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Australian BioCommons

Australian BioCommons is a research infrastructure project building digital capability for life science research in Australia.

Australian BioCommons https://tess.elixir-europe.org/content_providers/australian-biocommons Australian BioCommons is a research infrastructure project building digital capability for life science research in Australia. /system/content_providers/images/000/000/123/original/Australian-Biocommons-Logo-Horizontal-144dpi_%282%29_%281%29.jpg?1580547111
Showing 6 materials.
WEBINAR: Getting started with command line bioinformatics

This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Getting started with command line bioinformatics’. This webinar took place on 22 June 2021.

Scientific topics: Computational biology

Keywords: Command line

WEBINAR: Getting started with command line bioinformatics https://tess.elixir-europe.org/materials/webinar-getting-started-with-command-line-bioinformatics This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Getting started with command line bioinformatics’. This webinar took place on 22 June 2021. Carolyn Hogg Computational biology Command line
WORKSHOP: Variant calling in humans, animals and plants with Galaxy

This Zenodo record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021.

Scientific topics: Genetic variation

Keywords: Variant calling

WORKSHOP: Variant calling in humans, animals and plants with Galaxy https://tess.elixir-europe.org/materials/workshop-variant-calling-in-humans-animals-and-plants-with-galaxy This Zenodo record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021. Genetic variation Variant calling
WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset

This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021.

Scientific topics: Phylogeny, Phylogenetics

WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset https://tess.elixir-europe.org/materials/webinar-detection-of-and-phasing-of-hybrid-accessions-in-a-target-capture-dataset This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021. Phylogeny Phylogenetics
WEBINAR: Getting started with deep learning

This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Getting started with deep learning’. This webinar took place on 21 July 2021.

Scientific topics: Machine learning

Keywords: Deep learning

WEBINAR: Getting started with deep learning https://tess.elixir-europe.org/materials/webinar-getting-started-with-deep-learning This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Getting started with deep learning’. This webinar took place on 21 July 2021. Machine learning Deep learning
WEBINAR: Making sense of phosphoproteomics data with Phosphomatics

This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021.

Scientific topics: Protein modifications, Proteomics

Keywords: Phosphoproteomics

WEBINAR: Making sense of phosphoproteomics data with Phosphomatics https://tess.elixir-europe.org/materials/webinar-making-sense-of-phosphoproteomics-data-with-phosphomatics This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021. Protein modifications Proteomics Phosphoproteomics
WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation

This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021.

Scientific topics: Phylogenetics

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/materials/webinar-conflict-in-multi-gene-datasets-why-it-happens-and-what-to-do-about-it-deep-coalescence-paralogy-and-reticulation This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021. Phylogenetics
Showing 4 upcoming events. Found 41 past events. View all results.

