Contact: Melissa Burke (melissa@biocommons.org.au)
Australian BioCommons is a research infrastructure project building digital capability for life science research in Australia.
Australian BioCommons
https://www.biocommons.org.au/
https://dresa.org.au/content_providers/australian-biocommons
Australian BioCommons is a research infrastructure project building digital capability for life science research in Australia.
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Australian BioCommons YouTube Channel
The Australian BioCommons YouTube channel hosts a collection of recorded webinars on a variety of bioinformatics topics from genomics, to metabolomics, containers, machine learning and more.
Keywords: Bioinformatics
Resource type: video
Australian BioCommons YouTube Channel
https://www.youtube.com/c/AustralianBioCommonsChannel
https://dresa.org.au/materials/australian-biocommons-youtube-channel
The Australian BioCommons YouTube channel hosts a collection of recorded webinars on a variety of bioinformatics topics from genomics, to metabolomics, containers, machine learning and more.
Melissa (melissa@biocommons.org.au)
Bioinformatics
WEBINAR: Global data resources for human genomics and health
This record includes training materials associated with the Australian BioCommons webinar ‘Global data resources for human genomics and health’. This webinar took place on 20 September 2024.
Event description
Dr Mallory Freeberg takes us on a whirlwind tour of the human genomics data resources...
Keywords: Bioinformatics, Genomics
WEBINAR: Global data resources for human genomics and health
https://zenodo.org/records/13845933
https://dresa.org.au/materials/webinar-global-data-resources-for-human-genomics-and-health
This record includes training materials associated with the Australian BioCommons webinar ‘Global data resources for human genomics and health’. This webinar took place on 20 September 2024.
Event description
Dr Mallory Freeberg takes us on a whirlwind tour of the human genomics data resources available at EMBL's European Bioinformatics Institute (EMBL-EBI). Used by scientists across the world, these resources enable the discovery and exploration of genes, variants and their impact on human health and disease.
Resources that will be covered in this webinar include:
Ensembl: a genome browser that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation
DECIPHER: an interactive web-based database and suite of tools that aid the clinical interpretation of genomic variants
Federated EGA: a global resource for discovery and access of sensitive human omics and associated data consented for secondary use
Perturbation Catalogue: a new project from Open Targets that is building a catalogue of harmonised and curated human gene, variant, and expression data
EMBL-EBI’s comprehensive range of freely available and up-to-date molecular data resources are used by scientists globally. The teams running these resources collaborate closely with international experts and are key partners in human genomic data sharing communities including the Global Alliance for Genomics and Health.
Speaker: Dr Mallory Freeberg, Human Genomics Team Leader, EMBL European Bioinformatics Institute
Host: Dr Melissa Burke, Australian BioCommons
Training materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
20240920_Australian-Biocommons-Webinar_MFreeberg: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/5FAj1KffYnY
Melissa Burke (melissa@biocommons.org.au)
Freeberg, Mallory (orcid: 0000-0003-2949-3921)
Bioinformatics, Genomics
WEBINAR: Making sense of gene and protein lists with functional enrichment analysis
This record includes training materials associated with the Australian BioCommons webinar ‘Making sense of gene and protein lists with functional enrichment analysis’. This webinar took place on 23 October 2024.
Topic description
Do you have a long list of genes or proteins from omics experiments...
Keywords: Bioinformatics, Enrichment analysis
WEBINAR: Making sense of gene and protein lists with functional enrichment analysis
https://zenodo.org/records/14032116
https://dresa.org.au/materials/webinar-making-sense-of-gene-and-protein-lists-with-functional-enrichment-analysis
This record includes training materials associated with the Australian BioCommons webinar ‘Making sense of gene and protein lists with functional enrichment analysis’. This webinar took place on 23 October 2024.
Topic description
Do you have a long list of genes or proteins from omics experiments that you don’t know what to do with? This webinar explains how functional enrichment analysis can be used to understand what these lists mean by employing gene ontology and pathway information to highlight the underlying biology. We’ll discuss the statistics that underpin enrichment analysis methods and some of the most commonly used tools, databases and workflows.
Speakers:
Dr Hossein Valipour Kahrood, Bioinformatician, Monash Genomics and Bioinformatics Platform
Dr Cali Willet, Senior Research Bioinformatician, Sydney Informatics Hub, The University of Sydney
Host:
Dr Melissa Burke, Australian BioCommons
Training materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Functional_enrichment_webinar: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://www.youtube.com/watch?v=AvpH2WMNXxA
Melissa Burke (melissa@biocommons.org.au)
Valipour Kahrood, Hossein (orcid: 0000-0003-4166-0382)
Willet, Cali (orcid: 0000-0001-8449-1502)
Bioinformatics, Enrichment analysis
WEBINAR: Getting started with whole genome mapping and variant calling on the command line
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with whole genome mapping and variant calling on the command line’. This webinar took place on 24 August 2022.
Event description
Life scientists are increasingly using whole genome...
Keywords: Genome mapping, Variant calling, Bioinformatics, Workflows
WEBINAR: Getting started with whole genome mapping and variant calling on the command line
https://zenodo.org/records/7024058
https://dresa.org.au/materials/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line-2046f36b-0c7a-4523-9c21-08046900d3ff
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with whole genome mapping and variant calling on the command line’. This webinar took place on 24 August 2022.
Event description
Life scientists are increasingly using whole genome sequencing (WGS) to ask and answer research questions across the tree of life. Before any of this work can be done, there is the essential but challenging task of processing raw sequencing data. Processing WGS data is a computationally challenging, multi-step process used to create a map of an individual’s genome and identify genetic variant sites. The tools you use in this process and overall workflow design can look very different for different researchers, it all depends on your dataset and the research questions you’re asking. Luckily, there are lots of existing WGS processing tools and pipelines out there, but knowing where to start and what your specific needs are is hard work, no matter how experienced you are.
In this webinar we will walk through the essential steps and considerations for researchers who are running and building reproducible WGS mapping and variant calling pipelines at the command line interface. We will discuss how to choose and evaluate a pipeline that is right for your dataset and research questions, and how to get access to the compute resources you need
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
WGS mapping and variant calling _slides (PDF): A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/Q2EceFyizio
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Genome mapping, Variant calling, Bioinformatics, Workflows
WORKSHOP: RNA-Seq: reads to differential genes and pathways
This record includes training materials associated with the Australian BioCommons workshop ‘RNA-Seq: reads to differential genes and pathways’. This workshop took place over two, 3.5 hour sessions on 27 and 28 September 2022.
Event description
RNA sequencing (RNA-seq) is a common method used to...
Keywords: Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re
WORKSHOP: RNA-Seq: reads to differential genes and pathways
https://zenodo.org/records/7439804
https://dresa.org.au/materials/workshop-rna-seq-reads-to-differential-genes-and-pathways-5a384156-d3de-4d5d-9797-e689bf6592f8
This record includes training materials associated with the Australian BioCommons workshop ‘RNA-Seq: reads to differential genes and pathways’. This workshop took place over two, 3.5 hour sessions on 27 and 28 September 2022.
Event description
RNA sequencing (RNA-seq) is a common method used to understand the differences in gene expression and molecular pathways between two or more groups. This workshop introduces the fundamental concepts of RNA sequencing experiments and will allow you to try out the analysis using data from a study of Williams-Beuren Syndrome, a rare disease.
