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21 event found

Content provider: Australian BioCommons 

  • WEBINAR: Getting started with containers

    12 May 2021

    WEBINAR: Getting started with containers 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://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://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://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://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://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://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://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://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
  • 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://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
  • WORKSHOP: R - fundamental skills for biologists

    1 - 22 June 2022

    WORKSHOP: R - fundamental skills for biologists 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
  • WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software

    21 June 2022

    WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software https://dresa.org.au/events/webinar-bio-tools-making-it-easier-to-find-understand-and-cite-biological-tools-and-software [bio.tools](https://bio.tools/) provides easy access to essential scientific and technical information about software, command-line tools, databases and services. It’s backed by ELIXIR, the European Infrastructure for Biological Information, and is being used in Australia to register software (e.g.[ Galaxy Australia](https://bio.tools/galaxy_australia),[ prokka](https://bio.tools/prokka)). It underpins the information provided in the Australian BioCommons discovery service[ ToolFinder](https://australianbiocommons.github.io/2_tools.html). Hans Ienasescu joins us to explain how bio.tools uses a community driven, open science model to create this collection of resources and how it makes it easier to find, understand, utilise and cite them. He’ll delve into how bio.tools is using standard semantics (e.g. the EDAM ontology) and syntax (e.g. biotoolsSchema) to enrich the annotation and description of tools and resources. Finally, we’ll see how the community can contribute to bio.tools and take advantage of its key features to share and promote their own research software. **Speaker:** Hans Ienasescu, Scientific Programmer / Data Administrator / Lead Curator Technical University of Denmark Matus Kalas, Researcher, Computational Biology Unit, University of Bergen **Who the webinar is for:** Life scientists, bioinformaticians and those seeking to use, develop and share research software, tools, databases and services as well as those interested in supporting the visibility of research software. **Date/time:** 21 June 2022 - 15:00-16:00 AEST / 14:30 - 15:30 ACST / 13:00-14:00 AWST ([check in your timezone](https://www.timeanddate.com/worldclock/fixedtime.html?ah=1&iso=20220621T15&msg=Biotools%20webinar&p1=47)) **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_A6meGIuiQseViSsQp-9TwQ)** 2022-06-21 15:00:00 UTC 2022-06-21 16:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] 500 webinar open_to_all research softwareopen sciencebio.toolsToolsBioinformatics
  • MEETING: BioChats

    5 July 2022

    MEETING: BioChats https://dresa.org.au/events/meeting-biochats We're inviting all our researcher friends to join us for a regular online chat about life science research, bioinformatics and research infrastructure. It's a 30 min informal drop in session for researchers to share their work, trade secrets, offer tips and hacks, have a whinge - whatever. BioCommons wants to hear from life scientists about their wins and challenges when it comes to doing bioinformatics and research computing so we can help make it better. This week we will be hearing from: Dr Gareth Price, Service Manager Galaxy Australia, QLD Cyber Infrastructure Foundation on '“Code Free" bioinformatics' & Dr Kate Farquharson, Postdoctoral Bioinformatician, University of Sydney on 'Progress and challenges in the bioinformatics of non-model organisms' Please join us at the next BioChat - everyone is welcome! The link to join is here: https://aarnet.zoom.us/meeting/register/tZcof-msqTosHNXqzjwfLqD4MrTbNH3hRkQP We have a[ forward schedule of conversation starters](https://docs.google.com/document/d/1BdBYVCAdJ965dazCYS8kj6Hl76T7_P05wJBvKe0gPzo/edit?usp=sharing). We’d love you to[ volunteer a topic for a BioChat](https://docs.google.com/forms/d/e/1FAIpQLSdVX1HdC2w-Z52T4ETITI9Ut37maal9ZGYCpyeM19fbKr4_QQ/viewform). [Register](https://aarnet.zoom.us/meeting/register/tZcof-msqTosHNXqzjwfLqD4MrTbNH3hRkQP) anytime to receive joining instructions. 2022-07-05 12:00:00 UTC 2022-07-05 12:30:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Tiffanie Nelson tiff@biocommons.org.au [] [] 500 meeting open_to_all BioinformaticsCommunity
  • MEETING: International Galaxy Proteomics community

