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8 events found

Country: Australia 

  • 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: Interactive statistical and functional analysis of phosphoproteomics data with Phosphomatics

    2 June 2021

    Australia

    WEBINAR: Interactive statistical and functional analysis 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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