In the first part of the workshop you will learn how to convert sequence reads into analysis ready count data. To do this we will use nf-core/rnaseq - a portable, scalable, reproducible and publicly available workflow on Pawsey Nimbus Cloud. In the second part of the workshop you will use the count data you created to identify differential genes and pathways using R/Rstudio. By the end of the workshop, you should be able to perform your own RNA-seq analysis for differential gene expression and pathway analysis!
This workshop is presented by the Australian BioCommons and Sydney Informatics Hub with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
RNAseq reads to differential genes and pathways - Additional Resources (PDF): Additional resources compiled by the Sydney Informatics Hub
rnaseq_DE_analysis_Day2.html: HTML version of code used on day 2 of the workshop
rnaseq_DE_analysis_Day2.Rmd: R Markdown version of code used on day 2 of the workshop
RNAseq reads to differential genes and pathways_Q_and_A (PDF): Archive of questions and their answers from the workshop Slack Channel.
Materials shared elsewhere:
This workshop follows the tutorial ‘RNA-seq: reads to differential gene expression workshop series’ developed by the Sydney Informatics Hub.
https://sydney-informatics-hub.github.io/training.RNAseq.series-quarto/
Melissa Burke (melissa@biocommons.org.au)
Deshpande, Nandan (orcid: 0000-0002-0324-8728)
Chew, Tracy (orcid: 0000-0001-9529-7705)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re
WEBINAR: Protection of genomic data and the Australian Privacy Act: when is genomic data 'personal information'?
This record includes training materials associated with the Australian BioCommons webinar ‘Protection of genomic data and the Australian Privacy Act: when is genomic data ‘personal information’?’. This webinar took place on 6 April 2022.
Event description
It is easy to assume that genomic data...
Keywords: Bioinformatics, Genomics, Genetic data, Personal information, Health information, Privacy
WEBINAR: Protection of genomic data and the Australian Privacy Act: when is genomic data 'personal information'?
https://zenodo.org/records/6423621
https://dresa.org.au/materials/webinar-protection-of-genomic-data-and-the-australian-privacy-act-when-is-genomic-data-personal-information-1f7194f9-4034-468f-8a78-614f83ef67b0
This record includes training materials associated with the Australian BioCommons webinar ‘Protection of genomic data and the Australian Privacy Act: when is genomic data ‘personal information’?’. This webinar took place on 6 April 2022.
Event description
It is easy to assume that genomic data will be captured by legal definitions of ‘health information’ and ‘genetic information’, but the legal meaning of ‘genetic information’ need not align with scientific categories.
There are many different types of genomic data, with varied characteristics, uses and applications. Clarifying when genomic data is covered by the Privacy Act 1988 (Cth) is an ongoing evaluative exercise but is important for at least 3 reasons:
those subject to the Privacy Act need to be able to confidently navigate their responsibilities
understanding current controls is a prerequisite for meaningful external critique (and this is particularly important at a time when the Privacy Act is under review), and
while legislation that applies to state public sector agencies is generally distinct from the Privacy Act there are similarities that extend the relevance of the question when is genomic data ‘personal information’ under the Privacy Act?
In this presentation, Mark will explore the relationship between the legal concept of genetic information and the concept of genomic data relevant to health and medical research, reflect on the characteristics of each, and the possibility
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Taylor_Slides (PDF): A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/Iaei-9Gu-AI
Melissa Burke (melissa@biocommons.org.au)
Taylor, Mark (orcid: 0000-0003-2009-6284)
Bioinformatics, Genomics, Genetic data, Personal information, Health information, Privacy
WEBINAR: Getting started with proteomics
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023.
Event description
Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is...
Keywords: Bioinformatics, Proteomics, Mass spectrometry
WEBINAR: Getting started with proteomics
https://zenodo.org/records/8019318
https://dresa.org.au/materials/webinar-getting-started-with-proteomics-134c519c-0cea-4195-b444-1e73d551a20e
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023.
Event description
Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is the most common tool for proteomics and the wide array of methods, techniques and specialised approaches available have made it a popular method for probing cells, tissue and organisms in response to various stimuli or diseases.
Each proteomics method has unique experimental design considerations and optimum workflows for data analysis meaning that there is no one-size-fits all solution. The variety of approaches available provides flexibility but can be bewildering and a barrier to getting started.
This webinar sets you up with the foundational knowledge of what to look out for when designing and understanding proteomics experiments. It outlines what you can and can’t do with proteomics, the type of data to expect as well as common data analysis approaches and quality control steps.
This webinar was developed in collaboration with the Australian Core Facilities and Australian Proteomics Communities.
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Getting started with proteomics_slides: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/RSrk2yqklQo
Melissa Burke (melissa@biocommons.org.au)
Padula, Matt (orcid: 0000-0002-8283-0643)
Carroll, Luke (orcid: 0000-0002-8600-4023)
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Bioinformatics, Proteomics, Mass spectrometry
WORKSHOP: Online data analysis for biologists
This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 21 August 2024.
Topic description
Galaxy is a web-based platform that lets you conduct accessible, reproducible, and transparent...
Keywords: Bioinformatics, Data analysis, Galaxy
WORKSHOP: Online data analysis for biologists
https://zenodo.org/records/13948826
https://dresa.org.au/materials/workshop-online-data-analysis-for-biologists
This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 21 August 2024.
Topic description
Galaxy is a web-based platform that lets you conduct accessible, reproducible, and transparent computational biological research. Widely used by researchers world wide, Galaxy gives you access to 1000’s of popular tools for analysis and processing of biological data. It is perfect for working with a wide range of big and small datasets including genome assembly, annotation, epigenetics, metabolomics, metagenomics, proteomics, statistics, transcriptomics, variant analysis and visualisation.
This workshop provides an introduction to using Galaxy and available tools. Using an example dataset, you’ll practice uploading data, choosing and running tools, and viewing the results. We’ll share our top tips for managing your experiments and speeding up your analysis with workflows.
Lead trainer: Dr Gareth Price, Galaxy Australia
Facilitator: Mike Thang, Galaxy Australia / QCIF
Infrastructure provision: Galaxy Australia
Host: Dr Melissa Burke, Australian BioCommons
Training Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event_metadata_Online_data_analysis_for_biologists_210824 (PDF): Information about the event logistics including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Schedule_Online_data_analysis_for_biologists_210824 (PDF): Schedule for the workshop providing a breakdown of topics and timings
Materials shared elsewhere:
This workshop is based on the Galaxy Training Network tutorial ‘Galaxy basics for everyone’: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html
A recording of this workshop is available on the Australian BioCommons YouTube Channel: https://www.youtube.com/watch?v=PF39KjOvreM
Melissa Burke (melissa@biocommons.org.au)
Price, Gareth (orcid: 0000-0003-2439-8650)
Thang, Michael
Bioinformatics, Data analysis, Galaxy
WORKSHOP: Unlocking nf-core - customising workflows for your research
This record includes training materials associated with the Australian BioCommons workshop Unlocking nf-core - customising workflows for your research’. This workshop took place over two, 3 hour sessions on 18-19 May 2023.
Event description
Processing and analysing omics datasets poses many...