    20 July 2022

    MEETING: International Galaxy Proteomics community https://dresa.org.au/events/meeting-international-galaxy-proteomics-community The Galaxy Proteomics communities in the US, Australia and Europe regularly come together online to talk about topics of shared interest. All are welcome! The next international Galaxy Proteomics meeting will include a presentation on a topic of shared interest. Adam Edwinson (Mayo Clinic, Rochester, MN) will be presenting a talk on “Commensal microbiota-based regulation of intestinal proteolytic activity.” **Next meeting: July 20 2022, 2:00 AM AEST / 6:00 PM CET, 12:00 pm EDT in person at the Galaxy Community Conference!** **The meeting series aims to** 1. Introduce new users to Galaxy 1. Bring the proteomics community together in the context of Galaxy 2. Foster collaboration globally 3. Influence and build on the capabilities of Galaxy for proteomics **Let us know via email if** 1. You would like to attend, and/or 2. You use Galaxy for proteomics and would like to present in a future meeting. Visit the[ rolling meeting agenda](https://docs.google.com/document/d/10lECIsd9tqC4IXWjqcINZDSduKn-1afoN9Q5r7IW8vg/edit) for details on how to join, or send johan@biocommons.org.au a message to receive meeting instructions and updates via email. 2022-07-20 02:00:00 UTC 2022-07-20 03:00:00 UTC Galaxy Proteomics Community Online, Australia Online Australia Australian BiocommonsGalaxy International Community Johan Gustafsson johan@biocommons.org.au [] [] meeting open_to_all BioinformaticsGalaxy ProjectProteomics
  • MEETING: Australian metabolomics community

    26 July 2022

    MEETING: Australian metabolomics community https://dresa.org.au/events/meeting-australian-metabolomics-community Members of the Australian metabolomics community meet regularly to discuss bioinformatics methods and challenges in metabolomics. Everyone is welcome, so if you are interested please join the discussion. _The next meeting will be on the 26th of July 2022_ **The meeting series aims to** 1. Grow a community of metabolomics researchers interested in bioinformatics methods, tools and workflows 2. Provide further opportunities for collaboration within the community 3. Foster knowledge sharing within Australia and where possible also with international peer communities 4. Provide a forum for the BioCommons to continue consulting the metabolomics community regarding their challenges, and how Australian computational infrastructure can be made fit-for-purpose for metabolomics. Visit the[ rolling meeting agenda](https://docs.google.com/document/d/1vatTUWOkksio6qNf9qCVblpDk4G9FK-9WZTyX2_wBoE/edit#heading=h.ad4jz0hlay4q) for details on how to join. To receive joining instructions and updates via email, or keep up to date with events and announcements related to the Australian metabolomics community, you are invited to join the Australian BioCommons[ Metabolomics Community GoogleGroup](https://www.biocommons.org.au/metabolomics-community). 2022-07-26 13:30:00 UTC 2022-07-26 14:30:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons Johan Gustafsson johan@biocommons.org.au [] [] meeting open_to_all MetabolomicsBioinformaticsCommunity
  • MEETING: BioChats

    2 August 2022

    MEETING: BioChats https://dresa.org.au/events/meeting-biochats-e1f3c1fc-a09e-4c34-a6c3-e94d3c413811 We're inviting all our researcher friends to join us for a regular online chat about life science research, bioinformatics and research infrastructure. It's a 30 min informal drop in session for researchers to share their work, trade secrets, offer tips and hacks, have a whinge - whatever. BioCommons wants to hear from life scientists about their wins and challenges when it comes to doing bioinformatics and research computing so we can help make it better. This month we will be hearing from Dr Anna Syme, Bioinformatician, Melbourne Bioinformatics on 'Genomes - what are they good for?" & Ms Jess Chung, Bioinformatician, Melbourne Bioinformatics on 'Direct-to-Consumer Genomic Sequencing Considerations' Please join us at the next BioChat - everyone is welcome! We have a[ forward schedule of conversation starters](https://docs.google.com/document/d/1BdBYVCAdJ965dazCYS8kj6Hl76T7_P05wJBvKe0gPzo/edit?usp=sharing). We’d love you to[ volunteer a topic for a BioChat](https://docs.google.com/forms/d/e/1FAIpQLSdVX1HdC2w-Z52T4ETITI9Ut37maal9ZGYCpyeM19fbKr4_QQ/viewform). [Register](https://aarnet.zoom.us/meeting/register/tZcof-msqTosHNXqzjwfLqD4MrTbNH3hRkQP) anytime to receive joining instructions. 2022-08-02 12:00:00 UTC 2022-08-02 12:30:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Tiffanie Nelson tiff@biocommons.org.au [] [] 500 meeting open_to_all BioinformaticsCommunity
  • WORKSHOP: Single cell RNAseq analysis in R

