContainersWorkflows -
WEBINAR: Getting started with command line bioinformatics
22 June 2021
WEBINAR: Getting started with command line bioinformatics https://www.biocommons.org.au/events/command-line https://dresa.org.au/events/webinar-getting-started-with-command-line-bioinformatics Bioinformatics skills are in demand like never before and biologists are stepping up to the challenge of learning to analyse large and ever growing datasets. Learning how to use the command line can open up many options for data analysis but getting started can be a little daunting for those without a background in computer science. Parice Brandies and Carolyn Hogg have recently put together [ten simple rules for getting started with command-line bioinformatics](https://doi.org/10.1371/journal.pcbi.1008645) to help biologists begin their computational journeys. In this webinar Parice will walk you through their hints and tips for getting started with the command line. She’ll cover topics like learning tech speak, evaluating your data and workflows, assessing computational requirements, computing options, the basics of software installation, curating and testing scripts, a bit of bash and keeping good records. The webinar will be followed by a short Q&A session. **Who the webinar is for** Aspiring bioinformaticians and command line users from a variety of biological fields. **Presenter**: Parice Brandies, School of Life and Environmental Sciences, The University of Sydney **Date/time:** 22 June 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST **How to join** This webinar is free to join but you must register for a place in advance. **[Register here](https://unimelb.zoom.us/webinar/register/WN_fkETrWTbQNe35O9ye9OC9Q)** 2021-06-22 12:00:00 UTC 2021-06-22 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa (melissa@biocommons.org.au) [] [] 500 webinar open_to_all Command lineBioinformaticsData analysis -
WEBINAR: Getting started with deep learning
21 July 2021
WEBINAR: Getting started with deep learning https://www.biocommons.org.au/events/deep-learning-titus https://dresa.org.au/events/webinar-getting-started-with-deep-learning Are you wondering what deep learning is and how it might be useful in your research? This high level overview will introduce deep learning ‘in a nutshell’ and provide tips on which concepts and skills you will need to know to build a deep learning application. The presentation also provides pointers to various resources you can use to get started in deep learning. The webinar will be followed by a short Q&A session. **Who the webinar is for: **Complete beginners in machine learning, deep learning, or programming, who want to investigate the potential application of AI systems in their research. **Presenter**: Dr Titus Tang, Senior Deep Learning Engineer, Data Science and AI Platform, Monash University **Date/time:** 21 July 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST **How to join: **This webinar is free to join but you must register for a place in advance. **[Register here](https://unimelb.zoom.us/webinar/register/WN_jH3KjLZKQvatEil9PULIeA)** 2021-07-21 12:00:00 UTC 2021-07-21 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa (melissa@biocommons.org.au) [] [] 500 [] open_to_all Deep learningBioinformatics -
WEBINAR: Getting started with R
16 August 2021
WEBINAR: Getting started with R https://www.biocommons.org.au/events/r-intro https://dresa.org.au/events/webinar-getting-started-with-r Data 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. R 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. In this webinar Saskia Freytag, an R user with over a decade of experience and member of the [Bioconductor Community Advisory Board](https://www.bioconductor.org/about/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](https://www.rstudio.com/) 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&A session. **Who the webinar is for** Aspiring data analysts from a variety of biological fields **Presenter**: Dr Saskia Freytag, Postdoctoral Fellow, Harry Perkins Institute of Medical Research. **Date/time:** 16 August 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST **How to join** This webinar is free to join but you must register for a place in advance. **[Register here](https://unimelb.zoom.us/webinar/register/WN_j3bXauUDQwW_q64JgnvdpQ)** 2021-08-16 12:00:00 UTC 2021-08-16 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa (melissa@biocommons.org.au) [] [] 500 webinar open_to_all R softwareBioinformaticsComputer ScienceStatistics -
WORKSHOP: Hybrid de novo genome assembly
7 October 2021
WORKSHOP: Hybrid de novo genome assembly https://www.biocommons.org.au/events/hybrid-assembly https://dresa.org.au/events/workshop-hybrid-de-novo-genome-assembly It’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. In 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](https://github.com/fenderglass/Flye), [Pilon](https://github.com/broadinstitute/pilon/wiki), and [Unicycler](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005595) 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. All analyses will be performed using [Galaxy Australia](https://usegalaxy.org.au/), an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. **Date/time:** 2 - 5pm AEDT/ 1 - 4pm AEST/ 1:30 - 4:30pm ACDT/ 11am - 2pm AWST, Thursday 7 October 2021 **Lead Trainer:** Grace Hall, Melbourne Bioinformatics **Learning outcomes** By the end of this workshop you should be able to: 1. Describe how Nanopore and Illumina reads can be used together to produce a high quality assembly 2. Use genome assembly and polishing programs in Galaxy Australia 3. Assess the quality of a genome assembly with and without a reference genome 4. Assemble an unknown, previously undocumented genome to high-quality using Nanopore and Illumina reads The workshop will NOT provide an introduction to the basics of Galaxy. If you would like to learn about this topic there are several tutorials available via the [Galaxy Training Network](https://training.galaxyproject.org/training-material/). **Who the workshop is for** This workshop is for Australian researchers who are or will perform hybrid genome assembly as part of their projects. To get the most out of the workshops you must have experience with the basics of using Galaxy Australia such as setting up a history, uploading data and running tools. It is recommended that you complete the tutorial [Galaxy 101 for Everyone](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html). No programming experience is required. **How to apply** This workshop is free but participation is subject to application with selection. **_Applications close at 11:59pm AEST Wednesday 29 September 2021._** You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 1 October 2021. Successful applicants will be provided with a Zoom meeting link closer to the date. **Applications have closed** This workshop is presented by the [Australian BioCommons](https://www.biocommons.org.au/) and [Melbourne Bioinformatics](https://www.melbournebioinformatics.org.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative). To hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to the Australian BioCommons’ eNewsletter. 2021-10-07 14:00:00 UTC 2021-10-07 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] [] workshop expression_of_interest Genome assemblyde novo genome assemblyGalaxy Australia -
WORKSHOP: Refining genome annotations with Apollo
17 November 2021
