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108 events found

Keywords: Setonix  or Bioinformatics  or Science & Technology 

  • 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
  • Single Cell RNA-Seq Analysis Using Galaxy

    27 October 2021

    Single Cell RNA-Seq Analysis Using Galaxy https://dresa.org.au/events/single-cell-rna-seq-analysis-using-galaxy-10c1ee79-508a-44bf-8454-e2c928e8c5f5 This hands-on workshop will cover the basics of single cell RNAseq analysis, using the Galaxy platform. Starting from a table of gene counts we will evaluate, filter, annotate and visualise the data. We will also cover clustering, cell type identification and differential expression. Galaxy Australia is a platform that provides a simple and user-friendly interface to bioinformatics tools. The output we will generate is suitable for further analysis within Galaxy Australia, or locally. 2021-10-27 09:00:00 UTC 2021-10-27 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] Life scientists planning or running single cell RNAseq experiments (or mining public data), who want to perform their own analyses. 30 workshop open_to_all RNASeqGalaxy AustraliaBioinformatics
  • Australian BioCommons 2021 Showcase

    3 - 5 November 2021

    Australian BioCommons 2021 Showcase https://dresa.org.au/events/australian-biocommons-2021-showcase Australian BioCommons projects draw key players together to deliver complex enhancements and new solutions for the digital life sciences. Join us to discover the breadth of our activities, review the impact we’re having and connect over a collaborative vision for the future of Australian bioinformatics and bioscience research infrastructure. We’ll meet online over three afternoons to share achievements, challenges and future directions. We invite existing partners, potential contributors and interested colleagues to learn more about all aspects of the Australian BioCommons, and meet the wide network of peers working hard to make these collaborative projects a success. Join us for any or all of the sessions on Wed 3 Nov 3-6pm AEDT, Thu 4 Nov 2-5pm AEDT or Fri 5 Nov 2-5pm AEDT. **[Click here for program of speakers & registration details](https://www.biocommons.org.au/events/2021-showcase)** 2021-11-03 15:00:00 UTC 2021-11-05 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Christina Hall (christina@biocommons.org.au) [] [] 500 meeting open_to_all BioinformaticsReference Genomes Community engagementBioCloudHuman genomicsResearch infrastructure
  • 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
  • P’Con – Exascale Data Management with ADIOS

    7 December 2021

    P’Con – Exascale Data Management with ADIOS https://dresa.org.au/events/p-con-exascale-data-management-with-adios Speakers: Speaker: Scott Klasky, Norbert Podhorszki (Oak Ridge National Laboratories) ADIOS is a high performance publish/subscribe I/O framework which has been designed and developed for the exascale computing era. In a snapshot, ADIOS: - Is integrated into most of the popular analysis and visualization packages. - Has strict continuous integration practices, providing stable, portable and efficient I/O services. - Has a programming interface designed for easy switching from files to streams (on-HPC machines) to streams over the Wide Area Network. In this presentation, the speaker will introduce the ADIOS I/O framework and describe how it is being used, including: - In data intensive supercomputing simulations, using it for data storage and retrieval moving petabytes of data in a single job, - In coupled simulations using it for data movement between the simulation codes and to in situ analysis and in situ visualization services, - In AI applications, for collecting training data from ensembles of computations on the fly, and - In collaborations between experimental facilities and HPC centers to stream experimental data for near-real-time decision making. We will present how ADIOS was used in the 2020 Gordon Bell finalist paper from Pawsey and ORNL about the workflow for simulating and processing the full-scale low-frequency telescope data of SKA Phase 1 on the Summit supercomputer at ORNL. ADIOS is also a research framework for new I/O technologies, pushing the boundaries beyond current use cases. Our research focuses on data reduction with trusted lossy compression techniques, data refactoring for easier on-demand retrieval, hierarchical storage to speed up access to the most important data, asynchronous I/O techniques and others. The techniques in ADIOS have been developed for over 15 years through collaborations with science applications, and we are always seeking new collaborations and new challenges that will define the I/O landscape of the future. We hope this presentation will allow the audience to learn about how others are using extreme I/O in their fields and also stimulate the audience to bring new challenges to us. Exascale Data Management with ADIOS session, is part of the first PaCER Conference – P’con: A week where Pawsey continues setting the pace for exascale. 2021-12-07 09:30:00 UTC 2021-12-07 11:30:00 UTC Pawsey Supercomputing Research Centre Pawsey Supercomputing Research Centre training@pawsey.org.au [] [] webinarconference open_to_all ADIOSsupercomputersupercomputingPawseyPaCERSetonix
  • P’Con – Porting multi-GPU SELF-Fluids code to HIPFort

