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48 events found

Organizer: ELIXIR Estonia  or Australian BioCommons 

  • Unix Shell Basics training

    3 March 2020

    Tartu, Estonia

    Unix Shell Basics training https://tess.elixir-europe.org/events/unix-shell-basics-training Advanced computing power is hidden away in clouds/cluster/supercomputers that you do not have click and point access. As a general rule these high performance computer resources use Linux operating systems and are accessible only by a shell terminal. This course is aimed to provide basic survival skills in Linux and terminal environment. We will teach you how to access files and folders, move around and hopefully shake off the fear of getting stuck somewhere along the way. 2020-03-03 10:15:00 UTC 2020-03-03 14:00:00 UTC ELIXIR Estonia Auditorium 2005 (the Linux classroom), Narva mnt 18 (UT Delta Centre), Tartu, Estonia Auditorium 2005 (the Linux classroom), Narva mnt 18 (UT Delta Centre) Tartu Tartumaa Estonia 51009 University of Tartu, Institute of Computer Science [] [] 20 workshops_and_courses registration_of_interest Unix/LinuxCommand lineUnix Shell
  • WEBINAR: What is the Australian BioCommons?

    4 March 2020

    Online, Australia

    WEBINAR: What is the Australian BioCommons? https://tess.elixir-europe.org/events/webinar-what-is-the-australian-biocommons 2020-03-04 12:00:00 UTC 2020-03-04 01:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons [] [] [] [] bioinformaticslife-sciencesAustralia
  • WEBINAR SERIES: FAIR data and Open Infrastructures to tackle the COVID-19 pandemic

    1 - 29 May 2020

    WEBINAR SERIES: FAIR data and Open Infrastructures to tackle the COVID-19 pandemic https://tess.elixir-europe.org/events/webinar-series-fair-data-and-open-infrastructures-to-tackle-the-covid-19-pandemic 2020-05-01 01:00:00 UTC 2020-05-29 02:00:00 UTC Australian BioCommons Bioinformatics Australian Biocommons [] [] [] [] bioinformaticslife sciences
  • WEBINAR: Portable pipelines: build once and run everywhere with Janis

    5 May 2020

    Online, Australia

    WEBINAR: Portable pipelines: build once and run everywhere with Janis https://tess.elixir-europe.org/events/webinar-portable-pipelines-build-once-and-run-everywhere-with-janis 2020-05-05 12:00:00 UTC 2020-05-05 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Bioinformatics Australian Biocommons [] [] [] [] bioinformaticslife sciences
  • WEBINAR: Introduction to containers

    2 June 2020

    Online, Australia

    WEBINAR: Introduction to containers https://tess.elixir-europe.org/events/webinar-introduction-to-containers 2020-06-02 13:00:00 UTC 2020-06-02 14:00:00 UTC Australian BioCommons Online, Australia Online Australia Bioinformatics Australian Biocommons [] [] [] [] bioinformaticslife sciences
  • WEBINAR: Comparison of long read methods for sequencing and assembly of a plant genome

    2 July 2020

    Australia

    WEBINAR: Comparison of long read methods for sequencing and assembly of a plant genome https://tess.elixir-europe.org/events/webinar-comparison-of-long-read-methods-for-sequencing-and-assembly-of-a-plant-genome 2020-07-02 12:00:00 UTC 2020-07-02 13:00:00 UTC Australian BioCommons Australia, Australia Australia Australia Bioinformatics Australian Biocommons [] [] [] [] bioinformatics
  • Bioinformatics Community Conference 2020

    19 - 22 July 2020

    Australia

    Bioinformatics Community Conference 2020 https://tess.elixir-europe.org/events/bioinformatics-community-conference-2020 BCC2020 brings together the Galaxy Community Conference and Bioinformatics Open Source Conference to meet jointly online. To ensure that the event is truly global, Australian BioCommons / Galaxy Australian have taken the lead on organising sessions in the eastern hemisphere. BCC2020 events will be held twice: once in its original Toronto time zone, and again 12 hours later. 2020-07-19 12:00:00 UTC 2020-07-22 12:00:00 UTC Australian BioCommons Australia, Australia Australia Australia Bioinformatics Australian Biocommons [] [] [] [] bioinformaticslife sciences
  • WEBINAR: DNA Zoo – Facilitating conservation efforts through rapid and open release of high-quality genomes

    19 August 2020

    Australia

    WEBINAR: DNA Zoo – Facilitating conservation efforts through rapid and open release of high-quality genomes https://tess.elixir-europe.org/events/webinar-dna-zoo-facilitating-conservation-efforts-through-rapid-and-open-release-of-high-quality-genomes 2020-08-19 12:00:00 UTC 2020-08-19 13:00:00 UTC Australian BioCommons Australia, Australia Australia Australia [] [] [] workshops_and_courses [] bioinformaticsGenome Sequencing
  • WEBINAR: So you think your genome assembly is good enough?