Keywords: Bioinformatics, Workflows, Nextflow, nf-core
WORKSHOP: Unlocking nf-core - customising workflows for your research
https://zenodo.org/records/8026170
https://dresa.org.au/materials/workshop-unlocking-nf-core-customising-workflows-for-your-research-1584ff39-e007-4422-9fd5-4e407df6b6c5
This record includes training materials associated with the Australian BioCommons workshop Unlocking nf-core - customising workflows for your research’. This workshop took place over two, 3 hour sessions on 18-19 May 2023.
Event description
Processing and analysing omics datasets poses many challenges to life scientists, particularly when we need to share our methods with other researchers and scale up our research. Public and reproducible bioinformatics workflows, like those developed by nf-core, are invaluable resources for the life science community.
nf-core is a community-driven effort to provide high-quality bioinformatics workflows for common analyses including, RNAseq, mapping, variant calling, and single cell transcriptomics. A big advantage of using nf-core workflows is the ability to customise and optimise them for different computational environments, types and sizes of data and research goals.
This workshop will set you up with the foundational knowledge required to run and customise nf-core workflows in a reproducible manner. On day 1 you will learn about the nf-core tools utility, and step through the code structure of nf-core workflows. Then on day 2, using the nf-core/rnaseq workflow as an example, you will explore the various ways to adjust the workflow parameters, customise processes, and configure the workflow for your computational environment.
This workshop event and accompanying materials were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet). The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project (Australian Research Data Commons and NCRIS via Bioplatforms Australia).
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
nfcore_Schedule: Schedule for the workshop providing a breakdown of topics and timings
nfcore_Q_and_A: Archive of questions and their answers from the workshop Slack Channel.
Materials shared elsewhere:
This workshop follows the accompanying training materials that were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet).
https://sydney-informatics-hub.github.io/customising-nfcore-workshop
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Willet, Cali (orcid: 0000-0001-8449-1502)
Hakkaart, Chris (orcid: 0000-0001-5007-2684)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
Stott, Audrey (orcid: 0000-0003-0939-3173)
Ip, Alex (orcid: 0000-0001-8937-8904)
Cooke, Steele
Bioinformatics, Workflows, Nextflow, nf-core
WEBINAR: A practical guide to AI tools for life scientists
This record includes training materials associated with the Australian BioCommons webinar ‘A practical guide to AI tools for life scientists’. This webinar took place on 8 May 2024.
Event description
The widespread availability and application of AI tools like ChatGPT have fundamentally...
Keywords: Bioinformatics, Machine Learning, Artificial Intelligence, ChatGPT
WEBINAR: A practical guide to AI tools for life scientists
https://zenodo.org/records/11206329
https://dresa.org.au/materials/webinar-a-practical-guide-to-ai-tools-for-life-scientists
This record includes training materials associated with the Australian BioCommons webinar ‘A practical guide to AI tools for life scientists’. This webinar took place on 8 May 2024.
Event description
The widespread availability and application of AI tools like ChatGPT have fundamentally transformed our approach to work, creativity, learning, and communication. In the realm of scientific research, the impact of AI extends far beyond mere promises, already catalysing significant advances and discoveries.
This talk will explore how AI is reshaping scientific exploration and innovation. We explore how AI can accelerate research processes, from data analysis and code writing to hypothesis development. We will present some of the available and emerging AI and how we might effectively leverage these tools while acknowledging their limitations.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Speaker: Dr Michael Kuiper, Principal Research Scientist in Computational Biology and acting Group Leader of the Computational Modelling (CM) group at Data61 of CSIRO.
Host: Dr Patrick Capon, Australian BioCommons
Training materials
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Kuiper_May2024_b_version: A PDF copy of the slides presented during the webinar.
Q_and_A_AI-life-scientists: PDF copy of questions and answers from the webinar
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/NbYvq3OLEfo
Melissa Burke (melissa@biocommons.org.au)
Kuiper, Michael (orcid: 0000-0002-8213-8382)
Bioinformatics, Machine Learning, Artificial Intelligence, ChatGPT
WORKSHOP: Refining genome annotations with Apollo
This record includes training materials associated with the Australian BioCommons workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021.
Workshop description
Genome annotation is crucial to defining the function of genomic sequences. This process...
Keywords: Apollo Software, Bioinformatics, Analysis, Workflows, Genomics, Genome annotation
WORKSHOP: Refining genome annotations with Apollo
https://zenodo.org/records/5781812
https://dresa.org.au/materials/workshop-refining-genome-annotations-with-apollo-d8f95fb3-7dc4-40e0-87d5-e7a4b2ceaf16
This record includes training materials associated with the Australian BioCommons workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021.
Workshop description
Genome annotation is crucial to defining the function of genomic sequences. This process typically involves a round of automated annotation followed by manual curation. Manual curation allows you to visualise your annotations so you can understand what your organism looks like, and then to manually refine these annotations along with any additional data you might have. This process is typically performed collaboratively as part of a team effort.
Apollo is a popular tool for facilitating real-time collaborative, manual curation and genome annotation editing. In this workshop we will learn how to use Apollo to refine genome annotations using example data from an E. coli strain. We’ll focus on the basics like getting data into Apollo, viewing evidence tracks, editing and adding structural and functional annotation, visualising the results and collaborating on genome annotations.
This workshop made use of a training instance of the new Australian Apollo Service. This service enables Australian-based research groups and consortia to access Apollo and host genome assembly and supporting evidence files for free. This service has been made possible by The Australian BioCommons and partners at QCIF and Pawsey. To learn more about the Australian Apollo Service you can watch the Australian Apollo Launch Webinar.
This workshop was presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) .
The Australian Apollo Service is operated by QCIF and underpinned by computational resources provided by the Pawsey Supercomputing Research Centre and receives NCRIS funding through Bioplatforms Australia and the Australian Research Data Commons as well as Queensland Government RICF funding.
The training materials presented in this workshop were developed by Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet for the Galaxy Training Network. Helena and Anthony are part of the Gallantries project which is supported by Erasmus Programme of the European Union.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Schedule (PDF): A breakdown of the topics and timings for the workshop
2021 Apollo Training Intro (PPTX and PDF): Slides used to introduce the Australian Apollo Service
Augustus.gff3 (gff3): E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia.
Blastp_vs_swissprot.gff3: E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia.
Materials shared elsewhere:
This workshop is based on the tutorial ‘Refining genome annotations with Apollo’ which was developed for the Galaxy Training Network.
Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet, Erasmus Programme, 2021 Refining Genome Annotations with Apollo (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/tutorial.html Online; accessed Wed Dec 15 2021
See also:
Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012
Melissa Burke (melissa@biocommons.org.au)
Bretaudeau, Anthony (orcid: 0000-0003-0914-2470)
Rasche, Helena (orcid: 0000-0001-9760-8992)
Williams, Sarah
Nelson, Tiffanie (orcid: 0000-0002-5341-312X)
Thang, Mike
Lee, Justin
Apollo Software, Bioinformatics, Analysis, Workflows, Genomics, Genome annotation
WORKSHOP: Hybrid de novo genome assembly
This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021.
Workshop description
It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches...
Keywords: Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly
WORKSHOP: Hybrid de novo genome assembly
https://zenodo.org/records/5781781
https://dresa.org.au/materials/workshop-hybrid-de-novo-genome-assembly-714004ba-0348-47c8-a68f-038a1f8ccfb1
This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021.