  • WORKSHOP: Working with genomic sequences and features in R with Bioconductor

    23 September 2021

    Australia

    WORKSHOP: Working with genomic sequences and features in R with Bioconductor https://tess.elixir-europe.org/events/workshop-working-with-genomic-sequences-and-features-in-r-with-bioconductor Explore the many useful functions that the Bioconductor environment offers for working with genomic data and other biological sequences. DNA and proteins are often represented as files containing strings of nucleic acids or amino acids. They are associated with text files that provide additional contextual information such as genome annotations. This workshop provides hands-on experience with tools, software and packages available in R via Bioconductor for manipulating, exploring and extracting information from biological sequences and annotation files. We will look at tools for working with some commonly used file formats including FASTA, GFF3, GTF, methods for identifying regions of interest, and easy methods for obtaining data packages such as genome assemblies. **Date/time:** 10am-1pm AEST, Thursday 23 September 2021 **Lead Trainer:** Dr Paul Harrison, Monash Bioinformatics Platform **Learning outcomes** After attending this workshop, participants will be able to: 1. Work with data types in R representing DNA and amino-acid sequences, and genomic ranges (representing things such as genes, transcripts, exons, motif matches, or results of peak-calling). 2. Perform useful operations on genomic ranges such as finding overlaps between two sets of ranges. 3. Load and save data in commonly used file formats, appreciate some of the advantages and disadvantages of different formats. 4. Install Bioconductor packages, find relevant documentation, and be aware of differences between the Bioconductor and base R ways of doing things. **Who the workshop is for** This workshop is open to Australian students and researchers who are using Bioconductor to analyse their life science data. It is not suitable for absolute beginners. Some familiarity with R is assumed (prospective participants should already be comfortable with [basic R concepts](https://monashdatafluency.github.io/r-intro-2)). Participants will need to have [RStudio](https://rstudio.com/products/rstudio/download/) and[ R](https://cran.r-project.org/) ready for use on their laptop. Participants should have used a few Bioconductor packages, perhaps having worked through a tutorial vignette to perform a standard data analysis task. This workshop will assist those who are now interrogating their data in a way that requires going off the beaten path, or perhaps needing to better understand package vignettes mentioning things like "GRanges" and "TxDb". **How to apply** This workshop is free but participation is subject to application with selection. Applications close at 5pm AEST Thursday 9 Sep 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 Monday 13 Sep 2021. Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://bioconductor-genomics.eventbrite.com.au/)** This workshop is presented by the [Australian BioCommons](https://www.biocommons.org.au/) and[ Monash Bioinformatics Platform](https://www.monash.edu/researchinfrastructure/bioinformatics/home) with the assistance of a network of facilitators from the national [Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative). To hear when registrations open for other events, please [subscribe](https://www.biocommons.org.au/subscribe) to the Australian BioCommons’ eNewsletter. 2021-09-23 10:00:00 UTC 2021-09-23 13:00:00 UTC Australian BioCommons Australia Australia DNA Sequence analysis Genomics Australian Biocommons Melissa Burke melissa@biocommons.org.au [] [] 50 workshops_and_courses registration_of_interest RBioconductorGenomic sequences

  • WEBINAR: KBase - A knowledge base for systems biology

    22 September 2021

    Australia

    WEBINAR: KBase - A knowledge base for systems biology https://tess.elixir-europe.org/events/webinar-kbase-a-knowledge-base-for-systems-biology Developed for bench biologists and bioinformaticians, The Department of Energy Systems Biology Knowledgebase ([KBase](https://www.kbase.us/)) is a free, open source, software and data science platform designed to meet the grand challenge of systems biology: predicting and designing biological function. This webinar will provide an overview of the KBase mission and user community, as well as a tour of the online platform and basic functionality. You’ll learn how KBase can support your research: Upload data, run analysis tools (Apps), share your analysis with collaborators, and publish your data and reproducible workflows. We’ll highlight a brand new feature that enables users to link environment and measurement data to sequencing data. You’ll also find out how KBase supports findable, accessible, interoperable, and reusable (FAIR) research by providing open, reproducible, shareable bioinformatics workflows. **Who the webinar is for** Anyone interested in hearing about KBase. **Presenters**: Ellen Dow, PhD - KBase Communications and Outreach Specialist Elisha Wood-Charlson, PhD - KBase User Engagement Lead **Date/time:** 22 September 2021 - 9:00-10:00 AEST / 830 - 9:30 ACST / 7:00-8:00 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_uEqSBotLTQ-19cqr2nP99w)** 2021-09-22 09:00:00 UTC 2021-09-22 10:00:00 UTC Australian BioCommons Australia Australia Data management Systems biology [] Melissa Burke (melissa@biocommons.org.au) [] [] 500 workshops_and_courses first_come_first_served Systems biologyMicrobiome

  • WEBINAR: Launching the new Apollo Service: collaborative genome annotation for Australian researchers