    24 September 2020

    Australia

    WEBINAR: So you think your genome assembly is good enough? https://tess.elixir-europe.org/events/webinar-so-you-think-your-genome-assembly-is-good-enough 2020-09-24 16:00:00 UTC 2020-09-24 18:00:00 UTC Australian BioCommons Australia Australia Bioinformatics Australian Biocommons [] [] [] [] bioinformaticsGenome Assembly
  • Galaxy Australia: enabling online data analysis for the research community

    4 - 5 November 2020

    Australia

    Galaxy Australia: enabling online data analysis for the research community https://tess.elixir-europe.org/events/webinar-galaxy-australia-enabling-online-data-analysis-for-the-research-community Galaxy is your ultimate research buddy - an online platform for biological research that gives you access to computational data analysis tools and workflows without the need for programming experience. It is supported by a rich collection of training materials and an active community of scientists. In this webinar we explore how Galaxy can transform your research through access to high performance computing power coupled with open, reproducible computational workflows and support from the Galaxy community. We’ll look at real-life examples of how Galaxy workflows are being applied to integrative meta-omics of microbial communities and how Galaxy is being leveraged to address the global challenges of COVID-19 research. Presenters: Dr Gareth Price, Service Manager, Galaxy Australia & Dr Johan Gustafsson, Bioinformatics Engagement Officer, Australian BioCommons Who the webinar is for: This webinar is suitable for life-science researchers. No prior knowledge of Galaxy or programming is required. 2020-11-04 09:00:00 UTC 2020-11-05 00:00:00 UTC Australian BioCommons Australia Australia [] Gareth Price, Johan Gustafsson [] Life Science Researchers workshops_and_courses first_come_first_served []
  • WEBINAR: Back to basics: handling research data

    5 November 2020

    Australia

    WEBINAR: Back to basics: handling research data https://tess.elixir-europe.org/events/https-www-biocommons-org-au-events-basics-data-movement How does the internet work and does it impact on your research? Dealing with data is an everyday part of modern biology. From small files to enormous data sets we are constantly moving and sharing data across the globe. How we move this data can have a big impact on our time and productivity. Go back to basics in this interactive webinar to explore the factors that influence data movement and discover tools that can be used to move data efficiently. We'll cover topics such as jargon busting, types of networks, data movement solutions and introduce CloudStor as a tool for data storage, transfer and analysis. This interactive webinar includes a hands-on component. There will be opportunities for discussion and questions. 2020-11-05 13:00:00 UTC 2020-11-05 15:00:00 UTC Australian BioCommons Australia, Australia Australia Australia Bioinformatics Data management Biology [] [] Biologists 30 workshops_and_courses first_come_first_served bioinformaticslife sciencesdata managementData skills
  • WEBINAR: Unifying package managers, workflow engines, and containers: computational reproducibility with BioNix

    10 - 11 November 2020

    Australia

    WEBINAR: Unifying package managers, workflow engines, and containers: computational reproducibility with BioNix https://tess.elixir-europe.org/events/webinar-unifying-package-managers-workflow-engines-and-containers-computational-reproducibility-with-bionix 2020-11-10 13:00:00 UTC 2020-11-11 14:00:00 UTC Australian BioCommons Australia Australia Bioinformatics Australian Biocommons [] [] [] [] bioinformaticsworkflows
  • WORKSHOP: Online data analysis for biologists - November 2020

    12 November 2020

    Australia

    WORKSHOP: Online data analysis for biologists - November 2020 https://tess.elixir-europe.org/events/workshop-online-data-analysis-for-biologists-november-2020 Galaxy is an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. It is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It also captures run information so that workflows can be saved, repeated and shared efficiently via the web. This interactive beginners workshop will provide an introduction to the Galaxy interface, histories and available tools. The material covered in this workshop is freely available through the Galaxy Training Network. 2020-11-12 14:00:00 UTC 2020-11-12 17:00:00 UTC Australian BioCommons Australia, Australia Australia Australia Bioinformatics [] [] Biologists workshops_and_courses [] GalaxyData analysislifescience
  • WORKSHOP: Practical tools for managing, moving and analysing data