Workshop description
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, Pilon, and Unicycler 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, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience.
This workshop is presented by the Australian BioCommons and Melbourne Bioinformatics with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Schedule (PDF): A breakdown of the topics and timings for the workshop
Materials shared elsewhere:
This workshop follows the tutorial ‘Hybrid genome assembly - Nanopore and Illumina’ developed by Melbourne Bioinformatics.
https://www.melbournebioinformatics.org.au/tutorials/tutorials/hybrid_assembly/nanopore_assembly/
Melissa Burke (melissa@biocommons.org.au)
Hall, Grace (orcid: 0000-0002-5105-8347)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Makunin, Igor
Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly
WORKSHOP: Online data analysis for biologists
This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 9 September 2021.
Workshop description
Galaxy is an online platform for biological research that allows people to use computational data...
Keywords: Bioinformatics, Analysis, Workflows, Galaxy Australia
WORKSHOP: Online data analysis for biologists
https://zenodo.org/records/5775277
https://dresa.org.au/materials/workshop-online-data-analysis-for-biologists-08d66913-4ce3-4528-bdd6-0b0fcf234982
This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 9 September 2021.
Workshop description
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.
The workshop will be held via Zoom and involves a combination of presentations by the lead trainer and smaller breakout groups supported by experienced facilitators.
The materials are shared under a Creative Commons 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Schedule (PDF): schedule for the workshop
Online_data_analysis_for_biologists_extraslides (PPTX and PDF): Slides used to introduce the data set and emphasise the importance of workflows. These slides were developed by Ms Grace Hall.
Materials shared elsewhere:
The tutorial used in this workshop is available via the Galaxy Training Network.
Anne Fouilloux, Nadia Goué, Christopher Barnett, Michele Maroni, Olha Nahorna, Dave Clements, Saskia Hiltemann, 2021 Galaxy 101 for everyone (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html Online; accessed Fri Dec 10 2021
Melissa Burke (melissa@biocommons.org.au)
Hall, Grace (orcid: 0000-0002-5105-8347)
Perreau, Vicky (orcid: 0000-0002-0773-7246)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Bioinformatics, Analysis, Workflows, Galaxy Australia
WEBINAR: Launching the new Apollo Service: collaborative genome annotation for Australian researchers
This record includes training materials associated with the Australian BioCommons webinar ‘Launching the new Apollo Service: collaborative genome annotation for Australian researchers’. This webinar/workshop took place on 29 September 2021.
Event description
Genome annotation is crucial to...
Keywords: Genome Annotation, Genomics, Genome curation, Bioinformatics, Apollo software
WEBINAR: Launching the new Apollo Service: collaborative genome annotation for Australian researchers
https://zenodo.org/records/5775233
https://dresa.org.au/materials/webinar-launching-the-new-apollo-service-collaborative-genome-annotation-for-australian-researchers-3d6cb4b6-50b0-4bf4-ad3a-a60c79dc04ff
This record includes training materials associated with the Australian BioCommons webinar ‘Launching the new Apollo Service: collaborative genome annotation for Australian researchers’. This webinar/workshop took place on 29 September 2021.
Event description
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 Australian 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 and Pawsey are now offering the Apollo Service free to use for Australian-based 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 Australian Apollo Service.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Degnan Lab - Apollo Launch Webinar (PDF): Slides presented by Professors Sandie and Bernie Degnan
Nelson - Apollo Launch Webinar (PDF): Slides presented by Dr Tiffanie Nelson
Voelker - Apollo Launch Webinar (PDF): Slides presented by Julia Voelker
Rane - Apollo Launch Webinar (PDF): Slides presented by Dr Rahul Rane.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/o8jhRra-x4Y
Melissa Burke (melissa@biocommons.org.au)
Nelson, Tiffanie (orcid: 0000-0002-5341-312X)
Rane, Rahul (orcid: 0000-0003-4616-6244)
Degnan, Sandie (orcid: 0000-0001-8003-0426)
Degnan, Bernie (orcid: 0000-0001-7573-8518)
Voelker, Julia (orcid: 0000-0002-7615-0553)
Genome Annotation, Genomics, Genome curation, Bioinformatics, Apollo software
WORKSHOP: R: fundamental skills for biologists
This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.
Event description
Biologists need data analysis skills to be able to...
Keywords: Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
WORKSHOP: R: fundamental skills for biologists
https://zenodo.org/records/6766951
https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists-81aa00db-63ad-4962-a7ac-b885bf9f676b
This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.
Event description
Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets.
R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes.
Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R.
Topics covered in this workshop include:
Spreadsheets, organising data and first steps with R
Manipulating and analysing data with dplyr
Data visualisation
Summarized experiments and getting started with Bioconductor
This workshop is presented by the Australian BioCommons and Saskia Freytag from WEHI with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Schedule (PDF): A breakdown of the topics and timings for the workshop
Recommended resources (PDF): A list of resources recommended by trainers and participants
Q_and_A(PDF): Archive of questions and their answers from the workshop Slack Channel.
Materials shared elsewhere:
This workshop follows the tutorial ‘Introduction to data analysis with R and Bioconductor’ which is publicly available.
https://saskiafreytag.github.io/biocommons-r-intro/
This is derived from material produced as part of The Carpentries Incubator project
https://carpentries-incubator.github.io/bioc-intro/
Melissa Burke (melissa@biocommons.org.au)
Freytag, Saskia (orcid: 0000-0002-2185-7068)
Barugahare, Adele (orcid: 0000-0002-8976-0094)
Doyle, Maria
Ansell, Brendan (orcid: 0000-0003-0297-897X)
Varshney, Akriti
Bourke, Caitlin (orcid: 0000-0002-4466-6563)
Conradsen, Cara (orcid: 0000-0001-9797-3412)
Jung, Chol-Hee (orcid: 0000-0002-2992-3162)
Sandoval, Claudia
Chandrananda, Dineika (orcid: 0000-0002-8834-9500)
Zhang, Eden (orcid: 0000-0003-0294-3734)
Rosello, Fernando (orcid: 0000-0003-3885-8777)
Iacono, Giulia (orcid: 0000-0002-1527-0754)
Tarasova, Ilariya (orcid: 0000-0002-0895-9385)
Chung, Jessica (orcid: 0000-0002-0627-0955)
Moffet, Joel
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Ding, Ke
Feher, Kristen
Perlaza-Jimenez, Laura (orcid: 0000-0002-8511-1134)
Crowe, Mark (orcid: 0000-0002-9514-2487)
Ma, Mengyao
Kandhari, Nitika (orcid: 0000-0002-0261-727X)
Williams, Sarah
Nelson, Tiffanie (orcid: 0000-0002-5341-312X)
Schreiber, Veronika (orcid: 0000-0001-6088-7828)
Pinzon Perez, William
Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
WEBINAR: What exactly is bioinformatics?
This record includes training materials associated with the Australian BioCommons webinar ‘What exactly is bioinformatics?' This webinar took place on 7 August 2024.
Event description
‘Doing’ bioinformatics to extract, process, analyse, and interpret experimental results is something that all...