WORKSHOP: Refining genome annotations with Apollo https://www.biocommons.org.au/events/apollo-2021 https://dresa.org.au/events/workshop-refining-genome-annotations-with-apollo Genome 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. Apollo 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. This workshop will make use of a training instance of the new [Australian Apollo Service](https://apollo-portal.genome.edu.au/). 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 [join our webinar](https://www.biocommons.org.au/events/apollo-launch) on 29 September 2021. **Trainers** Dr Anthony Bretaudeau (French National Institute for Agriculture, Food, and Environment), Dr Helena Rasche (Erasmus Medical Center, The Netherlands), Dr Sarah Williams (QCIF), Dr Tiffanie Nelson (Australian BioCommons) **Date/Time** 3-6pm AEDT/ 2-5pm AEST/ 2:30-5:30pm ACDT / 12-3pm AWST, Wednesday 17 Nov 2021 **Learning outcomes** By the end of the workshop you should be able to: 1. Upload data to Apollo 2. Visualise your genome and associated automated annotations 3. Manually annotate genomes after automated annotations have been performed 4. Evaluate and visualise annotated genomic features 5. Use Apollo to collaborate on genome annotation This workshop is based on [training materials](https://training.galaxyproject.org/training-material//topics/genome-annotation/tutorials/apollo/tutorial.html) developed for the Galaxy Training Network and the [Apollo User Guide](https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html#). **Who the workshop is for** This workshop is for Australian researchers who have or will work on genome annotation and manual curation/editing as part of their projects. You should be familiar with the concepts of genome annotation and have, or soon have, genome annotation files that require manual annotation and curation. You do not need access to a personal or institutional instance of Apollo for this workshop. Access to a training instance of the Australian Apollo Service will be provided. **How to apply** This workshop is free but participation is subject to application with selection. **_Applications close at 11:59pm AEDT, Thursday 4 November 2021_**. You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 12 November 2021. Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://apollo-2021.eventbrite.com.au/)** This workshop is presented by the [Australian BioCommons](https://www.biocommons.org.au/) and [Queensland Cyber Infrastructure Foundation (QCIF)](https://www.qcif.edu.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative). This event is part of a series of [bioinformatics training events](https://www.biocommons.org.au/events). If you'd like to hear when registrations open for other events, please [subscribe](https://www.biocommons.org.au/subscribe) to Australian BioCommons 2021-11-17 15:00:00 UTC 2021-11-17 18:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa Burke melissa@biocommons.org.au [] [] workshop expression_of_interest Genome annotationBioinformaticsGenomics -
WEBINAR: Establishing Gen3 to enable better human genome data sharing in Australia
16 - 22 February 2022
WEBINAR: Establishing Gen3 to enable better human genome data sharing in Australia https://www.biocommons.org.au/events/gen3-webinar https://dresa.org.au/events/webinar-establishing-gen3-to-enable-better-human-genome-data-sharing-in-australia Australian human genome initiatives are generating vast amounts of human genome data. There is a desire and need to share data across projects 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. Australian BioCommons has brought together a team from[ Zero Childhood Cancer](https://www.zerochildhoodcancer.org.au/) (Zero), the[ University of Melbourne Centre for Cancer Research](https://mdhs.unimelb.edu.au/centre-for-cancer-research/home) (UMCCR),[ Australian Access Federation](https://aaf.edu.au/) and[ Melbourne Bioinformatics](https://www.melbournebioinformatics.org.au/) 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. [Gen3](https://gen3.org/) 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](https://gdc.cancer.gov/),[ BloodPAC](https://www.bloodpac.org/),[ BrainCommons](https://www.braincommons.org/),[ Kids First Data Commons](https://kidsfirstdrc.org/)). In 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. **Date/time:** 16 February 2022 - 13:00-14:00 AEDT/ 12:00-13:00 AEST / 12:30 - 13:30 ACDT / 10:00-11:00 AWST **How to join:** This webinar is free to join but you must [register for a place](https://unimelb.zoom.us/webinar/register/WN_ZDfeLU_RT9CS9anotCpzZQ) in advance. 2022-02-16 13:00:00 UTC 2022-02-22 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] [] 500 webinar open_to_all BioinformaticsResearch infrastructureHuman genomics -
WORKSHOP: Introduction to Metabarcoding using Qiime2
22 February 2022
WORKSHOP: Introduction to Metabarcoding using Qiime2 https://www.biocommons.org.au/events/metabarcoding-qiime2 https://dresa.org.au/events/workshop-introduction-to-metabarcoding-using-qiime2 Metabarcoding has revolutionized 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. This 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. **Date/time:** 12 - 5pm AEDT/ 11 - 4pm AEST/ 11:30 - 4:30 ACDT/ 9am - 2pm AWST, Tuesday 22 February 2022 **Lead Trainers:** Dr Ashley Dungan (School of Bioscience, University of Melbourne) and Dr Gayle Philip (Melbourne Bioinformatics) **Learning outcomes** By the end of this workshop you should be able to: 1. Understand data and metadata formats required for Qiime2 2. Use Qiime2 to: 1. Create and interpret sequence quality data 2. Generate taxonomy reports/tables and phylogenic trees based on amplicon sequence variants 3. Compare Alpha and Beta data analysis 4. Develop publication quality graphics and statistics using 16S sequencing data 3. Assess the results to determine the influence of genotype (an intrinsic factor) and environment (an extrinsic factor) on anemone-associated bacterial communities **Who the workshop is for** This workshop is for researchers studying microbiomes as part of their projects. The workshop will be conducted in a Unix environment so basic command line knowledge (e.g. logging in to a remote machine, navigating the directory structure and copy files between the computers) is a prerequisite You should be familiar with the concepts of microbial analysis a however no previous experience with Qiime2 is required. **How to apply** This workshop is free but participation is subject to application with selection. You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered. Applications close 8 February 2022. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://intro-qiime2.eventbrite.com.au/)** This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/) and[ Melbourne Bioinformatics](https://www.melbournebioinformatics.org.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative). To hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to the Australian BioCommons’ eNewsletter. 2022-02-22 12:00:00 UTC 2022-02-22 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] [] 30 workshop expression_of_interest BioinformaticsMicrobiomeMetabarcodingMetagenomics -
WEBINAR: Conservation genomics and the age of extinction
8 March 2022
WEBINAR: Conservation genomics and the age of extinction https://www.biocommons.org.au/events/conservation-genomics-webinar https://dresa.org.au/events/webinar-conservation-genomics-and-the-age-of-extinction Biodiversity 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. In this webinar Dr Carolyn Hogg speaks about the work she has been doing with the [Threatened Species Initiative](https://threatenedspeciesinitiative.com/) 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. **Speaker: **Dr Carolyn Hogg, Australasian Wildlife Genomics Group, The University of Sydney **Who the webinar is for:** Anyone with an interest in the application of genomics to conservation biology. **How to join:** This webinar is free to join but you must [register for a place in advance](https://unimelb.zoom.us/webinar/register/WN_QLLM7rRPTB2D3OQyGhSXgw). 2022-03-08 13:00:00 UTC 2022-03-08 14:00:00 UTC Australian BioCommons Online, Online, Australia Online Online Australia Australian Biocommons Melissa Burke (melissa@biocommons.org.au) [] [] [] open_to_all Conservation genomicsThreatened SpeciesBioplatforms AustraliaThreatened Species Initiative -
Working with Sensitive Data
4 April 2022
Working with Sensitive Data https://www.qcif.edu.au/trainingcourses/working-with-sensitive-data/ https://dresa.org.au/events/working-with-sensitive-data This workshop uses practical and discussion-based training to guide researchers about identifying what constitutes sensitive data, the risks of working with sensitive data, and how to appropriately manage those risks. It covers the 'Five Safes' framework and researchers' responsibilities, and introduces ways to promote data security and mitigate disclosure risks. 2022-04-04 09:00:00 UTC 2022-04-04 11:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] webinar open_to_all [] -
Longitudinal and Mixed Model Analysis with R
6 April 2022
Longitudinal and Mixed Model Analysis with R https://www.eventbrite.com.au/e/267298455877/ https://dresa.org.au/events/longitudinal-and-mixed-model-analysis-with-r This workshop will develop participants’ understanding of the principles, methods, and interpretation of statistical models for longitudinal data (i.e. repeated measures over time) using R. The course will cover the principles of Linear Mixed Models from simple models to more complex ones and includes practical sessions getting hands-on experience of longitudinal analysis in R. 2022-04-06 09:00:00 UTC 2022-04-06 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
WEBINAR: Protection of genomic data and the Australian Privacy Act: when is genomic data ‘personal information’?