    4 December 2020

    Australia

    WORKSHOP: Practical tools for managing, moving and analysing data https://tess.elixir-europe.org/events/workshop-practical-tools-for-managing-moving-and-analysing-data Are you constantly moving, storing, sharing and analysing data in complex scenarios throughout your research projects? Managing data well is now more important than ever for biological research but it can also be frustrating and difficult to know where to start! This hands-on workshop will explore and discuss data management challenges and introduce simple steps towards managing active research data. Participants will become familiar with CloudStor and its associated tools and services for organising, storing, sharing and analysing data, in a safe and secure way. Topics such as cloud storage, collaborative editing, versioning and data sharing will be discussed and demonstrated. You will learn how to set up an automatic way to move your data to the cloud so that your data is safe and secure. We’ll also show you how CloudStor integrates with data analysis solutions including Juypter Notebooks and Galaxy. This is a hands-on workshop using CloudStor (AARNet’s file sync, share and storage service). CloudStor is available to Australian researchers and provides one terabyte of storage to every individual researcher at AARNet-connected institutions. Trainer: This event will be led by Sara King, AARNet, and hosted by Australian BioCommons. Learning objectives: By the end of this workshop you should be able to: Identify common data management challenges Use CloudStor tools to store, move and manage data Describe methods for integrating CloudStor storage solutions with data analysis Who the workshop is for This hands-on workshop is tailored for biologists and requires no programming experience. Date/Time: 4 December 1:00pm - 4:00pm AEDT How to join The workshop is free but places are strictly limited to Australian life science researchers and students and registration requires an Australian institutional email address. Participation in this workshop requires access to a CloudStor account. You can check if you have access via your institutional subscription by finding your institution’s name on the CloudStor log-in list. If you do not have CloudStor access via your institution, you can still attend, but please advise us in advance so that arrangements can be made. 2020-12-04 13:00:00 UTC 2020-12-04 16:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons melissa@biocommons.org.au [] Biologists 30 workshops_and_courses first_come_first_served data managementToolslife sciences
  • WORKSHOP: Online data analysis for biologists - December 2020

    9 December 2020

    Australia

    WORKSHOP: Online data analysis for biologists - December 2020 https://tess.elixir-europe.org/events/workshop-online-data-analysis-for-biologists-december-2020 Galaxy is an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. It is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It also captures run information so that workflows can be saved, repeated and shared efficiently via the web. This interactive beginners workshop will provide an introduction to the Galaxy interface, histories and available tools. The material covered in this workshop is freely available through the Galaxy Training Network. 2020-12-09 14:00:00 UTC 2020-12-09 17:00:00 UTC Australian BioCommons Australia, Australia Australia Australia Bioinformatics [] [] Biologists workshops_and_courses [] bioinformaticslife sciences
  • WEBINAR: Plant genomics: chloroplast genome assembly using Galaxy Australia

    10 December 2020

    Australia

    WEBINAR: Plant genomics: chloroplast genome assembly using Galaxy Australia https://tess.elixir-europe.org/events/webinar-plant-genomics-chloroplast-genome-assembly-using-galaxy-australia-df405f97-a446-47f2-89a5-9bfaea1c9f9b 2020-12-10 01:00:00 UTC 2020-12-10 02:00:00 UTC Australian BioCommons Australia, Australia Australia Australia Bioinformatics Australian Biocommons [] [] [] [] bioinformaticslife sciences
  • WEBINAR: Harmonised analysis of childhood cancer data across international borders

    21 January 2021

    Australia

    WEBINAR: Harmonised analysis of childhood cancer data across international borders https://tess.elixir-europe.org/events/webinar-harmonised-analysis-of-childhood-cancer-data-across-international-borders The development of personalised treatments that target rare paediatric cancer subtypes can be enhanced through global collaboration. But geography and rules to protect personal data in different jurisdictions can make the sharing and comparing of essential data difficult or even impossible. The Australian BioCommons Zero Childhood Cancer Flagship project is a collaborative partnership between ZERO Childhood Cancer, D3b at Children’s Hospital of Philadelphia, Seven Bridges (SB), Australian Research Data Commons and the Australian BioCommons to unite and harmonise the analysis of paediatric cancer data sets from Australia (ZERO) and the US (Kids First Data Resource) using the cloud-based Cavatica analysis platform. The project allows ZERO and Kids First workflows and analysis tools to be used interchangeably and seamlessly across both datasets, effectively aggregating the separate datasets into a single virtual pan-continental dataset. This webinar will highlight the outcomes of the project and how the platform can be used to enhance human genomics studies and patient outcomes. Future plans will also be discussed. **Presenters**: Mark Cowley (Children's Cancer Institute), Jack DiGiovanna (Seven Bridges), Allison Heath (Children’s Hospital of Philadelphia) **Date/time**: 21 Jan 2021 - 11:00-12:00 AEDT / 10:00-11:00 AEST / 10:30 - 11:30 ACST / 8:00-9:00 AWST 2021-01-21 11:00:00 UTC 2021-01-21 12:00:00 UTC Australian BioCommons Australia, Australia Australia Australia [] [] [] 500 [] first_come_first_served CancergenomicsCloud computing
  • WEBINAR: AusTrakka: integrated pathogen genomics for SARS-CoV-2