    8 December 2021

    P’Con – Porting multi-GPU SELF-Fluids code to HIPFort https://dresa.org.au/events/p-con-porting-multi-gpu-self-fluids-code-to-hipfort Speaker: By Dr Joseph Schoonover, Fluid Numerics LLC During this talk, we will share our experience with porting process for SELF-Fluids from multi-GPU CUDA-Fortran to multi-GPU HIPFort. The talk will cover the design principles and roadmap for SELF and the strategy to port from Nvidia-only platforms to AMD & Nvidia GPUs. We’ll discuss hurdles encountered along the way and considerations for developing multi-GPU accelerated applications in Fortran. SELF is an object-oriented Fortran library that supports the implementation of Spectral Element Methods for solving partial differential equations. SELF-Fluids is an implementation of SELF that solves the compressible Navier Stokes equations on CPU only and GPU accelerated compute platforms using the Discontinuous Galerkin Spectral Element Method. The SELF API is designed based on the assumption that SEM developers and researchers need to be able to implement derivatives in 1-D and divergence, gradient, and curl in 2-D and 3-D on scalar, vector, and tensor functions using spectral collocation, continuous Galerkin, and discontinuous Galerkin spectral element methods. Additionally, as we enter the Exascale era, we are currently faced with a zoo of compute hardware that is available. Because of this, SELF routines provide support for GPU acceleration through AMD’s HIP and support for multi-core, multi-node, and multi-GPU platforms with MPI. SELF and SELF-Fluids are publicly available online at https://github.com/fluidnumerics/self Porting multi-GPU SELF-Fluids code to HIPFort, is part of the first PaCER Conference – P’con: A week where Pawsey continues setting the pace for exascale. 2021-12-08 09:30:00 UTC 2021-12-08 11:30:00 UTC Pawsey Supercomputing Research Centre Pawsey Supercomputing Research Centre training@pawsey.org.au [] [] webinarconference open_to_all GPUsHipFortsupercomputersupercomputingSetonix
  • 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
  • WORKSHOPS: Galaxy Training Smörgåsbord 2022

    14 - 18 March 2022

    WORKSHOPS: Galaxy Training Smörgåsbord 2022 https://dresa.org.au/events/workshops-galaxy-training-smorgasbord-2022 Learn how to analyse your data and use sophisticated computational workflows without the need for programming experience. The Galaxy Training Network is hosting a smörgåsbord of opportunities to learn how to use[ Galaxy](https://www.biocommons.org.au/galaxy-australia) (a free, online platform for reproducible data analysis) to analyse a huge variety of data including transcriptomics, proteomics, and next generation sequencing. Topics on offer include: 1. Introduction to Galaxy 2. NGS 3. RNA-Seq 4. Single Cell 5. Proteomics 6. SARS-CoV-2 Genomics 7. Galaxy Admin Training **Format** Online and asynchronous (at-your-own-pace) across all international time zones. All training sessions are pre-recorded, captioned and accompanied by live support from experienced instructors from the Galaxy Training community via chat and video conferencing. You can follow all of the sessions or just pick and choose the ones you’re most interested in, with the security of live help from the Galaxy Australia and Australian BioCommons teams. **Date/Time**: March 14-18, 2022 in your local timezone. **Who the workshop is for** These training sessions are suitable for researchers with no prior knowledge of Galaxy and no programming experience. **How to join** This workshop is free to join and open to everyone. Registrations are essential. **[More information and registrations](https://gallantries.github.io/posts/2021/12/14/smorgasbord2-tapas/)** _This workshop is presented by the Gallantries, Galaxy Training Network and Galaxy Training Community. The Australian BioCommons and its partners collaborate to provide the [Galaxy Australia Service](https://www.biocommons.org.au/galaxy-australia)._ 2022-03-14 09:00:00 UTC 2022-03-18 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] [] 1000 workshop open_to_all BioinformaticsGalaxy AustraliaNGSRNASeqSingle cell RNAseqProteomics
  • 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
  • What skills are needed in commercial bioinformatics?