    22 - 23 August 2022

    WORKSHOP: Single cell RNAseq analysis in R https://dresa.org.au/events/workshop-single-cell-rnaseq-analysis-in-r Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using[ Seurat](https://satijalab.org/seurat/index.html) - an R package for QC, analysis, and exploration of single-cell RNAseq data. We will discuss the ‘why’ behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data. **Lead trainers:** Dr Sarah Williams, Senior Bioinformatician, QCIF Mr Nick Matigan, Biostatistician and Bioinformatician, QCIF Dr Ahmed Mehdi, Senior Biostatistician, QCIF **Format** This online workshop will take place over two half-day sessions. You must attend both sessions. Expert trainers will guide you through each of the topics and provide activities to help you put your new skills into action. **Date/Time:** 22 and 23 August 2022, 1-5pm AEST/ ACST/AWST **Location:** Online **Learning outcomes:** By the end of the workshop you should be able to: 1. Load gene counts into a Seurat format 2. Perform QC and select cells for further analysis 3. Filter and normalise scRNAseq data 4. Cluster cells and identify cluster markers 5. Visualise scRNAseq expression data **Who the workshop is for:** This workshop is for Australian researchers who have or will work on scRNAseq data as part of their projects. You must be associated with an Australian organisation for your application to be considered. This workshop will not teach you the basics of R. While you don’t need to be an expert, you require some basic familiarity with R. For example you should be able to work with tables of data, know how to load an R package, make basic plots (ideally with ggplot2). You should also have basic knowledge of single cell RNA sequencing technology. **How to apply:** This workshop is free but participation is subject to application with selection. 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. Applications close at **11:59pm AEDT, Wednesday 10 August 2022**. **[Apply here](https://biocommons-scrnaseq.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_ 2022-08-22 13:00:00 UTC 2022-08-23 17:00:00 UTC Australian BioCommons Australian Biocommons training@biocommons.org.au [] [] [] expression_of_interest Single Cell technologiesscRNAseqSeuratR software
  • WEBINAR: Getting started with whole genome mapping and variant calling on the command line

    24 August 2022

    WEBINAR: Getting started with whole genome mapping and variant calling on the command line https://dresa.org.au/events/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line Life scientists are increasingly using whole genome sequencing (WGS) to ask and answer research questions across the tree of life. Before any of this work can be done, there is the essential but challenging task of processing raw sequencing data. Processing WGS data is a computationally challenging, multi-step process used to create a map of an individual’s genome and identify genetic variant sites. The tools you use in this process and overall workflow design can look very different for different researchers, it all depends on your dataset and the research questions you’re asking. Luckily, there are lots of existing WGS processing tools and pipelines out there, but knowing where to start and what your specific needs are is hard work, no matter how experienced you are. In this webinar we will walk through the essential steps and considerations for researchers who are running and building reproducible WGS mapping and variant calling pipelines at the command line interface. We will discuss how to choose and evaluate a pipeline that is right for your dataset and research questions, and how to get access to the compute resources you need. **Who the webinar is for** This webinar is intended for life scientists who are using and building whole genome sequencing mapping and variant calling pipelines. Some familiarity with the concepts of whole genome sequencing is recommended. **Presenter:** Dr Georgina Samaha, Sydney Informatics Hub, University of Sydney **Date/time:** 24 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_ekHib2_2QYazaH06VFMPgQ)** 2022-08-24 12:00:00 UTC 2022-08-24 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] 500 webinar open_to_all BioinformaticsworkflowsWhole genome sequencingVariant callingSequence mapping
  • MEETING: BioChats

    6 September 2022

    MEETING: BioChats https://dresa.org.au/events/meeting-biochats-2c842e85-7f7c-462d-8372-c0af5732a80e We're inviting all our researcher friends to join us for a regular online chat about life science research, bioinformatics and research infrastructure. It's a 30 min informal drop in session for researchers to share their work, trade secrets, offer tips and hacks, have a whinge - whatever. BioCommons wants to hear from life scientists about their wins and challenges when it comes to doing bioinformatics and research computing so we can help make it better. Please join us at the next BioChat - everyone is welcome! We have a[ forward schedule of conversation starters](https://docs.google.com/document/d/1BdBYVCAdJ965dazCYS8kj6Hl76T7_P05wJBvKe0gPzo/edit?usp=sharing). We’d love you to[ volunteer a topic for a BioChat](https://docs.google.com/forms/d/e/1FAIpQLSdVX1HdC2w-Z52T4ETITI9Ut37maal9ZGYCpyeM19fbKr4_QQ/viewform). [Register](https://aarnet.zoom.us/meeting/register/tZcof-msqTosHNXqzjwfLqD4MrTbNH3hRkQP) anytime to receive joining instructions. 2022-09-06 12:00:00 UTC 2022-09-06 12:30:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Tiffanie Nelson tiff@biocommons.org.au [] [] 500 meeting open_to_all BioinformaticsCommunity
  • WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud

    20 September 2022

    WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud https://dresa.org.au/events/webinar-portable-reproducible-and-scalable-bioinformatics-workflows-using-nextflow-and-pawsey-nimbus-cloud Bioinformatics workflows can support portable, reproducible and scalable analysis of omics datasets but using workflows can be challenging for both beginners and experienced bioinformaticians. Beginners face a steep learning curve to be able to build and deploy their own bioinformatics workflows while those with more experience face challenges productionising and scaling code for custom workflows and big data. Bioinformaticians across the world are using Nextflow to build and manage workflows. Many of these workflows are shared for others to use and supported by the community via [nf-co.re](https://nf-co.re/). So far, [39 workflows for omics data](https://nf-co.re/pipelines) are available with another 23 under development. These workflows cover common analyses such as RNAseq, mapping, variant calling, single cell transcriptomics and more and can be easily deployed by anyone, regardless of skill level. In this webinar, Nandan Deshpande from the Sydney Informatics Hub, University of Sydney, will discuss how you can deploy freely available Nextflow (nf.co-re) bioinformatics workflows with a single command. We describe how you can quickly get started deploying these workflows using Pawsey Nimbus Cloud. For advanced users, we show you how you can use Nextflow to build your own workflows that save you time and support reproducible, portable and scalable analysis. In the latter half of the webinar, Sarah Beecroft from the Pawsey Supercomputing Research Centre will talk about their Nimbus Cloud systems. While Nextflow supports portability and can run on many computing infrastructures, we describe why we specifically love using Nimbus with Nextflow for many bioinformatics projects. We will describe some of the nf.co-re workflows that we have used on Nimbus and the research outcomes. We will also cover when not to use Nimbus and the alternatives we recommend. **Speakers:** Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Sarah Beecroft, Bioinformatics Applications Specialist, Pawsey Supercomputing Research Centre. **Who the webinar is for:** This webinar is for biologists who are new to bioinformatics on the command-line and bioinformaticians and would like to use existing best practice workflows available through nf.co-re. **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_P54j05SaQ6qbQz8h0Su_Zw)** 2022-09-20 12:00:00 UTC 2022-09-20 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] webinar open_to_all Nextflownf-coreWorkflowsBioinformaticsReproducibility
  • WORKSHOP: RNA-Seq: reads to differential genes and pathways

    27 - 28 September 2022

    WORKSHOP: RNA-Seq: reads to differential genes and pathways https://dresa.org.au/events/workshop-rna-seq-reads-to-differential-genes-and-pathways RNA sequencing (RNA-seq) is a common method used to understand the differences in gene expression and molecular pathways between two or more groups. This workshop introduces the fundamental concepts of RNA sequencing experiments and will allow you to try out the analysis using data from a study of Williams-Beuren Syndrome, a rare disease. In the first part of the workshop you will learn how to convert sequence reads into analysis ready count data. To do this we will use[ nf-core/rnaseq](https://nf-co.re/rnaseq/usage) - a portable, scalable, reproducible and publicly available workflow on[ Pawsey Nimbus Cloud](https://pawsey.org.au/systems/nimbus-cloud-service/). In the second part of the workshop you will use the count data you created to identify differential genes and pathways using R/Rstudio. By the end of the workshop, you should be able to perform your own RNA-seq analysis for differential gene expression and pathway analysis! **Lead Trainers:** Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub **Date/Time**: 27 & 28 September 2022, 2-5pm AEST/1:30-4:30pm ACST/12-3pm AWST **Format:** This online workshop will take place over two three-hour sessions. You must attend both sessions in order to get the most out of the workshop. Expert trainers will introduce new topics and guide you through hands-on activities to help you put your new skills into action. **Learning outcomes:** By the end of the workshop you should be able to: 1. List the steps involved in analysis of RNA-seq data 2. Describe key concepts and considerations for RNA-seq experiments 3. Describe the benefits of using nf-core workflows 4. Deploy an RNA-seq nf-core workflow on Pawsey’s Nimbus Cloud to perform: 1. Quality control 2. Alignment 3. Quantification to generate raw counts 5. Use R/RStudio on Pawsey’s Nimbus Cloud to perform 4. Quality control 5. Identify differentially expressed genes using DESeq2 6. Perform functional enrichment/pathway analysis **Who the workshop is for:** This workshop is for Australian researchers who have or will work on RNAseq data as part of their projects. You must be associated with an Australian organisation for your application to be considered. The workshop will be conducted in a Unix environment and will use R/RStudio. Basic command line knowledge is required. You must know how to navigate the directory structure and copy files between the computers. If you need a refresher on Unix/Linux try[ this online tutorial](https://linuxjourney.com/lesson/the-shell). Basic knowledge of R/RStudio is required. You must know how to set up directories, run commands, reading in and outputting files. If you need a refresher on R/RStudio try the[ Introduction to R and RStudio section](https://swcarpentry.github.io/r-novice-gapminder/01-rstudio-intro/index.html) of this online tutorial. It’s recommended that you watch the webinar[ Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud](http://biocommons.org.au/events/nextflow-nimbus) in advance. You may join this webinar live on 20 September 2022. A recording will be posted on the[ Australian BioCommons YouTube Channel](https://www.youtube.com/c/AustralianBioCommonsChannel). **How to apply:** This workshop is free but participation is subject to application with selection. Applications close at **11:59pm AEST, Sunday 11 September 2022**. 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://biocommons-rnaseq-2022.eventbrite.com.au/)** _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/), Sydney Informatics Hub and Pawsey Supercomputing Research Centre 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_ 2022-09-27 14:00:00 UTC 2022-09-28 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] workshop expression_of_interest BioinformaticsRNA-seqGene ExpressionPathway analysisNextflownf-coreWorkflowsFunctional analysis
  • WEBINAR: Getting started with containers