    10 February 2021

    Australia

    WEBINAR: AusTrakka: integrated pathogen genomics for SARS-CoV-2 https://tess.elixir-europe.org/events/webinar-austrakka-integrated-pathogen-genomics-for-sars-cov-2 [AusTrakka](https://portal.austrakka.net.au/) is a platform to enable genomic surveillance of pathogen outbreaks at the national level. AusTrakka enables inter-jurisdictional sharing and analysis of genomic data, which is critical for the tracking of pathogen outbreaks across state boundaries. In 2020, AusTrakka development was accelerated and refocused in response to the COVID-19 pandemic, and AusTrakka was endorsed as the national SARS-Cov-2 data sharing platform. AusTrakka now hosts data for over 18,000 SARS-Cov-2 samples from all Australian states and territories, as well as New Zealand. Clare will discuss the efforts involved in setting up and developing a national genomics platform like AusTrakka, and the impact of the COVID-19 pandemic. Presenter: Dr Clare Sloggett, University of Melbourne Date/time: 10 Feb 2021 - 13:00-14:00 AEDT / 12:00-13:00 AEST / 12:30 - 13:30 ACST / 10:00-11:00 AWST [Register here](https://unimelb.zoom.us/webinar/register/WN_b0M6FWM3QW63pfyp_UMs1Q) 2021-02-10 13:00:00 UTC 2021-02-10 14:00:00 UTC Australian BioCommons Australia, Australia Australia Australia Australian Biocommons Melissa Burke: melissa@biocommons.org.au [] [] [] first_come_first_served MicrobiologyGenomicsdata sharingInfectious diseases
  • RNA-seq: from reads to differentially expressed genes

    23 - 25 February 2021

    Australia

    RNA-seq: from reads to differentially expressed genes https://tess.elixir-europe.org/events/workshop-rna-seq-from-reads-to-differentially-expressed-genes An introduction to RNA-seq analysis using the Galaxy Australia web platform **About this workshop** RNA-seq is a popular method for simultaneously measuring and comparing the expression of tens of thousands of genes in multiple samples. There are many steps involved in analysing RNA-Seq data. The analysis begins with sequencing reads (FASTQ files). These are usually aligned to a reference genome. The number of reads mapped to each gene can then be counted. This results in a table of counts, which is what we perform statistical analyses on to determine differentially expressed genes and pathways. This practical workshop provides a hands-on introduction to RNA-seq analysis from reads to counts, to differential expression. The workshop makes use of Galaxy, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. The workshop materials are based on the following Galaxy training workshops: - [RNA-seq reads to counts](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html) - [RNA-seq counts to genes](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html) **Who the workshop is for** Researchers who have, or will soon acquire, RNA-seq short read data that they need to analyse themselves. No prior experience with RNA-seq analysis is required. The workshop requires you to be familiar with using and navigating Galaxy Australia. If you are new to the Galaxy platform (an online platform for computational analysis) we recommend that you work through the Galaxy 101 For Everyone tutorial in advance of the workshop. **Date/Time: 23 - 24 February 2:00 - 5:00 pm AEDT** **How to apply** The workshop is free but due to anticipated high demand, participation is subject to application with selection. Places are strictly limited to 30 participants. Ineligible or incomplete applications will not be considered. For your application to be considered you must: - Have an Australian institutional email address - Have, or will soon acquire, RNA-seq data - Complete the application form 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 Tuesday 16 February 2021. Please complete the application form if you are interested in attending this workshop. Applications close 5pm AEDT Friday 5 February 2021. **[Apply here](https://biocommons-rnaseq.eventbrite.com.au/)** The 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 around Australia. 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 to Australian Biocommons](https://www.biocommons.org.au/subscribe). 2021-02-23 09:00:00 UTC 2021-02-25 00:00:00 UTC Australian BioCommons Australia, Australia Australia Australia [] Jessica Chung, Tom Harrop [] Biologists 30 workshops_and_courses registration_of_interest []
  • Using containers in bioinformatics

    25 - 26 March 2021

    Australia

    Using containers in bioinformatics https://tess.elixir-europe.org/events/using-containers-in-bioinformatics Are you wondering how your research could benefit from workflow containerisation? Containers enable you to package up an application and its dependencies and encourage reproducibility, portability and shareability of computational workflows. This workshop explores the merits, advantages and limitations of applying containers in bioinformatics. During the workshop you will: - learn and practice the basics of building, deploying and running applications in containers - explore real use cases related to biology - discuss tips and best practices, and have your questions answered. This workshop will be delivered online through a combination of presentations, demonstrations and hands-on interactive exercises supported by containers experts. On day 1 you will learn new skills through undertaking practical exercises and on day 2 you can bring your own pipeline to get advice and tips in a small group setting. **Learning outcomes** By the end of the workshop you should be able to: - Identify when you would benefit from using containers in your workflow - Download container images and run commands from inside a container using Singularity - Identify popular image registries - Discuss the pros & cons of building with Singularity vs Docker - Describe the basic syntax of a Dockerfile - Build and share an image with Docker - Convert a Docker image into the Singularity format **Lead trainer:** TBC **Date/time:** 12:30pm - 4:00pm AEDT/ 11:30am - 3:00pm AEST/ 12:00pm - 3:30pm ACDT / 9:30am - 1:00pm AWST Thursday 25 - Friday 26 March 2021 **Who the workshop is for** Basic familiarity with UNIX shell concepts and command line interactions are required. Participants do not need any previous experience with containers. This workshop is open to staff and students from Australian universities and research institutes. **How to apply** The workshop is free but participation is subject to application with selection. Please note that applications that do not nominate an Australian institute and do not provide an appropriate institutional email address will not be able to take part. 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 19 March 2021. Participants will be provided with a Zoom meeting link closer to the date. Please complete the application form if you are interested in attending this workshop. **Applications close 5pm AEDT Monday 15 March 2021.** [Apply here](https://biocommons-containers-2021.eventbrite.com.au/) The workshop is presented by the [Australian BioCommons](https://www.biocommons.org.au/) and [Pawsey Supercomputing Centre](https://pawsey.org.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. 2021-03-25 12:30:00 UTC 2021-03-26 16:00:00 UTC Australian BioCommons Australia, Australia Australia Australia Australian Biocommons Melissa Burke: melissa@biocommons.org.au [] [] 30 workshops_and_courses registration_of_interest WorkflowsContainers
  • Plant genomics: chloroplast genome assembly using Galaxy Australia