    6 July 2022

    What skills are needed in commercial bioinformatics? https://dresa.org.au/events/becoming-a-research-software-engineer-a43878db-e1ef-488a-b5ad-eab519e7e516 It is our pleasure to announce that for our very first COMBINE Fireside Chat we will have Dr David Wood from Microba sharing with us about invaluable skills in commercial bioinformatics. This program series is an excellent opportunity for upcoming student bioinformaticians to learn more about industry-related career pathways and from the successes of industry leaders in the field. # Abstract Despite frequent classification as a specialist activity, bioinformatics is a broad discipline. Bioinformaticians work in industries that have different goals and drivers, across multiple biological domains applying expert skills and technologies. As a student with a large informatics component to your work you may wonder what skills do commercial enterprises require of bioinformaticians? [Microba Life Sciences](https://microba.com/) is a precision microbiome company driven to improve human health. With world-leading technology for measuring the human gut microbiome, Microba is driving the discovery and development of novel therapeutics for major chronic diseases and delivering gut microbiome testing services globally to researchers, clinicians, and consumers. In this presentation I will describe how we conduct bioinformatics at Microba, and what are the key skills we require of bioinformaticians. Using our cloud-based, fast-turnaround bioinformatics platform as a case study, I will explain the role and skills required for each bioinformatics team member in its’ build, validation, operation, management and evolution. # About the speaker Dr David Wood leads the research and development of bioinformatic tools and data production at Microba. Dr Wood specialises in genome informatics and bioinformatics software development and has 20 years’ experience in industry and academia across diverse life science domains. He is an author on more than 30 scientific publications. His primary interest is in the application and advancement of high-throughput genomics technologies to improve public health. [You can submit your questions to the speaker anonymously](https://forms.gle/Z31vbn9ka9x5Cr4bA) to be answered during the event. To be informed of future events, [you can join the mailing list here](https://combine.us9.list-manage.com/subscribe?u=3f6e1d0b6a995d4581459ac68&id=a252376405). 2022-07-06 13:30:00 UTC 2022-07-06 14:30:00 UTC Australian Computational Biology and Bioinformatics Student Society (COMBINE) Virtual, Australia Virtual Australia Australian Computational Biology and Bioinformatics Student Society (COMBINE) combine@combine.org.au [] anybioinformaticiansstudentsresearch studentsresearcherresearchers [] open_to_all Bioinformaticssoftware publishingresearch softwarecommunity of practiceCommunity
  • Getting Started with Nectar Research Cloud Training

    7 July 2022

    Getting Started with Nectar Research Cloud Training https://dresa.org.au/events/getting-started-with-nectar-research-cloud-training Learn the basics of using the ARDC Nectar Cloud for your research. 2022-07-07 14:00:00 UTC 2022-07-07 16:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 10 [] open_to_all Science & TechnologyHigh Tech
  • Using Containers on the ARDC Nectar Research Cloud (Part 1: Docker)

    18 July 2022

    Using Containers on the ARDC Nectar Research Cloud (Part 1: Docker) https://dresa.org.au/events/using-containers-on-the-ardc-nectar-research-cloud-part-1-docker Learn the fundamentals of using Docker containers on the ARDC Nectar Research Cloud 2022-07-18 14:00:00 UTC 2022-07-18 16:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 10 [] open_to_all Science & TechnologyHigh Tech
  • Data Management Planning Interest Group #2