6 April 2022
WEBINAR: Protection of genomic data and the Australian Privacy Act: when is genomic data ‘personal information’? https://www.biocommons.org.au/events/law-genomic-data https://dresa.org.au/events/webinar-protection-of-genomic-data-and-the-australian-privacy-act-when-is-genomic-data-personal-information It 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. There 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: 1. those subject to the Privacy Act need to be able to confidently navigate their responsibilities 2. understanding 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 3. while 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? In 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 of more clearly identifying the legal rights and responsibilities which attach to the use and disclosure of genomic data in the future. **Speaker:** Mark Taylor, Professor in Health Law and Regulation, Melbourne Law School; Director, Health, Law and Emerging Technologies (HeLEX), University of Melbourne. **How to join:** This webinar is free to join but you must [register for a place in advance](https://unimelb.zoom.us/webinar/register/WN_zC3MlCjAQUq7sTVw8idvLA). 2022-04-06 12:00:00 UTC 2022-04-06 13:00:00 UTC Australian BioCommons Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] Life scientists 500 webinar open_to_all EthicsHuman genomicsData privacyBioinformatics -
Introduction to Unix
11 - 12 April 2022
Introduction to Unix https://www.qcif.edu.au/trainingcourses/introduction-to-unix/ https://dresa.org.au/events/introduction-to-unix The Unix shell has been around longer than most of its users have been alive. It has survived so long because it’s a power tool that allows people to do complex things with just a few keystrokes. More importantly, it helps them combine existing programs in new ways and automate repetitive tasks so they aren’t typing the same things over and over again. Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including 'high-performance computing' supercomputers). This Software Carpentry workshop will start you on a path towards using these resources effectively. 2022-04-11 09:00:00 UTC 2022-04-12 12:30:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Statistical Comparisons using R
12 April 2022
Statistical Comparisons using R https://www.qcif.edu.au/trainingcourses/statistics-for-comparisons/ https://dresa.org.au/events/statistical-comparisons-using-r This practical workshop will help participants to choose and use the appropriate standard statistical test for their data by introducing key concepts of inferential statistics in R. Participants will learn how to compute and interpret hypothesis tests for popular statistical models such as correlation, contingency tables, chi-square test, t-test and ANOVA. 2022-04-12 09:00:00 UTC 2022-04-12 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Genome Annotation with Apollo
21 April 2022
Genome Annotation with Apollo https://www.qcif.edu.au/trainingcourses/genome-annotation-apollo/ https://dresa.org.au/events/genome-annotation-with-apollo Genome 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. In this workshop we'll show you how to use Apollo to refine genome annotations using the Australian Apollo Service. 2022-04-21 09:00:00 UTC 2022-04-21 12:30:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Introduction to Programming: Plotting and Programming with Python
26 - 29 April 2022
Introduction to Programming: Plotting and Programming with Python https://www.qcif.edu.au/trainingcourses/plotting-and-programming-with-python/ https://dresa.org.au/events/introduction-to-programming-plotting-and-programming-with-python This Software Carpentry workshop will introduce the building blocks of the Python scripting environment. Participants will start by exploring the command-line interface and basic programming concepts using Unix, before moving on to learn about simple and complex data types, conditionals and looping in Python. This workshop will prepare participants to carry out batch analysis and equip them with the knowledge to start creating automated pipelines to increase data processing power and productivity. 2022-04-26 09:00:00 UTC 2022-04-29 12:30:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Exploring and Predicting using Linear Regression with R
11 May 2022
Exploring and Predicting using Linear Regression with R https://www.qcif.edu.au/trainingcourses/exploring-and-predicting-using-linear-regression/ https://dresa.org.au/events/exploring-and-predicting-using-linear-regression-with-r This workshop is designed to increase participants understanding of statistical relationships between data. It introduces principles and methods of regression models using R, and how to interpret relationships between variables. The course covers basic principles of regression methods through to interpreting the output of statistical analyses, and also includes practical sessions giving hands-on experience with regression analysis in R. 2022-05-11 09:00:00 UTC 2022-05-11 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Data Storytelling
11 May 2022
Data Storytelling https://www.qcif.edu.au/trainingcourses/data-storytelling/ https://dresa.org.au/events/data-storytelling Research communication is much more than just writing journal papers; to maximise the impact of your work, it's vital that you make your research findings accessible and engaging to a wide audience. Data storytelling is a powerful way achieving this, by conveying your ideas in a clear and memorable way. This interactive webinar focuses on developing your data storytelling skills by introducing a range of data visualisation techniques that you can use to combine the three elements of data, visuals and narrative into a meaningful and memorable story. By using these three elements, you can weave a story about your research for an array of audiences, in a way that they will connect with and remember. 2022-05-11 13:30:00 UTC 2022-05-11 15:30:00 UTC QCIF QCIF training@qcif.edu.au [] [] webinar open_to_all [] -
Introduction to SPSS
13 May 2022
Introduction to SPSS https://www.qcif.edu.au/trainingcourses/introduction-to-spss/ https://dresa.org.au/events/introduction-to-spss This workshop will provide a hands-on introduction to the widely-used SPSS statistical analysis package. Participants will learn how to import, manage and transform datasets, and how to summarise and present data. The workshop will also include a basic introduction to statistical testing using SPSS. 2022-05-13 09:00:00 UTC 2022-05-13 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Introduction to HPC
16 May 2022
Introduction to HPC https://www.qcif.edu.au/trainingcourses/introduction-to-hpc/ https://dresa.org.au/events/introduction-to-hpc High-Performance Computing, or HPC, is the use of computers orders of magnitude faster and more powerful than even the best desktop PC. As research becomes more and more data-intensive, an ever broader range of researchers are using HPC for their data analysis. This workshop will give you an introduction to using high-performance computing systems effectively (as well as their limitations), and will introduce the basics of how to access a HPC cluster, load and use software, and submit jobs to run. 2022-05-16 09:00:00 UTC 2022-05-16 13:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop host_institution [] -
Single-cell RNA-Seq Analysis using Galaxy
17 May 2022
Single-cell RNA-Seq Analysis using Galaxy https://www.qcif.edu.au/trainingcourses/scrna-seq-analysis/ https://dresa.org.au/events/single-cell-rna-seq-analysis-using-galaxy This hands-on workshop will cover the basics of single-cell RNA-Seq analysis, using the Galaxy platform. Starting from a table of gene counts we will evaluate, filter, annotate and visualise the data. We will also cover clustering, cell type identification and differential expression. The workshop will be based in Galaxy, a platform that provides a simple and user-friendly interface to bioinformatics tools. 2022-05-17 09:00:00 UTC 2022-05-17 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Making your Research Data FAIR
18 May 2022
Making your Research Data FAIR https://www.qcif.edu.au/trainingcourses/fair-data/ https://dresa.org.au/events/making-your-research-data-fair Making your Research Data FAIR is a 3-hour workshop aimed at introducing researchers to FAIR (Findable, Accessible, Interoperable and Reusable) principles. During the workshop researchers will reflect on reasons for making their research data FAIR and self-assess on how FAIR their research data is and then learn about resources available for researchers to make their data FAIR. 2022-05-18 09:00:00 UTC 2022-05-18 12:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop host_institution [] -
Introduction to Programming: R for Reproducible Scientific Analysis
23 - 26 May 2022