Keywords: Bioinformatics
WEBINAR: What exactly is bioinformatics?
https://zenodo.org/records/13283096
https://dresa.org.au/materials/webinar-what-exactly-is-bioinformatics
This record includes training materials associated with the Australian BioCommons webinar ‘What exactly is bioinformatics?' This webinar took place on 7 August 2024.
Event description
‘Doing’ bioinformatics to extract, process, analyse, and interpret experimental results is something that all life scientists do as part of their research. But what exactly is bioinformatics? And is there a right (or a wrong) way to do it?
In this webinar, Dr Georgie Samaha welcomes you to the vast world of bioinformatics. Georgie will illuminate key concepts including:
What does a typical experiment look like?
What kind of data will I work with?
What is involved in data-preprocessing?
What’s involved in data analysis?
Where can I do bioinformatics?
We explore common experimental use cases and share essential - but easy to overlook - practical tips for accessing data, software, and computing resources you need to get your research done.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Speaker: Dr Georgie Samaha - Product Owner of the Australian BioCommons BioCLI Project and Bioinformatics Group Lead at the Sydney Informatics Hub, The University of Sydney.
Host: Dr Patrick Capon, Australian BioCommons
Training materials
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Samaha_2024_what_is_bioinformatics_webinar: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/wmy2C-S-rMU
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Bioinformatics
WEBINAR: High performance bioinformatics: submitting your best NCMAS application
This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021.
Bioinformaticians are increasingly turning to specialised compute infrastructure and...
Keywords: Computational Biology, Bioinformatics, High Performance Computing, HPC, NCMAS
WEBINAR: High performance bioinformatics: submitting your best NCMAS application
https://zenodo.org/records/5239883
https://dresa.org.au/materials/webinar-high-performance-bioinformatics-submitting-your-best-ncmas-application-ee80822f-74ac-41af-a5a4-e162c10e6d78
This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021.
Bioinformaticians are increasingly turning to specialised compute infrastructure and efficient, scalable workflows as their research becomes more data intensive. Australian researchers that require extensive compute resources to process large datasets can apply for access to national high performance computing facilities (e.g. Pawsey and NCI) to power their research through the National Computational Merit Allocation Scheme (NCMAS). NCMAS is a competitive, merit-based scheme and requires applicants to carefully consider how the compute infrastructure and workflows will be applied.
This webinar provides life science researchers with insights into what makes a strong NCMAS application, with a focus on the technical assessment, and how to design and present effective and efficient bioinformatic workflows for the various national compute facilities. It will be followed by a short Q&A session.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
High performance bioinformatics: submitting your best NCMAS application - slides (PDF and PPTX): Slides presented during the webinar
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/HeFGjguwS0Y
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Chew, Tracy (orcid: 0000-0001-9529-7705)
Computational Biology, Bioinformatics, High Performance Computing, HPC, NCMAS
WEBINAR: BioSamples: supporting multi-omics data integration with FAIR sample records
This record includes training materials associated with the Australian BioCommons webinar 'BioSamples: supporting multi-omics data integration with FAIR sample records'. This webinar took place on 4 October 2023.Event description The BioSamples database at EMBL-EBI is the ELIXIR deposition...
Keywords: Bioinformatics, Metadata, Multiomics, BioSamples, Data integration
WEBINAR: BioSamples: supporting multi-omics data integration with FAIR sample records
https://zenodo.org/records/10005538
https://dresa.org.au/materials/webinar-biosamples-supporting-multi-omics-data-integration-with-fair-sample-records
This record includes training materials associated with the Australian BioCommons webinar 'BioSamples: supporting multi-omics data integration with FAIR sample records'. This webinar took place on 4 October 2023.Event description The BioSamples database at EMBL-EBI is the ELIXIR deposition database and EMBL-EBI's central institutional repository for information about biological samples (metadata). BioSamples can be used to search, submit and curate sample metadata across multiple projects and contexts. BioSamples records are the key point of connection between EMBL-EBI archives (e.g ENA, ArrayExpress) and other resources.This webinar will highlight how BioSamples can be used to enable multi-omic data sharing and integration including how to submit to the database in combination with other major public repositories. We will look at how BioSamples supports Findable, Accessible, Interoperable and Reusable (FAIR) principles for sample metadata management, and examine case studies where this has been beneficial, for example for integrating data to support the COVID-19 pandemic response.Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.Files and materials included in this record:Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.20231004_BioSamples_Slides: A PDF copy of the slides presented during the webinar.Materials shared elsewhere:A recording of this webinar is available on the Australian BioCommons YouTube Channel:https://youtu.be/bRQ_6zZ4ecE?si=AbU-J2FMK9qVL_JJ
Melissa Burke (melissa@biocommons.org.au)
Burdett, Tony (orcid: 0000-0002-2513-5396)
Bioinformatics, Metadata, Multiomics, BioSamples, Data integration
WEBINAR: Where to go when your bioinformatics outgrows your compute
This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.
Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute...
Keywords: Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
WEBINAR: Where to go when your bioinformatics outgrows your compute
https://zenodo.org/records/5240578
https://dresa.org.au/materials/webinar-where-to-go-when-your-bioinformatics-outgrows-your-compute-7a5a0ff8-8f4f-4fd0-af20-a88d515a6554
This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.
Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute resources. “I don’t know what compute resources I will need”, “My analysis won’t run and I don’t know why” and "Just getting it to work" are common pain points for researchers. In this webinar, you will learn how to understand the compute requirements for your bioinformatics workflows. You will also hear about ways of accessing compute that suits your needs as an Australian researcher, including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey. We also describe bioinformatics and computing support services available to Australian researchers.
This webinar was jointly organised with the Sydney Informatics Hub at the University of Sydney.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Where to go when your bioinformatics outgrows your compute - slides (PDF and PPTX): Slides presented during the webinar
Australian research computing resources cheat sheet (PDF): A list of resources and useful links mentioned during the webinar.
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/hNTbngSc-W0
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Chew, Tracy (orcid: 0000-0001-9529-7705)
Sadsad, Rosemarie (orcid: 0000-0003-2488-953X)
Coddington, Paul (orcid: 0000-0003-1336-9686)
Gladman, Simon (orcid: 0000-0002-6100-4385)
Edberg, Roger
Shaikh, Javed
Cytowski, Maciej (orcid: 0000-0002-0007-0979)
Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
WORKSHOP: Single cell RNAseq analysis in R
This record includes training materials associated with the Australian BioCommons workshop 'Single cell RNAseq analysis in R'. This workshop took place over two, 3.5 hour sessions on 26 and 27 October 2023.Event descriptionAnalysis and interpretation of single cell RNAseq (scRNAseq) data requires...