    29 September 2021

    Australia

    WEBINAR: Launching the new Apollo Service: collaborative genome annotation for Australian researchers https://tess.elixir-europe.org/events/webinar-launching-the-new-apollo-service-collaborative-genome-annotation-for-australian-researchers Genome annotation is crucial to defining the function of genomic sequences. Apollo is a popular tool for facilitating real-time collaborative curation and genome annotation editing. The technical obstacles faced by Australian researchers wanting to access and maintain this software have now been solved. The new Apollo Service can host your genome assembly and supporting evidence files, taking care of all the system administration so you and your team can focus on the annotation curation itself. The Australian BioCommons and partners at [QCIF](https://www.qcif.edu.au/) and [Pawsey](https://pawsey.org.au/) are now offering the [Apollo Service](https://apollo-portal.genome.edu.au/) free to use for [Australian-based](https://apollo-portal.genome.edu.au/termsofuse#AusUni) research groups and research consortia. As part of this launch, you’ll hear what’s possible from some of the early adopters who helped guide the development of the service. These Australian researchers will highlight the benefits that Apollo is bringing to their genome annotation and curation workflows. Join us to find out how you can get access to the Apollo Service. **Who the webinar is for** Anyone with an interest in genome annotation, editing and curation. **Presenters:** Dr Tiffanie Nelson, Australian BioCommons Featuring case studies from: - Dr Rahul Rane, CSIRO - Prof Sandie Degnan and Prof Bernie Degnan, University of Queensland - Dr Ramil ‘Mau’ Mauleon and Julia Voelker, Southern Cross University **Date/time:** 29 September 2021 12pm - 1 pm AEST / 11:30am - 12:30pm ACST / 10am - 11am 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_0bDQZvP9RJ2hqGK0R2ulxg)** 2021-09-29 12:00:00 UTC 2021-09-29 13:00:00 UTC Australian BioCommons Australia Australia Genomics [] Melissa Burke (melissa@biocommons.org.au) [] [] 500 workshops_and_courses first_come_first_served genome annotationgenome curation

  • WORKSHOP: Hybrid de novo genome assembly

    7 October 2021

    Australia

    WORKSHOP: Hybrid de novo genome assembly https://tess.elixir-europe.org/events/workshop-hybrid-de-novo-genome-assembly It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches which enable research on organisms for which reference genomes were not previously available. These approaches combine the strengths of short (Illumina) and long (PacBio or Nanopore) read technologies, resulting in improved assembly quality. In this workshop we will learn how to create and assess genome assemblies from Illumina and Nanopore reads using data from a _Bacillus Subtilis_ strain. We will demonstrate two hybrid-assembly methods using the tools [Flye](https://github.com/fenderglass/Flye), [Pilon](https://github.com/broadinstitute/pilon/wiki), and [Unicycler](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005595) to perform assembly and subsequent error correction. You will learn how to visualise input read sets and the assemblies produced at each stage and assess the quality of the final assembly. All analyses will be performed using [Galaxy Australia](https://usegalaxy.org.au/), an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. **Date/time:** 2 - 5pm AEDT/ 1 - 4pm AEST/ 1:30 - 4:30pm ACDT/ 11am - 2pm AWST, Thursday 7 October 2021 **Lead Trainer:** Grace Hall, Melbourne Bioinformatics **Learning outcomes** By the end of this workshop you should be able to: 1. Describe how Nanopore and Illumina reads can be used together to produce a high quality assembly 2. Use genome assembly and polishing programs in Galaxy Australia 3. Assess the quality of a genome assembly with and without a reference genome 4. Assemble an unknown, previously undocumented genome to high-quality using Nanopore and Illumina reads The workshop will NOT provide an introduction to the basics of Galaxy. If you would like to learn about this topic there are several tutorials available via the[ Galaxy Training Network](https://training.galaxyproject.org/training-material/). **Who the workshop is for** This workshop is for Australian researchers who are or will perform hybrid genome assembly as part of their projects. To get the most out of the workshops you must have experience with the basics of using Galaxy Australia such as setting up a history, uploading data and running tools. It is recommended that you complete the tutorial[ Galaxy 101 for Everyone](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html). No programming experience is required. **How to apply** This workshop is free but participation is subject to application with selection. **_Applications close at 11:59pm AEST Wednesday 29 September 2021._** You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 1 October 2021. Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://hybrid-assembly.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. 2021-10-07 14:00:00 UTC 2021-10-07 17:00:00 UTC Australian BioCommons Australia Australia Genomics [] Melissa Burke (melissa@biocommons.org.au) [] [] 50 workshops_and_courses registration_of_interest Hybrid genome assembly