    19 July 2022

    Data Management Planning Interest Group #2 https://dresa.org.au/events/data-management-planning-interest-group-2 We are an Australasian interest group for people interested in discussing, building and improving Data Management Plans (DMPs). 2022-07-19 14:00:00 UTC 2022-07-19 15:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 100 meeting open_to_all Science & TechnologyOther
  • 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
  • Getting Started with Nectar Research Cloud Training

    21 July 2022

    Getting Started with Nectar Research Cloud Training https://dresa.org.au/events/getting-started-with-nectar-research-cloud-training-c33e654b-be84-4546-b816-222ae438c870 Learn the basics of using the ARDC Nectar Cloud for your research. 2022-07-21 14:00:00 UTC 2022-07-21 16:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 20 [] open_to_all Science & TechnologyHigh Tech
  • 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
  • Introduction to the Virtual Desktop Service

    2 August 2022

    Introduction to the Virtual Desktop Service https://dresa.org.au/events/introduction-to-the-virtual-desktop-service Learn more about our brand new Virtual Desktop Service! 2022-08-02 13:00:00 UTC 2022-08-02 14:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 25 [] open_to_all Science & TechnologyHigh Tech
  • Bringing Data to Life: Co-Designing a Language Data Commons

    4 August 2022

    New Farm, Australia

    Bringing Data to Life: Co-Designing a Language Data Commons https://dresa.org.au/events/bringing-data-to-life-co-designing-a-language-data-commons You’re invited to co-design the Language Data Commons of Australia. 2022-08-04 08:30:00 UTC 2022-08-04 13:15:00 UTC Australian Research Data Commons Yagara Country, 119 Lamington St, New Farm, Australia Yagara Country, 119 Lamington St New Farm Australia 4005 Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 300 [] open_to_all Science & TechnologyOther
  • Come and Try the Nectar Research Cloud

    4 August 2022

    Come and Try the Nectar Research Cloud https://dresa.org.au/events/come-and-try-the-nectar-research-cloud Not sure if the Cloud is for you? Come to this session about why it's useful and get a taste of some basic skills. 2022-08-04 14:00:00 UTC 2022-08-04 14:40:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 20 [] open_to_all Science & TechnologyHigh Tech
  • Come and Try the Nectar Cloud

    4 August 2022

    Come and Try the Nectar Cloud https://dresa.org.au/events/come-and-try-the-nectar-cloud Not sure if the Cloud is for you? Come to this session about why it's useful and get a taste of some basic skills. 2022-08-04 14:00:00 UTC 2022-08-04 14:40:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 20 [] open_to_all Science & TechnologyHigh Tech
  • Getting Started with Nectar Research Cloud Training

    10 August 2022

    Getting Started with Nectar Research Cloud Training https://dresa.org.au/events/getting-started-with-nectar-research-cloud-training-8782de65-dab4-4fb2-a87b-516eb7df69df Learn the basics of using the ARDC Nectar Cloud for your research. 2022-08-10 13:00:00 UTC 2022-08-10 15:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 10 [] open_to_all Science & TechnologyHigh Tech
  • Using Supercomputers: Parts 1 and 2

    22 - 23 August 2022

    Using Supercomputers: Parts 1 and 2 https://dresa.org.au/events/using-supercomputers-parts-1-and-2 In this course, students will be introduced to supercomputers and what makes them different to other computers. A typical supercomputing architecture, parallelism, compute resource sharing, command line interfaces and other key concepts and practices will be discussed. Students will practice what they learn using Pawsey's new supercomputer Setonix. 2022-08-22 10:00:00 UTC 2022-08-23 13:00:00 UTC Pawsey Supercomputing Research Centre Pawsey Supercomputing Research Centre training@pawsey.org.au [] [] workshopwebinar open_to_all supercomputingsupercomputersUnixSetonix
  • 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
  • Single Cell RNA-Seq Analysis Using Galaxy