    21 - 22 April 2021

    Australia

    Plant genomics: chloroplast genome assembly using Galaxy Australia https://tess.elixir-europe.org/events/workshop-plant-genomics-chloroplast-genome-assembly-using-galaxy-australia It is becoming increasingly practical to use large genomic data sets to answer research questions in plant biology, but it can be difficult to know where to start. In this workshop, you will perform a genome assembly using chloroplast sequencing data and the Galaxy Australia web platform. You'll have the opportunity to try out the workflows on the same or other data, using the free Galaxy platform and its tools. Galaxy is an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. The material covered in this workshop is freely available through the Galaxy Training Network. The workshop will be held via Zoom and involve a combination of presentations by the lead trainer and smaller breakout groups supported by experienced facilitators. **Lead trainer:** Dr Anna Syme, Bioinformatician, Australian BioCommons, Melbourne Bioinformatics, University of Melbourne. Anna has a long history as a research scientist and has recently worked at the Royal Botanic Gardens Victoria. Her work on the Bioplatforms Australia project, Genomics for Australian Plants, and her current Australian BioCommons role sees her contributing to workforce transition of researchers working with genomic data. **Learning objectives** By the end of the workshop you should be able to: - Assemble a chloroplast genome from a test dataset of Oxford Nanopore long sequencing reads - Polish the assembly with short Illumina sequencing reads - View the assembly in a genome browser and an assembly graph viewer - Describe how common tools can be combined to produce a workflow for genome assembly **Who the workshop is for** This workshop is suitable for Australian researchers with an interest in using Galaxy Australia for genome assembly. The workshop requires some prior knowledge of genome assembly and the basics of using Galaxy Australia. If you are new to these topics we recommend that you work through the following tutorials in advance: - [A short introduction to Galaxy] (https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html) - [Introduction to Genome Assembly] (https://training.galaxyproject.org/training-material/topics/assembly/tutorials/general-introduction/tutorial.html) Additional tutorials on genome assembly can be found on the Galaxy Training Network. **Date/Time:** 21 April 1:00pm - 4:00pm AEST **How to join** The workshop is free but places are strictly limited and registration requires an Australian institutional email address. [Register here] (https://plant-genomics-galaxy.eventbrite.com.au/) The workshop is presented by the Australian Biocommons and Melbourne Bioinformatics with the assistance of a network of Facilitators from around Australia. This event is part of a series of bioinformatics training events in partnership with Galaxy Australia. If you'd like to hear when registrations open for other events, please subscribe to Australian Biocommons. 2021-04-21 09:00:00 UTC 2021-04-22 00:00:00 UTC Australian BioCommons Australia, Australia Australia Australia [] Anna Syme [] [] 30 workshops_and_courses first_come_first_served []
  • WEBINAR: Getting started with containers

    12 May 2021

    Australia

    WEBINAR: Getting started with containers https://tess.elixir-europe.org/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 Australia Australia Bioinformatics Computational biology Computer science Australian BiocommonsPawsey Supercomputing Centre Melissa Burke melissa@biocommons.org.au [] BiologistsBioinformaticians 500 workshops_and_courses first_come_first_served ContainerssupercomputerCloud computing
  • WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation

    20 May 2021

    Australia

    WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation https://tess.elixir-europe.org/events/webinar-conflict-in-multi-gene-datasets-why-it-happens-and-what-to-do-about-it-deep-coalescence-paralogy-and-reticulation Multi-gene datasets used in phylogenetic analyses, such as those produced by the sequence capture or target enrichment used in the Genomics for Australian Plants: Australian Angiosperm Tree of Life project, often show discordance between individual gene trees and between gene and species trees. This webinar will explore three different forms of discordance: deep coalescence, paralogy, and reticulation. In each case, it will consider underlying biological processes, how discordance presents in the data, and what bioinformatic or phylogenetic approaches and tools are available to address these challenges. It will cover Yang and Smith paralogy resolution and general information on options for phylogenetic analysis. **Presenter:** Dr Alexander Schmidt-Lebuhn, Centre for Australian National Biodiversity Research, CSIRO **Date/time:** 20 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_cZVHIdKxST-6xyw4pg3B4g) 2021-05-20 12:00:00 UTC 2021-05-20 13:00:00 UTC Australian BioCommons Australia Australia Phylogenetics Australian Biocommons Melissa Burke melissa@biocommons.org.au [] Biologistsbioinformaticians 500 workshops_and_courses first_come_first_served phylogenetics
  • WORKSHOP: Variant calling in humans, animals and plants with Galaxy

    25 May 2021

    Australia

    WORKSHOP: Variant calling in humans, animals and plants with Galaxy https://tess.elixir-europe.org/events/workshop-variant-calling-in-humans-animals-and-plants-with-galaxy-a5b051e8-6ceb-4384-b19d-4bd170eb738d Variant calling in polyploid organisms, including humans, plants and animals, can help determine single or multi-variant contributors to a phenotype. Further, sexual reproduction (as compared to asexual) combines variants in a novel manner; this can be used to determine previously unknown variant - phenotype combinations but also to track lineage and lineage associated traits (GWAS studies), that all rely on highly accurate variant calling. The ability to confidently call variants in polyploid organisms is highly dependent on the balance between the frequency of variant observations against the background of non-variant observations, and even further compounded when one considers multi-variant positions within the genome. These are some of the challenges that will be explored in the workshop. In this online workshop we focus on the tools and workflows available for variant calling in polyploid organisms in Galaxy Australia. During the workshop you will get hands-on experience using Freebayes for variant calling and SnpEff and GEMINI for variant annotation. The workshop makes use of data from a case study on diagnosing a genetic disease however the tools and workflows are equally applicable to other polyploid organisms and biological questions. Access to all of the tools covered in this workshop is via [Galaxy Australia](https://usegalaxy.org.au/), an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. You may also be interested in our workshops on variant calling in viruses and bacteria. See our[ events page](https://www.biocommons.org.au/events) for more information. **Date/time**: 1-5pm AEST, Tuesday 25 May 2021 **Lead Trainers:** Dr Gareth Price, Dr Igor Makunin, QCIF Bioinformatics. **Learning outcomes** The materials to be covered in the workshop are freely available via the [Galaxy Training Network](https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html). By the end of the workshop you should be able to: - Identify genetic variants in samples based on exome sequencing data - Identify causative variants associated with a given phenotype - Apply Freebayes for variant calling - Apply SnpEff and GEMINI for variant annotation The workshop will NOT provide an introduction to the basics of Galaxy or the use of Galaxy for sequencing analysis (e.g. quality control and mapping). If you would like to learn about these topics there are several tutorials available via the [Galaxy Training Network](https://training.galaxyproject.org/training-material/). **Who the workshop is for** This workshop is for Australian researchers who have or will work on variant calling in polyploid organisms as part of their projects. To get the most out of the workshops you must be familiar with the concepts of variant calling and have some experience with the basics of using Galaxy Australia such as setting up a history, uploading data and running tools. No programming experience is required. You will be required to watch an introductory webinar (either live or recorded) that will provide an overview of Galaxy Australia and introduce key functionalities of the service. If you are new to Galaxy we recommend that you work through the following tutorials in advance: [A short introduction to Galaxy](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html) and [Galaxy 101 for Everyone](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html). **How to apply** This workshop is free but participation is subject to application with selection. **_Applications close at 5pm AEST Wednesday 12 May 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 14 May 2021. Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://biocommons-variants-polyploid.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) and [Galaxy Australia](https://usegalaxy.org.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. 2021-05-25 13:00:00 UTC 2021-05-25 17:00:00 UTC Australian BioCommons Australia Australia Australian BiocommonsQCIF Melissa Burke melissa@biocommons.org.au [] Biologistsbioinformaticians 50 workshops_and_courses registration_of_interest Variant calling
  • WORKSHOP: Viral variant calling with Galaxy