Keywords: bioinformatics, transcriptomics, single cell RNA-seq, Seurat, R statistical software
WORKSHOP: Single cell RNAseq analysis in R
https://zenodo.org/records/10042919
https://dresa.org.au/materials/workshop-single-cell-rnaseq-analysis-in-r-6a1126cf-7105-43ec-bf55-7c492f758301
This record includes training materials associated with the Australian BioCommons workshop 'Single cell RNAseq analysis in R'. This workshop took place over two, 3.5 hour sessions on 26 and 27 October 2023.Event descriptionAnalysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using Seurat - an R package for QC, analysis, and exploration of single-cell RNAseq data. We will discuss the 'why' behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data.This workshop is presented by the Australian BioCommons, Queensland Cyber Infrastructure Foundation (QCIF) and the Monash Genomics and Bioinformatics Platform with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.Lead trainers: Sarah Williams, Adele Barugahare, Paul Harrison, Laura Perlaza JimenezFacilitators: Nick Matigan, Valentine Murigneux, Magdalena (Magda) AntczakInfrastructure provision: Uwe WinterCoordinator: Melissa BurkeTraining materialsMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.Files and materials included in this record:Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.scRNAseq_Schedule (PDF): A breakdown of the topics and timings for the workshopMaterials shared elsewhere:This workshop follows the tutorial 'scRNAseq Analysis in R with Seurat'https://swbioinf.github.io/scRNAseqInR_Doco/index.htmlSlides used to introduce key topics are available via GitHubhttps://github.com/swbioinf/scRNAseqInR_Doco/tree/main/slidesThis material is based on the introductory Guided Clustering Tutorial tutorial from Seurat.It is also drawing from a similar workshop held by Monash Bioinformatics Platform Single-Cell-Workshop, with material here.
Melissa Burke (melissa@biocommons.org.au)
Williams, Sarah
Barugahare, Adele (orcid: 0000-0002-8976-0094)
Harrison, Paul (orcid: 0000-0002-3980-268X)
Perlaza Jimenez, Laura (orcid: 0000-0002-8511-1134)
Matigan, Nicholas
Murigneux, Valentine (orcid: 0000-0002-1235-9462)
Antczak, Magdalena (orcid: 0000-0003-1503-1849)
Winter, Uwe
bioinformatics, transcriptomics, single cell RNA-seq, Seurat, R statistical software
WORKSHOP: Introduction to Metabarcoding using QIIME2
This record includes training materials associated with the Australian BioCommons workshop ‘Introduction to Metabarcoding using QIIME2’. This workshop took place on 22 February 2022.
Event description
Metabarcoding has revolutionised the study of biodiversity science. By combining DNA taxonomy...
Keywords: Bioinformatics, Analysis, Workflows, Microbial ecology, Metabarcoding, Microbiome
WORKSHOP: Introduction to Metabarcoding using QIIME2
https://zenodo.org/records/6350808
https://dresa.org.au/materials/workshop-introduction-to-metabarcoding-using-qiime2-d3a7ac82-63aa-47e6-9d8e-5126419f9982
This record includes training materials associated with the Australian BioCommons workshop ‘Introduction to Metabarcoding using QIIME2’. This workshop took place on 22 February 2022.
Event description
Metabarcoding has revolutionised the study of biodiversity science. By combining DNA taxonomy with high-throughput DNA sequencing, it offers the potential to observe a larger diversity in the taxa within a single sample, rapidly expanding the scope of microbial analysis and generating high-quality biodiversity data.
This workshop will introduce the topic of metabarcoding and how you can use Qiime2 to analyse 16S data and gain simultaneous identification of all taxa within a sample. Qiime2 is a popular tool used to perform powerful microbiome analysis that can transform your raw data into publication quality visuals and statistics. In this workshop, using example 16S data from the shallow-water marine anemone E. diaphana, you will learn how to use this pipeline to run essential steps in microbial analysis including generating taxonomic assignments and phylogenic trees, and performing both alpha- and beta- diversity analysis.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Schedule (PDF): A breakdown of the topics and timings for the workshop
Materials shared elsewhere:
This workshop follows the tutorial ‘Introduction to metabarcoding with QIIME2’ which has been made publicly available by Melbourne Bioinformatics.
https://www.melbournebioinformatics.org.au/tutorials/tutorials/qiime2/qiime2/
Melissa Burke (melissa@biocommons.org.au)
Dungan, Ashley (orcid: 0000-0003-0958-2177)
Philip, Gayle (orcid: 0000-0002-2671-5093)
Perry, Andrew (orcid: 0000-0001-9256-6068)
Ismail, Rania
Geissler, Laura
Tandon, Kshitij (orcid: 0000-0003-3022-0808)
Makunin, Igor
Bioinformatics, Analysis, Workflows, Microbial ecology, Metabarcoding, Microbiome
WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia
This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022.
Event description
Have you discovered a brilliant...
Keywords: Bioinformatics, Workflows, FAIR, Galaxy Australia
WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia
https://zenodo.org/records/7251310
https://dresa.org.au/materials/webinar-here-s-one-we-prepared-earlier-re-creating-bioinformatics-methods-and-workflows-with-galaxy-australia-134a8bf5-3801-421f-a454-e0f9020f4871
This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022.
Event description
Have you discovered a brilliant bioinformatics workflow but you’re not quite sure how to use it? In this webinar we will introduce the power of Galaxy for construction and (re)use of reproducible workflows, whether building workflows from scratch, recreating them from published descriptions and/or extracting from Galaxy histories.
Using an established bioinformatics method, we’ll show you how to:
Use the workflows creator in Galaxy Australia
Build a workflow based on a published method
Annotate workflows so that you (and others) can understand them
Make workflows finable and citable (important and very easy to do!)
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
GalaxyWorkflows_Slides (PDF): A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/IMkl6p7hkho
Melissa Burke (melissa@biocommons.org.au)
Price, Gareth (orcid: 0000-0003-2439-8650)
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Bioinformatics, Workflows, FAIR, Galaxy Australia
WEBINAR: Getting started with deep learning
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with deep learning’. This webinar took place on 21 July 2021.
Are you wondering what deep learning is and how it might be useful in your research? This high level overview introduces deep...
Keywords: Deep learning, Neural networks, Machine learning
WEBINAR: Getting started with deep learning
https://zenodo.org/records/5121004
https://dresa.org.au/materials/webinar-getting-started-with-deep-learning-986aa2d2-594a-4a7f-836c-44d6e9d5d017
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with deep learning’. This webinar took place on 21 July 2021.
Are you wondering what deep learning is and how it might be useful in your research? This high level overview introduces deep learning ‘in a nutshell’ and provides 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 is followed by a short Q&A session.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Getting Started with Deep Learning - Slides (PDF): Slides used in the presentation
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/I1TmpnZUuiQ
Melissa Burke (melissa@biocommons.org.au)
Tang, Titus (orcid: 0000-0001-7496-1152)
Deep learning, Neural networks, Machine learning
WEBINAR AND PANEL DISCUSSION: Sustainability of biodata resources
This record includes training materials associated with the Australian BioCommons webinar and panel discussion ‘Sustainability of biodata resources’. This event took place on 8 March 2023.
Event description
Environmental, agricultural and biomedical research is dependent on the availability of...
Keywords: Bioinformatics, Open science, Services and resources, Tools, Databases, Global Biodata Coalition
WEBINAR AND PANEL DISCUSSION: Sustainability of biodata resources
https://zenodo.org/records/7816268
https://dresa.org.au/materials/webinar-and-panel-discussion-sustainability-of-biodata-resources-55c612d7-08ea-4d9a-a1fa-6816067048d1
This record includes training materials associated with the Australian BioCommons webinar and panel discussion ‘Sustainability of biodata resources’. This event took place on 8 March 2023.