    27 October 2021

    Single Cell RNA-Seq Analysis Using Galaxy https://dresa.org.au/events/single-cell-rna-seq-analysis-using-galaxy-10c1ee79-508a-44bf-8454-e2c928e8c5f5 This hands-on workshop will cover the basics of single cell RNAseq analysis, using the Galaxy platform. Starting from a table of gene counts we will evaluate, filter, annotate and visualise the data. We will also cover clustering, cell type identification and differential expression. Galaxy Australia is a platform that provides a simple and user-friendly interface to bioinformatics tools. The output we will generate is suitable for further analysis within Galaxy Australia, or locally. 2021-10-27 09:00:00 UTC 2021-10-27 17:00:00 UTC QCIF QCIF training@qcif.edu.au [] Life scientists planning or running single cell RNAseq experiments (or mining public data), who want to perform their own analyses. 30 workshop open_to_all RNASeqGalaxy AustraliaBioinformatics
  • Australian BioCommons 2021 Showcase

    3 - 5 November 2021

    Australian BioCommons 2021 Showcase https://dresa.org.au/events/australian-biocommons-2021-showcase Australian BioCommons projects draw key players together to deliver complex enhancements and new solutions for the digital life sciences. Join us to discover the breadth of our activities, review the impact we’re having and connect over a collaborative vision for the future of Australian bioinformatics and bioscience research infrastructure. We’ll meet online over three afternoons to share achievements, challenges and future directions. We invite existing partners, potential contributors and interested colleagues to learn more about all aspects of the Australian BioCommons, and meet the wide network of peers working hard to make these collaborative projects a success. Join us for any or all of the sessions on Wed 3 Nov 3-6pm AEDT, Thu 4 Nov 2-5pm AEDT or Fri 5 Nov 2-5pm AEDT. **[Click here for program of speakers & registration details](https://www.biocommons.org.au/events/2021-showcase)** 2021-11-03 15:00:00 UTC 2021-11-05 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Christina Hall (christina@biocommons.org.au) [] [] 500 meeting open_to_all BioinformaticsReference Genomes Community engagementBioCloudHuman genomicsResearch infrastructure
  • 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
  • P’Con – Exascale Data Management with ADIOS

    7 December 2021

    P’Con – Exascale Data Management with ADIOS https://dresa.org.au/events/p-con-exascale-data-management-with-adios Speakers: Speaker: Scott Klasky, Norbert Podhorszki (Oak Ridge National Laboratories) ADIOS is a high performance publish/subscribe I/O framework which has been designed and developed for the exascale computing era. In a snapshot, ADIOS: - Is integrated into most of the popular analysis and visualization packages. - Has strict continuous integration practices, providing stable, portable and efficient I/O services. - Has a programming interface designed for easy switching from files to streams (on-HPC machines) to streams over the Wide Area Network. In this presentation, the speaker will introduce the ADIOS I/O framework and describe how it is being used, including: - In data intensive supercomputing simulations, using it for data storage and retrieval moving petabytes of data in a single job, - In coupled simulations using it for data movement between the simulation codes and to in situ analysis and in situ visualization services, - In AI applications, for collecting training data from ensembles of computations on the fly, and - In collaborations between experimental facilities and HPC centers to stream experimental data for near-real-time decision making. We will present how ADIOS was used in the 2020 Gordon Bell finalist paper from Pawsey and ORNL about the workflow for simulating and processing the full-scale low-frequency telescope data of SKA Phase 1 on the Summit supercomputer at ORNL. ADIOS is also a research framework for new I/O technologies, pushing the boundaries beyond current use cases. Our research focuses on data reduction with trusted lossy compression techniques, data refactoring for easier on-demand retrieval, hierarchical storage to speed up access to the most important data, asynchronous I/O techniques and others. The techniques in ADIOS have been developed for over 15 years through collaborations with science applications, and we are always seeking new collaborations and new challenges that will define the I/O landscape of the future. We hope this presentation will allow the audience to learn about how others are using extreme I/O in their fields and also stimulate the audience to bring new challenges to us. Exascale Data Management with ADIOS session, is part of the first PaCER Conference – P’con: A week where Pawsey continues setting the pace for exascale. 2021-12-07 09:30:00 UTC 2021-12-07 11:30:00 UTC Pawsey Supercomputing Research Centre Pawsey Supercomputing Research Centre training@pawsey.org.au [] [] webinarconference open_to_all ADIOSsupercomputersupercomputingPawseyPaCERSetonix
  • P’Con – Porting multi-GPU SELF-Fluids code to HIPFort