Introduction to Programming: R for Reproducible Scientific Analysis https://www.qcif.edu.au/trainingcourses/r-for-reproducible-scientific-analysis/ https://dresa.org.au/events/introduction-to-programming-r-for-reproducible-scientific-analysis This Software Carpentry workshop will introduce novice programmers to the R software environment, a powerful, popular and free statistical and graphical programming language. R is commonly used in many scientific disciplines for statistical analysis and its array of third-party packages. The emphasis of this workshop is to give attendees a strong foundation in the fundamentals of R, and to teach best practices for scientific computing: breaking down analyses into modular units, task automation, and encapsulation. 2022-05-23 09:00:00 UTC 2022-05-26 12:30:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
A Guide to Reproducible Research
25 May 2022
A Guide to Reproducible Research https://www.qcif.edu.au/trainingcourses/guide-to-reproducible-research/ https://dresa.org.au/events/a-guide-to-reproducible-research The idea that you can duplicate an experiment and get the same conclusion is the basis for all scientific discoveries. Reproducible research is data analysis that starts with the raw data and offers a transparent workflow to arrive at the same results and conclusions. However not all studies are replicable due to lack of information on the process. Therefore reproducibility in research is extremely important. Researchers genuinely want to make their research more reproducible, but sometimes don't know where to start and often don't have the available time to investigate or establish methods on how reproducible research can speed up every day work. We aim for the philosophy 'Be better than you were yesterday'. Reproducibility is a process, and we highlight there is no expectation to go from beginner to expert in a single workshop. Instead, we offer some steps you can take towards the reproducibility path following our Steps to Reproducible Research self paced program. 2022-05-25 13:30:00 UTC 2022-05-25 15:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] webinar open_to_all [] -
WORKSHOP: R - fundamental skills for biologists
1 - 22 June 2022
WORKSHOP: R - fundamental skills for biologists https://www.biocommons.org.au/events/fundamental-r https://dresa.org.au/events/workshop-r-fundamental-skills-for-biologists Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets. R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes. Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R. Topics covered in this workshop include: 1. Spreadsheets, organising data and first steps with R 2. Manipulating and analysing data with dplyr and joining tables 3. Data visualisation 4. Summarized experiments and getting started with Bioconductor **Lead Trainer:** Dr Saskia Freytag (Laboratory Head, Personalised Oncology Division, WEHI) **Format** This online workshop will take place over a series of three-hour sessions. You must attend all four sessions in order to get the most out of the workshop. Expert trainers will guide you through each of the topics and provide activities and take home exercises to help you put your new skills into action. Support will be provided via Slack between sessions. **Date/time:** 1, 8, 15, and 22 June 2022: 2 - 5pm AEST/ 1:30-4:30pm ACST/ 12-3pm AWST 1 June 2022: Spreadsheets, organising data and first steps with R 8 June 2022: Manipulating and analysing data with dplyr and joining tables 15 June 2022: Data visualisation 22 June 2022: Summarized experiments and getting started with Bioconductor Participants must attend all four sessions **Learning outcomes** By the end of the workshop you should be able to: 1. Organise your data for effective use 2. Use RStudio to structure your work in R and run R packages 3. Make use of objects, vectors and functions in R 4. Load, inspect and manipulate data in R 5. Use dplyr and tidyr and packages to manipulate and reshape data 6. Produce and customise scatter plots, box plots, line plots, etc. using ggplot 7. Combine data spread across multiple tables 8. Use the SummarizedExperiment package to store and handle omics data 9. Have some familiarity with Bioconductor 10. Identify sources of help and support from the R community **Who the workshop is for** This workshop is for Australian life science researchers who are using, or intend to use, R to analyse their data. This workshop is suitable for absolute beginners or those who wish to go back to basics to ensure they are using R and RStudio effectively. No prior knowledge of R is required. **How to apply** This workshop is free but participation is subject to application with selection. Applications close at **11:59pm AEST Wednesday 11 May 2022**. You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://r-fundamentals.eventbrite.com.au/)** This event is part of a series of[ bioinformatics training events](https://www.biocommons.org.au/events). If you'd like to hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to Australian BioCommons. 2022-06-01 12:00:00 UTC 2022-06-22 17:00:00 UTC Australian BioCommons Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] Life scientists 50 workshop expression_of_interest RRStudioBioinformaticsLife scienceData analysisData visualisation -
Statistical Comparisons using SPSS
6 June 2022
Statistical Comparisons using SPSS https://www.qcif.edu.au/trainingcourses/stat-comparisons-spss/ https://dresa.org.au/events/statistical-comparisons-using-spss This practical workshop will help participants to choose and use the appropriate standard statistical test for their data by introducing key concepts of inferential statistics in SPSS. Participants will learn how to compute and interpret hypothesis tests for popular statistical models such as correlation, contingency tables, chi-square test, t-test and ANOVA. 2022-06-06 09:00:00 UTC 2022-06-06 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Longitudinal and Mixed Model Analysis with R
9 June 2022
Longitudinal and Mixed Model Analysis with R https://www.qcif.edu.au/trainingcourses/longitudinal-and-mixed-model-analysis/ https://dresa.org.au/events/longitudinal-and-mixed-model-analysis-with-r-33c3cd7d-3991-4056-a363-6b33560de5ef This workshop will develop participants’ understanding of the principles, methods, and interpretation of statistical models for longitudinal data (i.e. repeated measures over time) using R. The course will cover the principles of Linear Mixed Models from simple models to more complex ones and includes practical sessions getting hands-on experience of longitudinal analysis in R. 2022-06-09 09:00:00 UTC 2022-06-09 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Statistical Comparisons using R
14 June 2022
Statistical Comparisons using R https://www.qcif.edu.au/trainingcourses/statistics-for-comparisons/ https://dresa.org.au/events/statistical-comparisons-using-r-0193b73f-58db-433b-bdf6-958245487b21 This practical workshop will help participants to choose and use the appropriate standard statistical test for their data by introducing key concepts of inferential statistics in R. Participants will learn how to compute and interpret hypothesis tests for popular statistical models such as correlation, contingency tables, chi-square test, t-test and ANOVA. 2022-06-14 09:00:00 UTC 2022-06-14 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Metagenomics Analysis using Galaxy
15 June 2022
Metagenomics Analysis using Galaxy https://www.qcif.edu.au/trainingcourses/metagenomics-analysis-using-galaxy/ https://dresa.org.au/events/metagenomics-analysis-using-galaxy This workshop will cover the concepts of 16S bacterial metagenomics analysis. You will learn about pre-processing and quality-filtering of your data, assembly of reads into Operational Taxonomic Units (OTUs), and visualisation and export of data for further analysis. The workshop will be based in Galaxy, a platform that provides a simple and user-friendly interface to bioinformatics tools. 2022-06-15 09:00:00 UTC 2022-06-15 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Introduction to Reproducible Research
17 June 2022
Introduction to Reproducible Research https://www.qcif.edu.au/trainingcourses/intro-to-reproducible-research/ https://dresa.org.au/events/introduction-to-reproducible-research An Introduction to Reproducible Research is a 3-hour workshop aimed at introducing researchers to concepts, tools and practices to make their research workflows, data and results reproducible. The workshop challenges participants to use available tools and existing support to increase their research impact, quality and reproducibility through traditional and non-traditional outputs. 2022-06-17 09:00:00 UTC 2022-06-17 12:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop host_institution []
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WEBINAR: Getting started with containers
12 May 2021