Event description
Environmental, agricultural and biomedical research is dependent on the availability of high quality data that is made available through biodata resources and databases hosted locally, nationally and internationally. The reality is that funding for development, maintenance and sustainability of biodata resources is often short-term and piecemeal leaving the resources that life scientists depend on in a precarious position. The Global Biodata Coalition was formed in response to this challenge to provide a forum for research funders and others around the globe to better coordinate and share approaches for the efficient management and growth of biodata resources worldwide.
In this extended webinar we discuss the theme of development and sustainability of biodata resources with a panel of guests. We’ll hear about the goals and activities of the Global Biodata Coalition and the challenges faced by well established and highly curated Australian and international data resources (Stemformatics, Community for Antimicrobial Drug Discovery (CO-ADD) Database and InnateDB) in sustaining these resources.
The presentations and panel discussion will be followed by questions from the audience.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/T5Z5prXkvEA
Melissa Burke (melissa@biocommons.org.au)
Cochrane, Guy (orcid: 0000-0001-7954-7057)
Wells, Christine (orcid: 0000-0003-3133-3628)
Zuegg, Johannes (orcid: 0000-0001-6240-6020)
Lynn, David (orcid: 0000-0003-4664-1404)
Bioinformatics, Open science, Services and resources, Tools, Databases, Global Biodata Coalition
WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software
This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.
Event description
bio.tools provides easy access to essential scientific...
Keywords: Bioinformatics, Research software, EDAM, Workflows, FAIR
WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software
https://zenodo.org/records/7024050
https://dresa.org.au/materials/webinar-bio-tools-making-it-easier-to-find-understand-and-cite-biological-tools-and-software-aea38c9e-0b40-4308-bafd-f7580563f520
This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.
Event description
bio.tools provides easy access to essential scientific and technical information about software, command-line tools, databases and services. It’s backed by ELIXIR, the European Infrastructure for Biological Information, and is being used in Australia to register software (e.g. Galaxy Australia, prokka). It underpins the information provided in the Australian BioCommons discovery service ToolFinder.
Hans Ienasescu and Matúš Kalaš join us to explain how bio.tools uses a community driven, open science model to create this collection of resources and how it makes it easier to find, understand, utilise and cite them. They’ll delve into how bio.tools is using standard semantics (e.g. the EDAM ontology) and syntax (e.g. biotoolsSchema) to enrich the annotation and description of tools and resources. Finally, we’ll see how the community can contribute to bio.tools and take advantage of its key features to share and promote their own research software.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
biotools_EDAM_slides (PDF): A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/K0J4_bAUG3Y
Melissa Burke (melissa@biocommons.org.au)
Ienasescu, Hans
Kalaš, Matúš (orcid: 0000-0002-1509-4981)
Bioinformatics, Research software, EDAM, Workflows, FAIR
WEBINAR: Establishing Gen3 to enable better human genome data sharing in Australia
This record includes training materials associated with the Australian BioCommons webinar ‘Establishing Gen3 to enable better human genome data sharing in Australia’. This webinar took place on 16 February 2022.
Event description
Australian human genome initiatives are generating vast amounts...
Keywords: Bioinformatics, Genomics, Human genomics, Digital infrastructure, Gen3, Data sharing, Data management
WEBINAR: Establishing Gen3 to enable better human genome data sharing in Australia
https://zenodo.org/records/6233075
https://dresa.org.au/materials/webinar-establishing-gen3-to-enable-better-human-genome-data-sharing-in-australia-d8caf8c8-d447-4218-be01-95dfd0377f3e
This record includes training materials associated with the Australian BioCommons webinar ‘Establishing Gen3 to enable better human genome data sharing in Australia’. This webinar took place on 16 February 2022.
Event description
Australian human genome initiatives are generating vast amounts of human genome data. There is a desire and need to share data with collaborators but researchers face significant infrastructural, technical and administrative barriers in achieving this. To efficiently share and distribute their genome data they need scalable services and infrastructure that: is easily administered; allows for the efficient data management; enables sharing and interoperability; and is aligned with global standards for human genome data sharing.
Australian BioCommons has brought together a team from Zero Childhood Cancer (Zero), the University of Melbourne Centre for Cancer Research (UMCCR) and Australian Access Federation to explore the use of Gen3 technology. Establishing systems for easier management and sharing of their human genome data holdings is no simple task, and the group wants to ensure that other Australian providers and Institutions can benefit from their experience and easily deploy the same solution in the future.
Gen3 is an open source software suite that makes use of private and public clouds to tackle the challenges of data management, interoperability, data sharing and analysis. It has been used in several very large NIH-funded projects that collectively house and describe data derived from hundreds of thousands of human samples (e.g. NCI Genomic Data Commons, BioData Catalyst, BloodPAC, BrainCommons, Kids First Data Commons).
In this webinar you’ll hear from UMCCR and Zero about their experiences and progress towards establishing Gen3 instances to better enable better human genome data sharing in Australia. They will outline the challenges and opportunities that have arisen through this Australian BioCommons project and demonstrate the capabilities of Gen3 for human genome research.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Gen3_Webinar_Slides (PDF): Slides presented during the webinar
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/1F6B03Byigk
Melissa Burke (melissa@biocommons.org.au)
Pope, Bernie (orcid: 0000-0002-4840-1095)
Hofmann, Oliver (orcid: 0000-0002-7738-1513)
Wong-Erasmus, Marie (orcid: 0000-0003-0066-6606)
Taouk, Kamile (orcid: 0000-0001-8389-510X)
Bioinformatics, Genomics, Human genomics, Digital infrastructure, Gen3, Data sharing, Data management
WORKSHOP: Make your bioinformatics workflows findable and citable
This record includes training materials associated with the Australian BioCommons workshop ‘Make your bioinformatics workflows findable and citable’. This workshop took place on 21 March 2023.
Event description
Computational workflows are invaluable resources for research communities. They help...
Keywords: Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science
WORKSHOP: Make your bioinformatics workflows findable and citable
https://zenodo.org/records/7787488
https://dresa.org.au/materials/workshop-make-your-bioinformatics-workflows-findable-and-citable-74e85d1c-d869-429e-b942-8391f4bab23d
This record includes training materials associated with the Australian BioCommons workshop ‘Make your bioinformatics workflows findable and citable’. This workshop took place on 21 March 2023.
Event description
Computational workflows are invaluable resources for research communities. They help us standardise common analyses, collaborate with other researchers, and support reproducibility. Bioinformatics workflow developers invest significant time and expertise to create, share, and maintain these resources for the benefit of the wider community and being able to easily find and access workflows is an essential factor in their uptake by the community.
Increasingly, the research community is turning to workflow registries to find and access public workflows that can be applied to their research. Workflow registries support workflow findability and citation by providing a central repository and allowing users to search for and discover them easily.
This workshop will introduce you to workflow registries and support attendees to register their workflows on the popular workflow registry, WorkflowHub. We’ll kick off the workshop with an introduction to the concepts underlying workflow findability, how it can benefit workflow developers, and how you can make the most of workflow registries to share your computational workflows with the research community. You will then have the opportunity to register your own workflows in WorkflowHub with support from our trainers.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
2023-03-21_Workflows_slides (PDF): A copy of the slides presented during the workshop
Materials shared elsewhere:
A recording of the first part of this workshop is available on the Australian BioCommons YouTube Channel: https://youtu.be/2kGKxaPuQN8
Melissa Burke (melissa@biocommons.org.au)
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science
WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud
This record includes training materials associated with the Australian BioCommons webinar ‘Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud’. This webinar took place on 20 September 2022.