    8 December 2021

    P’Con – Porting multi-GPU SELF-Fluids code to HIPFort https://dresa.org.au/events/p-con-porting-multi-gpu-self-fluids-code-to-hipfort Speaker: By Dr Joseph Schoonover, Fluid Numerics LLC During this talk, we will share our experience with porting process for SELF-Fluids from multi-GPU CUDA-Fortran to multi-GPU HIPFort. The talk will cover the design principles and roadmap for SELF and the strategy to port from Nvidia-only platforms to AMD & Nvidia GPUs. We’ll discuss hurdles encountered along the way and considerations for developing multi-GPU accelerated applications in Fortran. SELF is an object-oriented Fortran library that supports the implementation of Spectral Element Methods for solving partial differential equations. SELF-Fluids is an implementation of SELF that solves the compressible Navier Stokes equations on CPU only and GPU accelerated compute platforms using the Discontinuous Galerkin Spectral Element Method. The SELF API is designed based on the assumption that SEM developers and researchers need to be able to implement derivatives in 1-D and divergence, gradient, and curl in 2-D and 3-D on scalar, vector, and tensor functions using spectral collocation, continuous Galerkin, and discontinuous Galerkin spectral element methods. Additionally, as we enter the Exascale era, we are currently faced with a zoo of compute hardware that is available. Because of this, SELF routines provide support for GPU acceleration through AMD’s HIP and support for multi-core, multi-node, and multi-GPU platforms with MPI. SELF and SELF-Fluids are publicly available online at https://github.com/fluidnumerics/self Porting multi-GPU SELF-Fluids code to HIPFort, is part of the first PaCER Conference – P’con: A week where Pawsey continues setting the pace for exascale. 2021-12-08 09:30:00 UTC 2021-12-08 11:30:00 UTC Pawsey Supercomputing Research Centre Pawsey Supercomputing Research Centre training@pawsey.org.au [] [] webinarconference open_to_all GPUsHipFortsupercomputersupercomputingSetonix
  • 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
  • WORKSHOPS: Galaxy Training Smörgåsbord 2022

    14 - 18 March 2022

    WORKSHOPS: Galaxy Training Smörgåsbord 2022 https://dresa.org.au/events/workshops-galaxy-training-smorgasbord-2022 Learn how to analyse your data and use sophisticated computational workflows without the need for programming experience. The Galaxy Training Network is hosting a smörgåsbord of opportunities to learn how to use[ Galaxy](https://www.biocommons.org.au/galaxy-australia) (a free, online platform for reproducible data analysis) to analyse a huge variety of data including transcriptomics, proteomics, and next generation sequencing. Topics on offer include: 1. Introduction to Galaxy 2. NGS 3. RNA-Seq 4. Single Cell 5. Proteomics 6. SARS-CoV-2 Genomics 7. Galaxy Admin Training **Format** Online and asynchronous (at-your-own-pace) across all international time zones. All training sessions are pre-recorded, captioned and accompanied by live support from experienced instructors from the Galaxy Training community via chat and video conferencing. You can follow all of the sessions or just pick and choose the ones you’re most interested in, with the security of live help from the Galaxy Australia and Australian BioCommons teams. **Date/Time**: March 14-18, 2022 in your local timezone. **Who the workshop is for** These training sessions are suitable for researchers with no prior knowledge of Galaxy and no programming experience. **How to join** This workshop is free to join and open to everyone. Registrations are essential. **[More information and registrations](https://gallantries.github.io/posts/2021/12/14/smorgasbord2-tapas/)** _This workshop is presented by the Gallantries, Galaxy Training Network and Galaxy Training Community. The Australian BioCommons and its partners collaborate to provide the [Galaxy Australia Service](https://www.biocommons.org.au/galaxy-australia)._ 2022-03-14 09:00:00 UTC 2022-03-18 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons Melissa Burke (melissa@biocommons.org.au) [] [] 1000 workshop open_to_all BioinformaticsGalaxy AustraliaNGSRNASeqSingle cell RNAseqProteomics
  • 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
  • What skills are needed in commercial bioinformatics?