WEBINAR: Getting started with containers https://www.biocommons.org.au/events/containers-for-beginners https://dresa.org.au/events/webinar-getting-started-with-containers What are containers? Who uses them? When, and why? You'll hear an expert's overview of using containers on supercomputers and the Cloud, and learn from real life examples of simple, domain-agnostic use. Absolute beginners are welcome to come along and ask the questions you’ve been too embarrassed to ask! This webinar is a collaboration between Pawsey Supercomputing Centre and Australian BioCommons to celebrate Data Science Week. **Presenter:** Dr Sarah Beecroft, HPC Research Fellow, Pawsey Supercomputing Centre **Date/time:** 12 May 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST [**Register here**](https://unimelb.zoom.us/webinar/register/WN_s5vlb2ZqRJGdcN6mGHFsGw) 2021-05-12 12:00:00 UTC 2021-05-12 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] [] 500 webinar open_to_all BioinformaticsContainersWorkflows -
WEBINAR: Getting started with command line bioinformatics
22 June 2021
WEBINAR: Getting started with command line bioinformatics https://www.biocommons.org.au/events/command-line https://dresa.org.au/events/webinar-getting-started-with-command-line-bioinformatics Bioinformatics skills are in demand like never before and biologists are stepping up to the challenge of learning to analyse large and ever growing datasets. Learning how to use the command line can open up many options for data analysis but getting started can be a little daunting for those without a background in computer science. Parice Brandies and Carolyn Hogg have recently put together [ten simple rules for getting started with command-line bioinformatics](https://doi.org/10.1371/journal.pcbi.1008645) to help biologists begin their computational journeys. In this webinar Parice will walk you through their hints and tips for getting started with the command line. She’ll cover topics like learning tech speak, evaluating your data and workflows, assessing computational requirements, computing options, the basics of software installation, curating and testing scripts, a bit of bash and keeping good records. The webinar will be followed by a short Q&A session. **Who the webinar is for** Aspiring bioinformaticians and command line users from a variety of biological fields. **Presenter**: Parice Brandies, School of Life and Environmental Sciences, The University of Sydney **Date/time:** 22 June 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST **How to join** This webinar is free to join but you must register for a place in advance. **[Register here](https://unimelb.zoom.us/webinar/register/WN_fkETrWTbQNe35O9ye9OC9Q)** 2021-06-22 12:00:00 UTC 2021-06-22 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa (melissa@biocommons.org.au) [] [] 500 webinar open_to_all Command lineBioinformaticsData analysis -
WEBINAR: Getting started with deep learning
21 July 2021
WEBINAR: Getting started with deep learning https://www.biocommons.org.au/events/deep-learning-titus https://dresa.org.au/events/webinar-getting-started-with-deep-learning Are you wondering what deep learning is and how it might be useful in your research? This high level overview will introduce deep learning ‘in a nutshell’ and provide tips on which concepts and skills you will need to know to build a deep learning application. The presentation also provides pointers to various resources you can use to get started in deep learning. The webinar will be followed by a short Q&A session. **Who the webinar is for: **Complete beginners in machine learning, deep learning, or programming, who want to investigate the potential application of AI systems in their research. **Presenter**: Dr Titus Tang, Senior Deep Learning Engineer, Data Science and AI Platform, Monash University **Date/time:** 21 July 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST **How to join: **This webinar is free to join but you must register for a place in advance. **[Register here](https://unimelb.zoom.us/webinar/register/WN_jH3KjLZKQvatEil9PULIeA)** 2021-07-21 12:00:00 UTC 2021-07-21 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa (melissa@biocommons.org.au) [] [] 500 [] open_to_all Deep learningBioinformatics -
WEBINAR: Getting started with R
16 August 2021
WEBINAR: Getting started with R https://www.biocommons.org.au/events/r-intro https://dresa.org.au/events/webinar-getting-started-with-r Data 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. R 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. In this webinar Saskia Freytag, an R user with over a decade of experience and member of the [Bioconductor Community Advisory Board](https://www.bioconductor.org/about/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](https://www.rstudio.com/) 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&A session. **Who the webinar is for** Aspiring data analysts from a variety of biological fields **Presenter**: Dr Saskia Freytag, Postdoctoral Fellow, Harry Perkins Institute of Medical Research. **Date/time:** 16 August 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST **How to join** This webinar is free to join but you must register for a place in advance. **[Register here](https://unimelb.zoom.us/webinar/register/WN_j3bXauUDQwW_q64JgnvdpQ)** 2021-08-16 12:00:00 UTC 2021-08-16 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa (melissa@biocommons.org.au) [] [] 500 webinar open_to_all R softwareBioinformaticsComputer ScienceStatistics -
WORKSHOP: Hybrid de novo genome assembly
7 October 2021
WORKSHOP: Hybrid de novo genome assembly https://www.biocommons.org.au/events/hybrid-assembly https://dresa.org.au/events/workshop-hybrid-de-novo-genome-assembly It’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. In 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](https://github.com/fenderglass/Flye), [Pilon](https://github.com/broadinstitute/pilon/wiki), and [Unicycler](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005595) 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. All analyses will be performed using [Galaxy Australia](https://usegalaxy.org.au/), an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. **Date/time:** 2 - 5pm AEDT/ 1 - 4pm AEST/ 1:30 - 4:30pm ACDT/ 11am - 2pm AWST, Thursday 7 October 2021 **Lead Trainer:** Grace Hall, Melbourne Bioinformatics **Learning outcomes** By the end of this workshop you should be able to: 1. Describe how Nanopore and Illumina reads can be used together to produce a high quality assembly 2. Use genome assembly and polishing programs in Galaxy Australia 3. Assess the quality of a genome assembly with and without a reference genome 4. Assemble an unknown, previously undocumented genome to high-quality using Nanopore and Illumina reads The workshop will NOT provide an introduction to the basics of Galaxy. If you would like to learn about this topic there are several tutorials available via the [Galaxy Training Network](https://training.galaxyproject.org/training-material/). **Who the workshop is for** This workshop is for Australian researchers who are or will perform hybrid genome assembly as part of their projects. To get the most out of the workshops you must have experience with the basics of using Galaxy Australia such as setting up a history, uploading data and running tools. It is recommended that you complete the tutorial [Galaxy 101 for Everyone](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html). No programming experience is required. **How to apply** This workshop is free but participation is subject to application with selection. **_Applications close at 11:59pm AEST Wednesday 29 September 2021._** You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 1 October 2021. Successful applicants will be provided with a Zoom meeting link closer to the date. **Applications have closed** This workshop is presented by the [Australian BioCommons](https://www.biocommons.org.au/) and [Melbourne Bioinformatics](https://www.melbournebioinformatics.org.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative). To hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to the Australian BioCommons’ eNewsletter. 2021-10-07 14:00:00 UTC 2021-10-07 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] [] workshop expression_of_interest Genome assemblyde novo genome assemblyGalaxy Australia -
WORKSHOP: Refining genome annotations with Apollo
17 November 2021