    26 May 2021

    Australia

    WORKSHOP: Viral variant calling with Galaxy https://tess.elixir-europe.org/events/workshop-viral-variant-calling-with-galaxy The analysis of a viral genome and its variants has unique challenges, most notably the inability to culture the virus outside of the host organism. Furthermore, many viruses have a high mutational rate which, coupled with the culturing restrictions, make determining viral variants more of a heterogeneous population exercise. In this online workshop we focus on the tools and workflows available for variant calling in viruses in Galaxy Australia. During the workshop you will get hands-on experience using BWA-MEM for alignment, lofreq for variant calling and SnpEff for annotating variant effects. The workshop makes use of COVID-19 variant calling data however the tools and workflows are equally applicable to other viruses and biological questions. Access to all of the tools covered in this workshop is via [Galaxy Australia](https://usegalaxy.org.au/), an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. You may also be interested in our workshops on variant calling in polyploid organisms (e.g. humans, plants and animals) and bacteria. See our [events page](https://www.biocommons.org.au/events) for more information. **Date/time**: 1-5pm AEST, Wednesday 26 May 2021 **Lead Trainers:** Dr Gareth Price, Dr Igor Makunin, QCIF Bioinformatics. **Learning outcomes** The materials to be covered in the workshop are freely available via the [Galaxy Training Network](https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html). By the end of the workshop you should be able to: - Download and import reference genome data - Align reads using BWA-MEM - Call variants using lofreq - Annotate variant effects with SnpEff The workshop will NOT provide an introduction to the basics of Galaxy or the use of Galaxy for sequencing analysis (e.g. quality control and mapping). If you would like to learn about these topics there are several tutorials available via the [Galaxy Training Network](https://training.galaxyproject.org/training-material/). **Who the workshop is for** This workshop is for Australian researchers who have or will work on variant calling in viruses as part of their projects. To get the most out of the workshops you must be familiar with the concepts of variant calling and have some experience with the basics of using Galaxy Australia such as setting up a history, uploading data and running tools. No programming experience is required. You will be required to watch an introductory webinar (either live or recorded) that will provide an overview of Galaxy Australia and introduce key functionalities of the service. If you are new to Galaxy we recommend that you work through the following tutorials in advance: [A short introduction to Galaxy](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html) and [Galaxy 101 for Everyone](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html). **How to apply** This workshop is free but participation is subject to application with selection. **_Applications close at 5pm AEST Wednesday 12 May 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 14 May 2021. Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://biocommons-variants-viruses.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) and [Galaxy Australia](https://usegalaxy.org.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. 2021-05-26 13:00:00 UTC 2021-05-26 17:00:00 UTC Australian BioCommons Australia Australia Genetic variation Australian BiocommonsQCIF Melissa Burke melissa@biocommons.org.au [] Biologistsbioinformaticians 50 workshops_and_courses registration_of_interest Variant callingGenetic Variation
  • WORKSHOP: Bacterial variant calling with Galaxy

    27 May 2021

    Australia

    WORKSHOP: Bacterial variant calling with Galaxy https://tess.elixir-europe.org/events/workshop-bacterial-variant-calling-with-galaxy Bacteria evolve rapidly, acquiring and purging DNA changes in response to their changing environments. Many bacteria can be cultured, allowing researchers to study DNA variants from a single organism source, unlike variant analysis in polyploids. Comparison of variants between single organisms gives insight not only into their individual characteristics (such as antimicrobial resistance) but at a population level allows for phylogenetic mapping to determine the relatedness between samples. In this online workshop we focus on the tools and workflows available for variant calling in bacteria in Galaxy Australia. During the workshop you will get hands-on experience using Snippy for genetic variation detection and annotation, and JBrowse to visualise variants. The workshop makes use of data from a case study on antimicrobial resistance in Mycobacterium tuberculosis however the tools and workflows are equally applicable to other bacteria and biological questions. Access to all of the tools covered in this workshop is via [Galaxy Australia](https://usegalaxy.org.au/), an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. You may also be interested in our workshops on variant calling in polyploid organisms (e.g animals, plants, humans) and viruses. See our [events listings](https://www.biocommons.org.au/events) for more information on other workshops and events. **Date/time**: 1-5pm AEST, Thursday 27 May 2021 **Lead Trainers:** Dr Gareth Price, and Dr Igor Makunin, QCIF Bioinformatics. **Learning outcomes** The materials to be covered in the workshop are freely available via the [Galaxy Training Network](https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html). By the end of the workshop you should be able to: - Detect genetic variation in microbial genomes using Snippy - Visualise variants in a genome browser (JBrowse) - Use annotations to infer changes to phenotype The workshop will NOT provide an introduction to the basics of Galaxy or the use of Galaxy for sequencing analysis (e.g. quality control and mapping). If you would like to learn about these topics there are several tutorials available via the [Galaxy Training Network](https://training.galaxyproject.org/training-material/). **Who the workshop is for** This workshop is for Australian researchers who have or will work on variant calling in bacteria as part of their projects. To get the most out of the workshops you must be familiar with the concepts of variant calling and have some experience with the basics of using Galaxy Australia such as setting up a history, uploading data and running tools. No programming experience is required. You will be required to watch an introductory webinar (either live or recorded) that will provide an overview of Galaxy Australia and introduce key functionalities of the service. If you are new to Galaxy we recommend that you work through the following tutorials in advance: [A short introduction to Galaxy](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html) and [Galaxy 101 for Everyone](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html). **How to apply** This workshop is free but participation is subject to application with selection. **_Applications close at 5pm AEST Wednesday 12 May 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 14 May 2021. Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://biocommons-variants-bacterial.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) and [Galaxy Australia](https://usegalaxy.org.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. 2021-05-27 13:00:00 UTC 2021-05-27 17:00:00 UTC Australian BioCommons Australia Australia Genetic variation Australian BiocommonsQCIF Melissa Burke melissa@biocommons.org.au [] Biologistsbioinformaticians 50 workshops_and_courses registration_of_interest Variant callingGenetic Variation
  • WEBINAR: Making sense of phosphoproteomics data with Phosphomatics