    6 July 2022

    What skills are needed in commercial bioinformatics? https://dresa.org.au/events/becoming-a-research-software-engineer-a43878db-e1ef-488a-b5ad-eab519e7e516 It is our pleasure to announce that for our very first COMBINE Fireside Chat we will have Dr David Wood from Microba sharing with us about invaluable skills in commercial bioinformatics. This program series is an excellent opportunity for upcoming student bioinformaticians to learn more about industry-related career pathways and from the successes of industry leaders in the field. # Abstract Despite frequent classification as a specialist activity, bioinformatics is a broad discipline. Bioinformaticians work in industries that have different goals and drivers, across multiple biological domains applying expert skills and technologies. As a student with a large informatics component to your work you may wonder what skills do commercial enterprises require of bioinformaticians? [Microba Life Sciences](https://microba.com/) is a precision microbiome company driven to improve human health. With world-leading technology for measuring the human gut microbiome, Microba is driving the discovery and development of novel therapeutics for major chronic diseases and delivering gut microbiome testing services globally to researchers, clinicians, and consumers. In this presentation I will describe how we conduct bioinformatics at Microba, and what are the key skills we require of bioinformaticians. Using our cloud-based, fast-turnaround bioinformatics platform as a case study, I will explain the role and skills required for each bioinformatics team member in its’ build, validation, operation, management and evolution. # About the speaker Dr David Wood leads the research and development of bioinformatic tools and data production at Microba. Dr Wood specialises in genome informatics and bioinformatics software development and has 20 years’ experience in industry and academia across diverse life science domains. He is an author on more than 30 scientific publications. His primary interest is in the application and advancement of high-throughput genomics technologies to improve public health. [You can submit your questions to the speaker anonymously](https://forms.gle/Z31vbn9ka9x5Cr4bA) to be answered during the event. To be informed of future events, [you can join the mailing list here](https://combine.us9.list-manage.com/subscribe?u=3f6e1d0b6a995d4581459ac68&id=a252376405). 2022-07-06 13:30:00 UTC 2022-07-06 14:30:00 UTC Australian Computational Biology and Bioinformatics Student Society (COMBINE) Virtual, Australia Virtual Australia Australian Computational Biology and Bioinformatics Student Society (COMBINE) combine@combine.org.au [] anybioinformaticiansstudentsresearch studentsresearcherresearchers [] open_to_all Bioinformaticssoftware publishingresearch softwarecommunity of practiceCommunity
  • Getting Started with Nectar Research Cloud Training

    7 July 2022

    Getting Started with Nectar Research Cloud Training https://dresa.org.au/events/getting-started-with-nectar-research-cloud-training Learn the basics of using the ARDC Nectar Cloud for your research. 2022-07-07 14:00:00 UTC 2022-07-07 16:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 10 [] open_to_all Science & TechnologyHigh Tech
  • Using Containers on the ARDC Nectar Research Cloud (Part 1: Docker)

    18 July 2022

    Using Containers on the ARDC Nectar Research Cloud (Part 1: Docker) https://dresa.org.au/events/using-containers-on-the-ardc-nectar-research-cloud-part-1-docker Learn the fundamentals of using Docker containers on the ARDC Nectar Research Cloud 2022-07-18 14:00:00 UTC 2022-07-18 16:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 10 [] open_to_all Science & TechnologyHigh Tech
  • Data Management Planning Interest Group #2