WORKSHOP: Refining genome annotations with Apollo https://www.biocommons.org.au/events/apollo-2021 https://dresa.org.au/events/workshop-refining-genome-annotations-with-apollo Genome 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. Apollo 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. This workshop will make use of a training instance of the new [Australian Apollo Service](https://apollo-portal.genome.edu.au/). 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 [join our webinar](https://www.biocommons.org.au/events/apollo-launch) on 29 September 2021. **Trainers** Dr Anthony Bretaudeau (French National Institute for Agriculture, Food, and Environment), Dr Helena Rasche (Erasmus Medical Center, The Netherlands), Dr Sarah Williams (QCIF), Dr Tiffanie Nelson (Australian BioCommons) **Date/Time** 3-6pm AEDT/ 2-5pm AEST/ 2:30-5:30pm ACDT / 12-3pm AWST, Wednesday 17 Nov 2021 **Learning outcomes** By the end of the workshop you should be able to: 1. Upload data to Apollo 2. Visualise your genome and associated automated annotations 3. Manually annotate genomes after automated annotations have been performed 4. Evaluate and visualise annotated genomic features 5. Use Apollo to collaborate on genome annotation This workshop is based on [training materials](https://training.galaxyproject.org/training-material//topics/genome-annotation/tutorials/apollo/tutorial.html) developed for the Galaxy Training Network and the [Apollo User Guide](https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html#). **Who the workshop is for** This workshop is for Australian researchers who have or will work on genome annotation and manual curation/editing as part of their projects. You should be familiar with the concepts of genome annotation and have, or soon have, genome annotation files that require manual annotation and curation. You do not need access to a personal or institutional instance of Apollo for this workshop. Access to a training instance of the Australian Apollo Service will be provided. **How to apply** This workshop is free but participation is subject to application with selection. **_Applications close at 11:59pm AEDT, Thursday 4 November 2021_**. You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 12 November 2021. Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://apollo-2021.eventbrite.com.au/)** This workshop is presented by the [Australian BioCommons](https://www.biocommons.org.au/) and [Queensland Cyber Infrastructure Foundation (QCIF)](https://www.qcif.edu.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative). This event is part of a series of [bioinformatics training events](https://www.biocommons.org.au/events). If you'd like to hear when registrations open for other events, please [subscribe](https://www.biocommons.org.au/subscribe) to Australian BioCommons 2021-11-17 15:00:00 UTC 2021-11-17 18:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa Burke melissa@biocommons.org.au [] [] workshop expression_of_interest Genome annotationBioinformaticsGenomics -
WEBINAR: Establishing Gen3 to enable better human genome data sharing in Australia
16 - 22 February 2022
WEBINAR: Establishing Gen3 to enable better human genome data sharing in Australia https://www.biocommons.org.au/events/gen3-webinar https://dresa.org.au/events/webinar-establishing-gen3-to-enable-better-human-genome-data-sharing-in-australia Australian human genome initiatives are generating vast amounts of human genome data. There is a desire and need to share data across projects 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. Australian BioCommons has brought together a team from[ Zero Childhood Cancer](https://www.zerochildhoodcancer.org.au/) (Zero), the[ University of Melbourne Centre for Cancer Research](https://mdhs.unimelb.edu.au/centre-for-cancer-research/home) (UMCCR),[ Australian Access Federation](https://aaf.edu.au/) and[ Melbourne Bioinformatics](https://www.melbournebioinformatics.org.au/) 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. [Gen3](https://gen3.org/) 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](https://gdc.cancer.gov/),[ BloodPAC](https://www.bloodpac.org/),[ BrainCommons](https://www.braincommons.org/),[ Kids First Data Commons](https://kidsfirstdrc.org/)). In 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. **Date/time:** 16 February 2022 - 13:00-14:00 AEDT/ 12:00-13:00 AEST / 12:30 - 13:30 ACDT / 10:00-11:00 AWST **How to join:** This webinar is free to join but you must [register for a place](https://unimelb.zoom.us/webinar/register/WN_ZDfeLU_RT9CS9anotCpzZQ) in advance. 2022-02-16 13:00:00 UTC 2022-02-22 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] [] 500 webinar open_to_all BioinformaticsResearch infrastructureHuman genomics -
WORKSHOP: Introduction to Metabarcoding using Qiime2
22 February 2022
WORKSHOP: Introduction to Metabarcoding using Qiime2 https://www.biocommons.org.au/events/metabarcoding-qiime2 https://dresa.org.au/events/workshop-introduction-to-metabarcoding-using-qiime2 Metabarcoding has revolutionized 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. This 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. **Date/time:** 12 - 5pm AEDT/ 11 - 4pm AEST/ 11:30 - 4:30 ACDT/ 9am - 2pm AWST, Tuesday 22 February 2022 **Lead Trainers:** Dr Ashley Dungan (School of Bioscience, University of Melbourne) and Dr Gayle Philip (Melbourne Bioinformatics) **Learning outcomes** By the end of this workshop you should be able to: 1. Understand data and metadata formats required for Qiime2 2. Use Qiime2 to: 1. Create and interpret sequence quality data 2. Generate taxonomy reports/tables and phylogenic trees based on amplicon sequence variants 3. Compare Alpha and Beta data analysis 4. Develop publication quality graphics and statistics using 16S sequencing data 3. Assess the results to determine the influence of genotype (an intrinsic factor) and environment (an extrinsic factor) on anemone-associated bacterial communities **Who the workshop is for** This workshop is for researchers studying microbiomes as part of their projects. The workshop will be conducted in a Unix environment so basic command line knowledge (e.g. logging in to a remote machine, navigating the directory structure and copy files between the computers) is a prerequisite You should be familiar with the concepts of microbial analysis a however no previous experience with Qiime2 is required. **How to apply** This workshop is free but participation is subject to application with selection. You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered. Applications close 8 February 2022. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://intro-qiime2.eventbrite.com.au/)** This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/) and[ Melbourne Bioinformatics](https://www.melbournebioinformatics.org.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative). To hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to the Australian BioCommons’ eNewsletter. 2022-02-22 12:00:00 UTC 2022-02-22 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] [] 30 workshop expression_of_interest BioinformaticsMicrobiomeMetabarcodingMetagenomics -
WEBINAR: Conservation genomics and the age of extinction
8 March 2022
WEBINAR: Conservation genomics and the age of extinction https://www.biocommons.org.au/events/conservation-genomics-webinar https://dresa.org.au/events/webinar-conservation-genomics-and-the-age-of-extinction Biodiversity 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. In this webinar Dr Carolyn Hogg speaks about the work she has been doing with the [Threatened Species Initiative](https://threatenedspeciesinitiative.com/) 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. **Speaker: **Dr Carolyn Hogg, Australasian Wildlife Genomics Group, The University of Sydney **Who the webinar is for:** Anyone with an interest in the application of genomics to conservation biology. **How to join:** This webinar is free to join but you must [register for a place in advance](https://unimelb.zoom.us/webinar/register/WN_QLLM7rRPTB2D3OQyGhSXgw). 2022-03-08 13:00:00 UTC 2022-03-08 14:00:00 UTC Australian BioCommons Online, Online, Australia Online Online Australia Australian Biocommons Melissa Burke (melissa@biocommons.org.au) [] [] [] open_to_all Conservation genomicsThreatened SpeciesBioplatforms AustraliaThreatened Species Initiative -
Working with Sensitive Data
4 April 2022
Working with Sensitive Data https://www.qcif.edu.au/trainingcourses/working-with-sensitive-data/ https://dresa.org.au/events/working-with-sensitive-data This workshop uses practical and discussion-based training to guide researchers about identifying what constitutes sensitive data, the risks of working with sensitive data, and how to appropriately manage those risks. It covers the 'Five Safes' framework and researchers' responsibilities, and introduces ways to promote data security and mitigate disclosure risks. 2022-04-04 09:00:00 UTC 2022-04-04 11:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] webinar open_to_all [] -
Longitudinal and Mixed Model Analysis with R
6 April 2022
Longitudinal and Mixed Model Analysis with R https://www.eventbrite.com.au/e/267298455877/ https://dresa.org.au/events/longitudinal-and-mixed-model-analysis-with-r This workshop will develop participants’ understanding of the principles, methods, and interpretation of statistical models for longitudinal data (i.e. repeated measures over time) using R. The course will cover the principles of Linear Mixed Models from simple models to more complex ones and includes practical sessions getting hands-on experience of longitudinal analysis in R. 2022-04-06 09:00:00 UTC 2022-04-06 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
WEBINAR: Protection of genomic data and the Australian Privacy Act: when is genomic data ‘personal information’?