    12 May 2021

    WEBINAR: Getting started with containers 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://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://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://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://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://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://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://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://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
  • 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://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
  • WORKSHOP: R - fundamental skills for biologists

    1 - 22 June 2022

    WORKSHOP: R - fundamental skills for biologists 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
  • WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software

    21 June 2022

    WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software https://dresa.org.au/events/webinar-bio-tools-making-it-easier-to-find-understand-and-cite-biological-tools-and-software [bio.tools](https://bio.tools/) provides easy access to essential scientific and technical information about software, command-line tools, databases and services. It’s backed by ELIXIR, the European Infrastructure for Biological Information, and is being used in Australia to register software (e.g.[ Galaxy Australia](https://bio.tools/galaxy_australia),[ prokka](https://bio.tools/prokka)). It underpins the information provided in the Australian BioCommons discovery service[ ToolFinder](https://australianbiocommons.github.io/2_tools.html). Hans Ienasescu joins us to explain how bio.tools uses a community driven, open science model to create this collection of resources and how it makes it easier to find, understand, utilise and cite them. He’ll delve into how bio.tools is using standard semantics (e.g. the EDAM ontology) and syntax (e.g. biotoolsSchema) to enrich the annotation and description of tools and resources. Finally, we’ll see how the community can contribute to bio.tools and take advantage of its key features to share and promote their own research software. **Speaker:** Hans Ienasescu, Scientific Programmer / Data Administrator / Lead Curator Technical University of Denmark Matus Kalas, Researcher, Computational Biology Unit, University of Bergen **Who the webinar is for:** Life scientists, bioinformaticians and those seeking to use, develop and share research software, tools, databases and services as well as those interested in supporting the visibility of research software. **Date/time:** 21 June 2022 - 15:00-16:00 AEST / 14:30 - 15:30 ACST / 13:00-14:00 AWST ([check in your timezone](https://www.timeanddate.com/worldclock/fixedtime.html?ah=1&iso=20220621T15&msg=Biotools%20webinar&p1=47)) **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_A6meGIuiQseViSsQp-9TwQ)** 2022-06-21 15:00:00 UTC 2022-06-21 16:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] 500 webinar open_to_all research softwareopen sciencebio.toolsToolsBioinformatics
  • MEETING: BioChats

    5 July 2022

    MEETING: BioChats https://dresa.org.au/events/meeting-biochats We're inviting all our researcher friends to join us for a regular online chat about life science research, bioinformatics and research infrastructure. It's a 30 min informal drop in session for researchers to share their work, trade secrets, offer tips and hacks, have a whinge - whatever. BioCommons wants to hear from life scientists about their wins and challenges when it comes to doing bioinformatics and research computing so we can help make it better. This week we will be hearing from: Dr Gareth Price, Service Manager Galaxy Australia, QLD Cyber Infrastructure Foundation on '“Code Free" bioinformatics' & Dr Kate Farquharson, Postdoctoral Bioinformatician, University of Sydney on 'Progress and challenges in the bioinformatics of non-model organisms' Please join us at the next BioChat - everyone is welcome! The link to join is here: https://aarnet.zoom.us/meeting/register/tZcof-msqTosHNXqzjwfLqD4MrTbNH3hRkQP We have a[ forward schedule of conversation starters](https://docs.google.com/document/d/1BdBYVCAdJ965dazCYS8kj6Hl76T7_P05wJBvKe0gPzo/edit?usp=sharing). We’d love you to[ volunteer a topic for a BioChat](https://docs.google.com/forms/d/e/1FAIpQLSdVX1HdC2w-Z52T4ETITI9Ut37maal9ZGYCpyeM19fbKr4_QQ/viewform). [Register](https://aarnet.zoom.us/meeting/register/tZcof-msqTosHNXqzjwfLqD4MrTbNH3hRkQP) anytime to receive joining instructions. 2022-07-05 12:00:00 UTC 2022-07-05 12:30:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Tiffanie Nelson tiff@biocommons.org.au [] [] 500 meeting open_to_all BioinformaticsCommunity
  • MEETING: International Galaxy Proteomics community