    19 July 2022

    Data Management Planning Interest Group #2 https://dresa.org.au/events/data-management-planning-interest-group-2 We are an Australasian interest group for people interested in discussing, building and improving Data Management Plans (DMPs). 2022-07-19 14:00:00 UTC 2022-07-19 15:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 100 meeting open_to_all Science & TechnologyOther
  • 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
  • Getting Started with Nectar Research Cloud Training

    21 July 2022

    Getting Started with Nectar Research Cloud Training https://dresa.org.au/events/getting-started-with-nectar-research-cloud-training-c33e654b-be84-4546-b816-222ae438c870 Learn the basics of using the ARDC Nectar Cloud for your research. 2022-07-21 14:00:00 UTC 2022-07-21 16:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 20 [] open_to_all Science & TechnologyHigh Tech
  • 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
  • Introduction to the Virtual Desktop Service

    2 August 2022

    Introduction to the Virtual Desktop Service https://dresa.org.au/events/introduction-to-the-virtual-desktop-service Learn more about our brand new Virtual Desktop Service! 2022-08-02 13:00:00 UTC 2022-08-02 14:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 25 [] open_to_all Science & TechnologyHigh Tech
  • Bringing Data to Life: Co-Designing a Language Data Commons

    4 August 2022

    New Farm, Australia

    Bringing Data to Life: Co-Designing a Language Data Commons https://dresa.org.au/events/bringing-data-to-life-co-designing-a-language-data-commons You’re invited to co-design the Language Data Commons of Australia. 2022-08-04 08:30:00 UTC 2022-08-04 13:15:00 UTC Australian Research Data Commons Yagara Country, 119 Lamington St, New Farm, Australia Yagara Country, 119 Lamington St New Farm Australia 4005 Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 300 [] open_to_all Science & TechnologyOther
  • Come and Try the Nectar Research Cloud

    4 August 2022

    Come and Try the Nectar Research Cloud https://dresa.org.au/events/come-and-try-the-nectar-research-cloud Not sure if the Cloud is for you? Come to this session about why it's useful and get a taste of some basic skills. 2022-08-04 14:00:00 UTC 2022-08-04 14:40:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 20 [] open_to_all Science & TechnologyHigh Tech
  • Come and Try the Nectar Cloud

    4 August 2022

    Come and Try the Nectar Cloud https://dresa.org.au/events/come-and-try-the-nectar-cloud Not sure if the Cloud is for you? Come to this session about why it's useful and get a taste of some basic skills. 2022-08-04 14:00:00 UTC 2022-08-04 14:40:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 20 [] open_to_all Science & TechnologyHigh Tech
  • Getting Started with Nectar Research Cloud Training

    10 August 2022

    Getting Started with Nectar Research Cloud Training https://dresa.org.au/events/getting-started-with-nectar-research-cloud-training-8782de65-dab4-4fb2-a87b-516eb7df69df Learn the basics of using the ARDC Nectar Cloud for your research. 2022-08-10 13:00:00 UTC 2022-08-10 15:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) Kathryn Unsworth (kathryn.unsworth@ardc.edu.au) [] [] 10 [] open_to_all Science & TechnologyHigh Tech
  • Using Supercomputers: Parts 1 and 2

    22 - 23 August 2022

    Using Supercomputers: Parts 1 and 2 https://dresa.org.au/events/using-supercomputers-parts-1-and-2 In this course, students will be introduced to supercomputers and what makes them different to other computers. A typical supercomputing architecture, parallelism, compute resource sharing, command line interfaces and other key concepts and practices will be discussed. Students will practice what they learn using Pawsey's new supercomputer Setonix. 2022-08-22 10:00:00 UTC 2022-08-23 13:00:00 UTC Pawsey Supercomputing Research Centre Pawsey Supercomputing Research Centre training@pawsey.org.au [] [] workshopwebinar open_to_all supercomputingsupercomputersUnixSetonix

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