6 April 2022
WEBINAR: Protection of genomic data and the Australian Privacy Act: when is genomic data ‘personal information’? https://www.biocommons.org.au/events/law-genomic-data https://dresa.org.au/events/webinar-protection-of-genomic-data-and-the-australian-privacy-act-when-is-genomic-data-personal-information It 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. There 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: 1. those subject to the Privacy Act need to be able to confidently navigate their responsibilities 2. understanding 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 3. while 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? In 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 of more clearly identifying the legal rights and responsibilities which attach to the use and disclosure of genomic data in the future. **Speaker:** Mark Taylor, Professor in Health Law and Regulation, Melbourne Law School; Director, Health, Law and Emerging Technologies (HeLEX), University of Melbourne. **How to join:** This webinar is free to join but you must [register for a place in advance](https://unimelb.zoom.us/webinar/register/WN_zC3MlCjAQUq7sTVw8idvLA). 2022-04-06 12:00:00 UTC 2022-04-06 13:00:00 UTC Australian BioCommons Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] Life scientists 500 webinar open_to_all EthicsHuman genomicsData privacyBioinformatics -
Introduction to Unix
11 - 12 April 2022
Introduction to Unix https://www.qcif.edu.au/trainingcourses/introduction-to-unix/ https://dresa.org.au/events/introduction-to-unix The Unix shell has been around longer than most of its users have been alive. It has survived so long because it’s a power tool that allows people to do complex things with just a few keystrokes. More importantly, it helps them combine existing programs in new ways and automate repetitive tasks so they aren’t typing the same things over and over again. Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including 'high-performance computing' supercomputers). This Software Carpentry workshop will start you on a path towards using these resources effectively. 2022-04-11 09:00:00 UTC 2022-04-12 12:30:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Statistical Comparisons using R
12 April 2022
Statistical Comparisons using R https://www.qcif.edu.au/trainingcourses/statistics-for-comparisons/ https://dresa.org.au/events/statistical-comparisons-using-r This practical workshop will help participants to choose and use the appropriate standard statistical test for their data by introducing key concepts of inferential statistics in R. Participants will learn how to compute and interpret hypothesis tests for popular statistical models such as correlation, contingency tables, chi-square test, t-test and ANOVA. 2022-04-12 09:00:00 UTC 2022-04-12 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Genome Annotation with Apollo
21 April 2022
Genome Annotation with Apollo https://www.qcif.edu.au/trainingcourses/genome-annotation-apollo/ https://dresa.org.au/events/genome-annotation-with-apollo Genome 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. In this workshop we'll show you how to use Apollo to refine genome annotations using the Australian Apollo Service. 2022-04-21 09:00:00 UTC 2022-04-21 12:30:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Introduction to Programming: Plotting and Programming with Python
26 - 29 April 2022
Introduction to Programming: Plotting and Programming with Python https://www.qcif.edu.au/trainingcourses/plotting-and-programming-with-python/ https://dresa.org.au/events/introduction-to-programming-plotting-and-programming-with-python This Software Carpentry workshop will introduce the building blocks of the Python scripting environment. Participants will start by exploring the command-line interface and basic programming concepts using Unix, before moving on to learn about simple and complex data types, conditionals and looping in Python. This workshop will prepare participants to carry out batch analysis and equip them with the knowledge to start creating automated pipelines to increase data processing power and productivity. 2022-04-26 09:00:00 UTC 2022-04-29 12:30:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Exploring and Predicting using Linear Regression with R
11 May 2022
Exploring and Predicting using Linear Regression with R https://www.qcif.edu.au/trainingcourses/exploring-and-predicting-using-linear-regression/ https://dresa.org.au/events/exploring-and-predicting-using-linear-regression-with-r This workshop is designed to increase participants understanding of statistical relationships between data. It introduces principles and methods of regression models using R, and how to interpret relationships between variables. The course covers basic principles of regression methods through to interpreting the output of statistical analyses, and also includes practical sessions giving hands-on experience with regression analysis in R. 2022-05-11 09:00:00 UTC 2022-05-11 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Data Storytelling
11 May 2022
Data Storytelling https://www.qcif.edu.au/trainingcourses/data-storytelling/ https://dresa.org.au/events/data-storytelling Research communication is much more than just writing journal papers; to maximise the impact of your work, it's vital that you make your research findings accessible and engaging to a wide audience. Data storytelling is a powerful way achieving this, by conveying your ideas in a clear and memorable way. This interactive webinar focuses on developing your data storytelling skills by introducing a range of data visualisation techniques that you can use to combine the three elements of data, visuals and narrative into a meaningful and memorable story. By using these three elements, you can weave a story about your research for an array of audiences, in a way that they will connect with and remember. 2022-05-11 13:30:00 UTC 2022-05-11 15:30:00 UTC QCIF QCIF training@qcif.edu.au [] [] webinar open_to_all [] -
Introduction to SPSS
13 May 2022
Introduction to SPSS https://www.qcif.edu.au/trainingcourses/introduction-to-spss/ https://dresa.org.au/events/introduction-to-spss This workshop will provide a hands-on introduction to the widely-used SPSS statistical analysis package. Participants will learn how to import, manage and transform datasets, and how to summarise and present data. The workshop will also include a basic introduction to statistical testing using SPSS. 2022-05-13 09:00:00 UTC 2022-05-13 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Introduction to HPC
16 May 2022
Introduction to HPC https://www.qcif.edu.au/trainingcourses/introduction-to-hpc/ https://dresa.org.au/events/introduction-to-hpc High-Performance Computing, or HPC, is the use of computers orders of magnitude faster and more powerful than even the best desktop PC. As research becomes more and more data-intensive, an ever broader range of researchers are using HPC for their data analysis. This workshop will give you an introduction to using high-performance computing systems effectively (as well as their limitations), and will introduce the basics of how to access a HPC cluster, load and use software, and submit jobs to run. 2022-05-16 09:00:00 UTC 2022-05-16 13:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop host_institution [] -
Single-cell RNA-Seq Analysis using Galaxy
17 May 2022
Single-cell RNA-Seq Analysis using Galaxy https://www.qcif.edu.au/trainingcourses/scrna-seq-analysis/ https://dresa.org.au/events/single-cell-rna-seq-analysis-using-galaxy This hands-on workshop will cover the basics of single-cell RNA-Seq analysis, using the Galaxy platform. Starting from a table of gene counts we will evaluate, filter, annotate and visualise the data. We will also cover clustering, cell type identification and differential expression. The workshop will be based in Galaxy, a platform that provides a simple and user-friendly interface to bioinformatics tools. 2022-05-17 09:00:00 UTC 2022-05-17 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Making your Research Data FAIR
18 May 2022
Making your Research Data FAIR https://www.qcif.edu.au/trainingcourses/fair-data/ https://dresa.org.au/events/making-your-research-data-fair Making your Research Data FAIR is a 3-hour workshop aimed at introducing researchers to FAIR (Findable, Accessible, Interoperable and Reusable) principles. During the workshop researchers will reflect on reasons for making their research data FAIR and self-assess on how FAIR their research data is and then learn about resources available for researchers to make their data FAIR. 2022-05-18 09:00:00 UTC 2022-05-18 12:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop host_institution [] -
Introduction to Programming: R for Reproducible Scientific Analysis
23 - 26 May 2022