    20 July 2022

    MEETING: International Galaxy Proteomics community https://dresa.org.au/events/meeting-international-galaxy-proteomics-community The Galaxy Proteomics communities in the US, Australia and Europe regularly come together online to talk about topics of shared interest. All are welcome! The next international Galaxy Proteomics meeting will include a presentation on a topic of shared interest. Adam Edwinson (Mayo Clinic, Rochester, MN) will be presenting a talk on “Commensal microbiota-based regulation of intestinal proteolytic activity.” **Next meeting: July 20 2022, 2:00 AM AEST / 6:00 PM CET, 12:00 pm EDT in person at the Galaxy Community Conference!** **The meeting series aims to** 1. Introduce new users to Galaxy 1. Bring the proteomics community together in the context of Galaxy 2. Foster collaboration globally 3. Influence and build on the capabilities of Galaxy for proteomics **Let us know via email if** 1. You would like to attend, and/or 2. You use Galaxy for proteomics and would like to present in a future meeting. Visit the[ rolling meeting agenda](https://docs.google.com/document/d/10lECIsd9tqC4IXWjqcINZDSduKn-1afoN9Q5r7IW8vg/edit) for details on how to join, or send johan@biocommons.org.au a message to receive meeting instructions and updates via email. 2022-07-20 02:00:00 UTC 2022-07-20 03:00:00 UTC Galaxy Proteomics Community Online, Australia Online Australia Australian BiocommonsGalaxy International Community Johan Gustafsson johan@biocommons.org.au [] [] meeting open_to_all BioinformaticsGalaxy ProjectProteomics
  • MEETING: Australian metabolomics community

    26 July 2022

    MEETING: Australian metabolomics community https://dresa.org.au/events/meeting-australian-metabolomics-community Members of the Australian metabolomics community meet regularly to discuss bioinformatics methods and challenges in metabolomics. Everyone is welcome, so if you are interested please join the discussion. _The next meeting will be on the 26th of July 2022_ **The meeting series aims to** 1. Grow a community of metabolomics researchers interested in bioinformatics methods, tools and workflows 2. Provide further opportunities for collaboration within the community 3. Foster knowledge sharing within Australia and where possible also with international peer communities 4. Provide a forum for the BioCommons to continue consulting the metabolomics community regarding their challenges, and how Australian computational infrastructure can be made fit-for-purpose for metabolomics. Visit the[ rolling meeting agenda](https://docs.google.com/document/d/1vatTUWOkksio6qNf9qCVblpDk4G9FK-9WZTyX2_wBoE/edit#heading=h.ad4jz0hlay4q) for details on how to join. To receive joining instructions and updates via email, or keep up to date with events and announcements related to the Australian metabolomics community, you are invited to join the Australian BioCommons[ Metabolomics Community GoogleGroup](https://www.biocommons.org.au/metabolomics-community). 2022-07-26 13:30:00 UTC 2022-07-26 14:30:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons Johan Gustafsson johan@biocommons.org.au [] [] meeting open_to_all MetabolomicsBioinformaticsCommunity
  • MEETING: BioChats

    2 August 2022

    MEETING: BioChats https://dresa.org.au/events/meeting-biochats-e1f3c1fc-a09e-4c34-a6c3-e94d3c413811 We're inviting all our researcher friends to join us for a regular online chat about life science research, bioinformatics and research infrastructure. It's a 30 min informal drop in session for researchers to share their work, trade secrets, offer tips and hacks, have a whinge - whatever. BioCommons wants to hear from life scientists about their wins and challenges when it comes to doing bioinformatics and research computing so we can help make it better. This month we will be hearing from Dr Anna Syme, Bioinformatician, Melbourne Bioinformatics on 'Genomes - what are they good for?" & Ms Jess Chung, Bioinformatician, Melbourne Bioinformatics on 'Direct-to-Consumer Genomic Sequencing Considerations' Please join us at the next BioChat - everyone is welcome! We have a[ forward schedule of conversation starters](https://docs.google.com/document/d/1BdBYVCAdJ965dazCYS8kj6Hl76T7_P05wJBvKe0gPzo/edit?usp=sharing). We’d love you to[ volunteer a topic for a BioChat](https://docs.google.com/forms/d/e/1FAIpQLSdVX1HdC2w-Z52T4ETITI9Ut37maal9ZGYCpyeM19fbKr4_QQ/viewform). [Register](https://aarnet.zoom.us/meeting/register/tZcof-msqTosHNXqzjwfLqD4MrTbNH3hRkQP) anytime to receive joining instructions. 2022-08-02 12:00:00 UTC 2022-08-02 12:30:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Tiffanie Nelson tiff@biocommons.org.au [] [] 500 meeting open_to_all BioinformaticsCommunity
  • WORKSHOP: Single cell RNAseq analysis in R