    2 June 2021

    Australia

    WEBINAR: Making sense of phosphoproteomics data with Phosphomatics https://tess.elixir-europe.org/events/webinar-interactive-statistical-and-functional-analysis-of-phosphoproteomics-data-with-phosphomatics Mass spectrometry-based phosphoproteomics is one of the most powerful tools available for investigating the detailed molecular events that occur in response to cellular stimuli. Experiments can routinely detect and quantify thousands of phosphorylated peptides, and interpreting this data, and extracting biological meaning, remains challenging. This webinar will provide an overview of the phosphoproteomics data analysis website, Phosphomatics, that incorporates a suite of tools and resources for statistical and functional analysis that aim to simplify the process of extracting meaningful insights from experimental results. Phosphomatics can natively import search and quantitation results from major search engines including MaxQuant and Proteome Discoverer and employs intuitive ‘wizards’ to guide user through data preprocessing routines such as filtering, normalization and transformation. A graphical platform of interactive univariate and multivariate analysis features is provided that allow subgroups of the uploaded data containing phosphosites of statistical interest to be created and interrogated through further functional analysis. A range of databases have been integrated that, for example, provide ligand and inhibitor information for key proteins or highlight key modification sites known to be involved in functional state regulation. At each step, published literature is natively incorporated along with a ‘bibliography builder’ that allows references of interest to be assembled and exported in various formats. Taken together, these expanded features aim to provide a ‘one-stop-shop’ for phosphoproteomics data analysis. Presenter: Dr Michael Leeming, Research Fellow, Mass Spectrometry and Proteomics Facility, University of Melbourne Date/time: 2 June 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_kqno1eeTQK6pYZ0LYuqV2Q) 2021-06-02 12:00:00 UTC 2021-06-02 13:00:00 UTC Australian BioCommons Australia Australia Australian Biocommons Melissa Burke melissa@biocommons.org.au [] Biologistsbioinformaticians 500 workshops_and_courses first_come_first_served PhosphoproteomicsPhosphorylationmassspectrometry
  • WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset

    10 June 2021

    Australia

    WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset https://tess.elixir-europe.org/events/https-unimelb-zoom-us-webinar-register-wn_czvhidkxst-6xyw4pg3b4g Hybridisation plays an important role in evolution, leading to the exchange of genes between species and in some cases generate new lineages. The use of molecular methods has revealed the frequency and importance of reticulation events is higher than previously thought and this insight continues with the ongoing development of phylogenomic methods that allow novel insights into the role and extent of hybridisation. Hybrids notoriously provide challenges for the reconstruction of evolutionary relationships, as they contain conflicting genetic information from their divergent parental lineages. However, this also provides the opportunity to gain insights into the origin of hybrids (including autopolyploids). This webinar explores some of the challenges and opportunities that occur when hybrids are included in a target capture sequence dataset. In particular, it describes the impact of hybrid accessions on sequence assembly and phylogenetic analysis and further explores how the information of the conflicting phylogenetic signal can be used to detect and resolve hybrid accessions. The webinar will showcase a novel bioinformatic workflow, [HybPhaser](https://www.biorxiv.org/content/10.1101/2020.10.27.354589v2), that can be used to detect and phase hybrids in target capture datasets and will provide the theoretical background and concepts behind the workflow. **Presenter:** Dr Lars Nauheimer, Australian Tropical Herbarium **Date/time:** 10 June 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_AZ-ezvarRhqH-eg6TFMG5w) 2021-06-10 12:00:00 UTC 2021-06-10 13:00:00 UTC Australian BioCommons Australia Australia Phylogenetics Australian Biocommons Melissa Burke melissa@biocommons.org.au [] BioinformaticiansBiologists 500 workshops_and_courses first_come_first_served phylogenetics
  • WEBINAR: Getting started with command line bioinformatics

    22 June 2021

    Australia

    WEBINAR: Getting started with command line bioinformatics https://tess.elixir-europe.org/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 Australia Australia Bioinformatics Australian Biocommons Melissa Burke melissa@biocommons.org.au [] Biologists 500 workshops_and_courses first_come_first_served Command lineBioinformaticsCoding
  • WEBINAR: Getting started with deep learning

    21 July 2021

    Australia

    WEBINAR: Getting started with deep learning https://tess.elixir-europe.org/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 Australia Australia Australian Biocommons Melissa Burke melissa@biocommons.org.au [] Biologistsbioinformaticians 500 workshops_and_courses first_come_first_served Deep learningMachine Learning and Artificial Intelligence Course

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