Introduction to Programming: R for Reproducible Scientific Analysis https://www.qcif.edu.au/trainingcourses/r-for-reproducible-scientific-analysis/ https://dresa.org.au/events/introduction-to-programming-r-for-reproducible-scientific-analysis This Software Carpentry workshop will introduce novice programmers to the R software environment, a powerful, popular and free statistical and graphical programming language. R is commonly used in many scientific disciplines for statistical analysis and its array of third-party packages. The emphasis of this workshop is to give attendees a strong foundation in the fundamentals of R, and to teach best practices for scientific computing: breaking down analyses into modular units, task automation, and encapsulation. 2022-05-23 09:00:00 UTC 2022-05-26 12:30:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
A Guide to Reproducible Research
25 May 2022
A Guide to Reproducible Research https://www.qcif.edu.au/trainingcourses/guide-to-reproducible-research/ https://dresa.org.au/events/a-guide-to-reproducible-research The idea that you can duplicate an experiment and get the same conclusion is the basis for all scientific discoveries. Reproducible research is data analysis that starts with the raw data and offers a transparent workflow to arrive at the same results and conclusions. However not all studies are replicable due to lack of information on the process. Therefore reproducibility in research is extremely important. Researchers genuinely want to make their research more reproducible, but sometimes don't know where to start and often don't have the available time to investigate or establish methods on how reproducible research can speed up every day work. We aim for the philosophy 'Be better than you were yesterday'. Reproducibility is a process, and we highlight there is no expectation to go from beginner to expert in a single workshop. Instead, we offer some steps you can take towards the reproducibility path following our Steps to Reproducible Research self paced program. 2022-05-25 13:30:00 UTC 2022-05-25 15:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] webinar open_to_all [] -
WORKSHOP: R - fundamental skills for biologists
1 - 22 June 2022
WORKSHOP: R - fundamental skills for biologists https://www.biocommons.org.au/events/fundamental-r https://dresa.org.au/events/workshop-r-fundamental-skills-for-biologists Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets. R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes. Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R. Topics covered in this workshop include: 1. Spreadsheets, organising data and first steps with R 2. Manipulating and analysing data with dplyr and joining tables 3. Data visualisation 4. Summarized experiments and getting started with Bioconductor **Lead Trainer:** Dr Saskia Freytag (Laboratory Head, Personalised Oncology Division, WEHI) **Format** This online workshop will take place over a series of three-hour sessions. You must attend all four sessions in order to get the most out of the workshop. Expert trainers will guide you through each of the topics and provide activities and take home exercises to help you put your new skills into action. Support will be provided via Slack between sessions. **Date/time:** 1, 8, 15, and 22 June 2022: 2 - 5pm AEST/ 1:30-4:30pm ACST/ 12-3pm AWST 1 June 2022: Spreadsheets, organising data and first steps with R 8 June 2022: Manipulating and analysing data with dplyr and joining tables 15 June 2022: Data visualisation 22 June 2022: Summarized experiments and getting started with Bioconductor Participants must attend all four sessions **Learning outcomes** By the end of the workshop you should be able to: 1. Organise your data for effective use 2. Use RStudio to structure your work in R and run R packages 3. Make use of objects, vectors and functions in R 4. Load, inspect and manipulate data in R 5. Use dplyr and tidyr and packages to manipulate and reshape data 6. Produce and customise scatter plots, box plots, line plots, etc. using ggplot 7. Combine data spread across multiple tables 8. Use the SummarizedExperiment package to store and handle omics data 9. Have some familiarity with Bioconductor 10. Identify sources of help and support from the R community **Who the workshop is for** This workshop is for Australian life science researchers who are using, or intend to use, R to analyse their data. This workshop is suitable for absolute beginners or those who wish to go back to basics to ensure they are using R and RStudio effectively. No prior knowledge of R is required. **How to apply** This workshop is free but participation is subject to application with selection. Applications close at **11:59pm AEST Wednesday 11 May 2022**. You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://r-fundamentals.eventbrite.com.au/)** This event is part of a series of[ bioinformatics training events](https://www.biocommons.org.au/events). If you'd like to hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to Australian BioCommons. 2022-06-01 12:00:00 UTC 2022-06-22 17:00:00 UTC Australian BioCommons Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] Life scientists 50 workshop expression_of_interest RRStudioBioinformaticsLife scienceData analysisData visualisation -
Statistical Comparisons using SPSS
6 June 2022
Statistical Comparisons using SPSS https://www.qcif.edu.au/trainingcourses/stat-comparisons-spss/ https://dresa.org.au/events/statistical-comparisons-using-spss This practical workshop will help participants to choose and use the appropriate standard statistical test for their data by introducing key concepts of inferential statistics in SPSS. Participants will learn how to compute and interpret hypothesis tests for popular statistical models such as correlation, contingency tables, chi-square test, t-test and ANOVA. 2022-06-06 09:00:00 UTC 2022-06-06 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Longitudinal and Mixed Model Analysis with R
9 June 2022
Longitudinal and Mixed Model Analysis with R https://www.qcif.edu.au/trainingcourses/longitudinal-and-mixed-model-analysis/ https://dresa.org.au/events/longitudinal-and-mixed-model-analysis-with-r-33c3cd7d-3991-4056-a363-6b33560de5ef This workshop will develop participants’ understanding of the principles, methods, and interpretation of statistical models for longitudinal data (i.e. repeated measures over time) using R. The course will cover the principles of Linear Mixed Models from simple models to more complex ones and includes practical sessions getting hands-on experience of longitudinal analysis in R. 2022-06-09 09:00:00 UTC 2022-06-09 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Statistical Comparisons using R
14 June 2022
Statistical Comparisons using R https://www.qcif.edu.au/trainingcourses/statistics-for-comparisons/ https://dresa.org.au/events/statistical-comparisons-using-r-0193b73f-58db-433b-bdf6-958245487b21 This practical workshop will help participants to choose and use the appropriate standard statistical test for their data by introducing key concepts of inferential statistics in R. Participants will learn how to compute and interpret hypothesis tests for popular statistical models such as correlation, contingency tables, chi-square test, t-test and ANOVA. 2022-06-14 09:00:00 UTC 2022-06-14 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Metagenomics Analysis using Galaxy
15 June 2022
Metagenomics Analysis using Galaxy https://www.qcif.edu.au/trainingcourses/metagenomics-analysis-using-galaxy/ https://dresa.org.au/events/metagenomics-analysis-using-galaxy This workshop will cover the concepts of 16S bacterial metagenomics analysis. You will learn about pre-processing and quality-filtering of your data, assembly of reads into Operational Taxonomic Units (OTUs), and visualisation and export of data for further analysis. The workshop will be based in Galaxy, a platform that provides a simple and user-friendly interface to bioinformatics tools. 2022-06-15 09:00:00 UTC 2022-06-15 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop open_to_all [] -
Introduction to Reproducible Research
17 June 2022
Introduction to Reproducible Research https://www.qcif.edu.au/trainingcourses/intro-to-reproducible-research/ https://dresa.org.au/events/introduction-to-reproducible-research An Introduction to Reproducible Research is a 3-hour workshop aimed at introducing researchers to concepts, tools and practices to make their research workflows, data and results reproducible. The workshop challenges participants to use available tools and existing support to increase their research impact, quality and reproducibility through traditional and non-traditional outputs. 2022-06-17 09:00:00 UTC 2022-06-17 12:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop host_institution []

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