    22 - 23 August 2022

    WORKSHOP: Single cell RNAseq analysis in R https://dresa.org.au/events/workshop-single-cell-rnaseq-analysis-in-r Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using[ Seurat](https://satijalab.org/seurat/index.html) - an R package for QC, analysis, and exploration of single-cell RNAseq data. We will discuss the ‘why’ behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data. **Lead trainers:** Dr Sarah Williams, Senior Bioinformatician, QCIF Mr Nick Matigan, Biostatistician and Bioinformatician, QCIF Dr Ahmed Mehdi, Senior Biostatistician, QCIF **Format** This online workshop will take place over two half-day sessions. You must attend both sessions. Expert trainers will guide you through each of the topics and provide activities to help you put your new skills into action. **Date/Time:** 22 and 23 August 2022, 1-5pm AEST/ ACST/AWST **Location:** Online **Learning outcomes:** By the end of the workshop you should be able to: 1. Load gene counts into a Seurat format 2. Perform QC and select cells for further analysis 3. Filter and normalise scRNAseq data 4. Cluster cells and identify cluster markers 5. Visualise scRNAseq expression data **Who the workshop is for:** This workshop is for Australian researchers who have or will work on scRNAseq data as part of their projects. You must be associated with an Australian organisation for your application to be considered. This workshop will not teach you the basics of R. While you don’t need to be an expert, you require some basic familiarity with R. For example you should be able to work with tables of data, know how to load an R package, make basic plots (ideally with ggplot2). You should also have basic knowledge of single cell RNA sequencing technology. **How to apply:** This workshop is free but participation is subject to application with selection. 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. Applications close at **11:59pm AEDT, Wednesday 10 August 2022**. **[Apply here](https://biocommons-scrnaseq.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_ 2022-08-22 13:00:00 UTC 2022-08-23 17:00:00 UTC Australian BioCommons Australian Biocommons training@biocommons.org.au [] [] [] expression_of_interest Single Cell technologiesscRNAseqSeuratR software
  • WEBINAR: Getting started with whole genome mapping and variant calling on the command line

    24 August 2022

    WEBINAR: Getting started with whole genome mapping and variant calling on the command line https://dresa.org.au/events/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line Life scientists are increasingly using whole genome sequencing (WGS) to ask and answer research questions across the tree of life. Before any of this work can be done, there is the essential but challenging task of processing raw sequencing data. Processing WGS data is a computationally challenging, multi-step process used to create a map of an individual’s genome and identify genetic variant sites. The tools you use in this process and overall workflow design can look very different for different researchers, it all depends on your dataset and the research questions you’re asking. Luckily, there are lots of existing WGS processing tools and pipelines out there, but knowing where to start and what your specific needs are is hard work, no matter how experienced you are. In this webinar we will walk through the essential steps and considerations for researchers who are running and building reproducible WGS mapping and variant calling pipelines at the command line interface. We will discuss how to choose and evaluate a pipeline that is right for your dataset and research questions, and how to get access to the compute resources you need. **Who the webinar is for** This webinar is intended for life scientists who are using and building whole genome sequencing mapping and variant calling pipelines. Some familiarity with the concepts of whole genome sequencing is recommended. **Presenter:** Dr Georgina Samaha, Sydney Informatics Hub, University of Sydney **Date/time:** 24 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_ekHib2_2QYazaH06VFMPgQ)** 2022-08-24 12:00:00 UTC 2022-08-24 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] 500 webinar open_to_all BioinformaticsworkflowsWhole genome sequencingVariant callingSequence mapping
  • MEETING: BioChats

    6 September 2022

    MEETING: BioChats https://dresa.org.au/events/meeting-biochats-2c842e85-7f7c-462d-8372-c0af5732a80e We're inviting all our researcher friends to join us for a regular online chat about life science research, bioinformatics and research infrastructure. It's a 30 min informal drop in session for researchers to share their work, trade secrets, offer tips and hacks, have a whinge - whatever. BioCommons wants to hear from life scientists about their wins and challenges when it comes to doing bioinformatics and research computing so we can help make it better. Please join us at the next BioChat - everyone is welcome! We have a[ forward schedule of conversation starters](https://docs.google.com/document/d/1BdBYVCAdJ965dazCYS8kj6Hl76T7_P05wJBvKe0gPzo/edit?usp=sharing). We’d love you to[ volunteer a topic for a BioChat](https://docs.google.com/forms/d/e/1FAIpQLSdVX1HdC2w-Z52T4ETITI9Ut37maal9ZGYCpyeM19fbKr4_QQ/viewform). [Register](https://aarnet.zoom.us/meeting/register/tZcof-msqTosHNXqzjwfLqD4MrTbNH3hRkQP) anytime to receive joining instructions. 2022-09-06 12:00:00 UTC 2022-09-06 12:30:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Tiffanie Nelson tiff@biocommons.org.au [] [] 500 meeting open_to_all BioinformaticsCommunity
  • WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud

    20 September 2022

    WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud https://dresa.org.au/events/webinar-portable-reproducible-and-scalable-bioinformatics-workflows-using-nextflow-and-pawsey-nimbus-cloud Bioinformatics workflows can support portable, reproducible and scalable analysis of omics datasets but using workflows can be challenging for both beginners and experienced bioinformaticians. Beginners face a steep learning curve to be able to build and deploy their own bioinformatics workflows while those with more experience face challenges productionising and scaling code for custom workflows and big data. Bioinformaticians across the world are using Nextflow to build and manage workflows. Many of these workflows are shared for others to use and supported by the community via [nf-co.re](https://nf-co.re/). So far, [39 workflows for omics data](https://nf-co.re/pipelines) are available with another 23 under development. These workflows cover common analyses such as RNAseq, mapping, variant calling, single cell transcriptomics and more and can be easily deployed by anyone, regardless of skill level. In this webinar, Nandan Deshpande from the Sydney Informatics Hub, University of Sydney, will discuss how you can deploy freely available Nextflow (nf.co-re) bioinformatics workflows with a single command. We describe how you can quickly get started deploying these workflows using Pawsey Nimbus Cloud. For advanced users, we show you how you can use Nextflow to build your own workflows that save you time and support reproducible, portable and scalable analysis. In the latter half of the webinar, Sarah Beecroft from the Pawsey Supercomputing Research Centre will talk about their Nimbus Cloud systems. While Nextflow supports portability and can run on many computing infrastructures, we describe why we specifically love using Nimbus with Nextflow for many bioinformatics projects. We will describe some of the nf.co-re workflows that we have used on Nimbus and the research outcomes. We will also cover when not to use Nimbus and the alternatives we recommend. **Speakers:** Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Sarah Beecroft, Bioinformatics Applications Specialist, Pawsey Supercomputing Research Centre. **Who the webinar is for:** This webinar is for biologists who are new to bioinformatics on the command-line and bioinformaticians and would like to use existing best practice workflows available through nf.co-re. **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_P54j05SaQ6qbQz8h0Su_Zw)** 2022-09-20 12:00:00 UTC 2022-09-20 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] webinar open_to_all Nextflownf-coreWorkflowsBioinformaticsReproducibility
  • WORKSHOP: RNA-Seq: reads to differential genes and pathways

    27 - 28 September 2022

    WORKSHOP: RNA-Seq: reads to differential genes and pathways https://dresa.org.au/events/workshop-rna-seq-reads-to-differential-genes-and-pathways RNA sequencing (RNA-seq) is a common method used to understand the differences in gene expression and molecular pathways between two or more groups. This workshop introduces the fundamental concepts of RNA sequencing experiments and will allow you to try out the analysis using data from a study of Williams-Beuren Syndrome, a rare disease. In the first part of the workshop you will learn how to convert sequence reads into analysis ready count data. To do this we will use[ nf-core/rnaseq](https://nf-co.re/rnaseq/usage) - a portable, scalable, reproducible and publicly available workflow on[ Pawsey Nimbus Cloud](https://pawsey.org.au/systems/nimbus-cloud-service/). In the second part of the workshop you will use the count data you created to identify differential genes and pathways using R/Rstudio. By the end of the workshop, you should be able to perform your own RNA-seq analysis for differential gene expression and pathway analysis! **Lead Trainers:** Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub **Date/Time**: 27 & 28 September 2022, 2-5pm AEST/1:30-4:30pm ACST/12-3pm AWST **Format:** This online workshop will take place over two three-hour sessions. You must attend both sessions in order to get the most out of the workshop. Expert trainers will introduce new topics and guide you through hands-on activities to help you put your new skills into action. **Learning outcomes:** By the end of the workshop you should be able to: 1. List the steps involved in analysis of RNA-seq data 2. Describe key concepts and considerations for RNA-seq experiments 3. Describe the benefits of using nf-core workflows 4. Deploy an RNA-seq nf-core workflow on Pawsey’s Nimbus Cloud to perform: 1. Quality control 2. Alignment 3. Quantification to generate raw counts 5. Use R/RStudio on Pawsey’s Nimbus Cloud to perform 4. Quality control 5. Identify differentially expressed genes using DESeq2 6. Perform functional enrichment/pathway analysis **Who the workshop is for:** This workshop is for Australian researchers who have or will work on RNAseq data as part of their projects. You must be associated with an Australian organisation for your application to be considered. The workshop will be conducted in a Unix environment and will use R/RStudio. Basic command line knowledge is required. You must know how to navigate the directory structure and copy files between the computers. If you need a refresher on Unix/Linux try[ this online tutorial](https://linuxjourney.com/lesson/the-shell). Basic knowledge of R/RStudio is required. You must know how to set up directories, run commands, reading in and outputting files. If you need a refresher on R/RStudio try the[ Introduction to R and RStudio section](https://swcarpentry.github.io/r-novice-gapminder/01-rstudio-intro/index.html) of this online tutorial. It’s recommended that you watch the webinar[ Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud](http://biocommons.org.au/events/nextflow-nimbus) in advance. You may join this webinar live on 20 September 2022. A recording will be posted on the[ Australian BioCommons YouTube Channel](https://www.youtube.com/c/AustralianBioCommonsChannel). **How to apply:** This workshop is free but participation is subject to application with selection. Applications close at **11:59pm AEST, Sunday 11 September 2022**. 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://biocommons-rnaseq-2022.eventbrite.com.au/)** _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/), Sydney Informatics Hub and Pawsey Supercomputing Research Centre 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_ 2022-09-27 14:00:00 UTC 2022-09-28 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] workshop expression_of_interest BioinformaticsRNA-seqGene ExpressionPathway analysisNextflownf-coreWorkflowsFunctional analysis

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