Event description
Bioinformatics workflows can support...
Keywords: Bioinformatics, Workflows, Nextflow, Containerisation
WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud
https://zenodo.org/records/7095271
https://dresa.org.au/materials/webinar-portable-reproducible-and-scalable-bioinformatics-workflows-using-nextflow-and-pawsey-nimbus-cloud-824bc004-4dcb-4bb5-b0dc-a207c44bbbe6
This record includes training materials associated with the Australian BioCommons webinar ‘Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud’. This webinar took place on 20 September 2022.
Event description
Bioinformatics workflows can support portable, reproducible and scalable analysis of omics datasets but using workflows can be challenging for both beginners and experienced bioinformaticians. Beginners face a steep learning curve to be able to build and deploy their own bioinformatics workflows while those with more experience face challenges productionising and scaling code for custom workflows and big data.
Bioinformaticians across the world are using Nextflow to build and manage workflows. Many of these workflows are shared for others to use and supported by the community via nf-co.re. So far, 39 workflows for omics data are available with another 23 under development. These workflows cover common analyses such as RNAseq, mapping, variant calling, single cell transcriptomics and more and can be easily deployed by anyone, regardless of skill level.
In this webinar, Nandan Deshpande from the Sydney Informatics Hub, University of Sydney, will discuss how you can deploy freely available Nextflow (nf.co-re) bioinformatics workflows with a single command. We describe how you can quickly get started deploying these workflows using Pawsey Nimbus Cloud. For advanced users, we introduce you to Nextflow concepts to get you started with building your own workflows that will save you time and support reproducible, portable and scalable analysis.
In the latter half of the webinar, Sarah Beecroft from the Pawsey Supercomputing Research Centre will talk about their Nimbus Cloud systems. While Nextflow supports portability and can run on many computing infrastructures, we describe why we specifically love using Nimbus with Nextflow for many bioinformatics projects. We will describe some of the nf.co-re workflows that we have used on Nimbus and the research outcomes. We will also cover when not to use Nimbus and the alternatives we recommend.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Nextflow_Nimbus_slides (PDF): A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/VnLX63yXbJU
Melissa Burke (melissa@biocommons.org.au)
Deshpande, Nandan (orcid: 0000-0002-0324-8728)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
Bioinformatics, Workflows, Nextflow, Containerisation
WEBINAR: Getting started with command line bioinformatics
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with command line bioinformatics’. This webinar took place on 22 June 2021.
Bioinformatics skills are in demand like never before and biologists are stepping up to the challenge of...
Keywords: Bioinformatics, Command line, Workflows, Bash, Computational biology
WEBINAR: Getting started with command line bioinformatics
https://zenodo.org/records/5068997
https://dresa.org.au/materials/webinar-getting-started-with-command-line-bioinformatics-248027d1-0773-485a-b511-831e2fd4cc64
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with command line bioinformatics’. This webinar took place on 22 June 2021.
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 to help biologists begin their computational journeys. In this webinar Parice walks you through their hints and tips for getting started with the command line. She covers 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.
The slides were created by Parice Brandies and are based on the publication ‘Ten simple rules for getting started with command-line bioinformatics’ (https://doi.org/10.1371/journal.pcbi.1008645). The slides are shared under a Creative Commons Attribution 4.0 International unless otherwise specified and were current at the time of the webinar.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Getting started with command line bioinformatics - slides (PDF): Slides presented during the webinar
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel
https://youtu.be/p7pA4OLB2X4
Melissa Burke (melissa@biocommons.org.au)
Brandies, Parice (orcid: 0000-0003-1702-2938)
Hogg, Carolyn (type: Supervisor)
Bioinformatics, Command line, Workflows, Bash, Computational biology
WEBINAR: Multivariate integration of multi-omics data with mixOmics
This record includes training materials associated with the Australian BioCommons webinar ‘Multivariate integration of multi-omics data with mixOmics’. This webinar took place on 6 March 2024.
Event description
Multi-omics data (eg. transcriptomics, proteomics) collected from the same set of...
Keywords: Bioinformatics, Omics, Multiomics, Multi-omics, Data integration
WEBINAR: Multivariate integration of multi-omics data with mixOmics
https://zenodo.org/records/10828246
https://dresa.org.au/materials/webinar-multivariate-integration-of-multi-omics-data-with-mixomics
This record includes training materials associated with the Australian BioCommons webinar ‘Multivariate integration of multi-omics data with mixOmics’. This webinar took place on 6 March 2024.
Event description
Multi-omics data (eg. transcriptomics, proteomics) collected from the same set of biospecimens or individuals is a powerful way to understand the underlying molecular mechanisms of a biological system.
mixOmics, a popular R package, integrates omics data from a wide range of sources into a single, unified view making it easier to explore and reveal interactions between omics layers. It overcomes many of the challenges of multi-omic data integration arising from data that are complex and large, with few samples (<50) and many molecules (>10,000), and generated using different technologies.
Prof Kim-Anh Lê Cao, head of the mixOmics team, is delivering this webinar to outline the different methods implemented in mixOmics and how statistical data integration is defined in this context. She will demonstrate how these approaches are applied to analysis of different multi-omics studies and outline the latest methodological developments in this area. From a study of human newborns, to multi-omics microbiomes, and multi-omics in single cells, these examples illustrate how mixOmics is used to perform variable selection and identify a signature of omics markers that characterise a specific phenotype or disease status.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Speaker: Prof Kim-Anh Lê Cao, Director of Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne.
Host: Dr Melissa Burke, Australian BioCommons
Training materials
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Mixomics_BioCommons: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/5XpmQ5X89lA
Melissa Burke (melissa@biocommons.org.au)
Lê Cao, Kim-Anh (orcid: 0000-0003-3923-1116)
Bioinformatics, Omics, Multiomics, Multi-omics, Data integration
WEBINAR: Managing hands-on data analysis training with Galaxy
This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023.
Event description
Looking for flexible, scalable, real-world solutions that enable data analysis skills to...
Keywords: Bioinformatics, Galaxy, Training, Training infrastructure
WEBINAR: Managing hands-on data analysis training with Galaxy
https://zenodo.org/records/8185398
https://dresa.org.au/materials/webinar-managing-hands-on-data-analysis-training-with-galaxy-6d3e8b36-69f2-4fec-9290-d5acd068624a
This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023.
Event description
Looking for flexible, scalable, real-world solutions that enable data analysis skills to be taught to anyone and anywhere?
Galaxy Australia, a national web service supporting 1000s of bioinformatics tools and workflows is a fantastic solution for training on bioinformatics concepts. Their "Training Infrastructure as a Service”, or TIaaS provides free compute and back-end support for data analysis training. It is paired with 100’s of easy-to-follow tutorials developed and maintained by the worldwide community on the Galaxy Training Network (GTN). TIaaS frees trainers from setting up and maintaining computational resources for their training events so that they can focus on student needs and learning outcomes
This webinar will show you how to make the most of Galaxy Australia, TIaaS and the Galaxy Training Network for bioinformatics training. We’ll highlight all the nifty features you can use to plan, manage and deliver training to any size audience efficiently.
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Managing data analysis training with Galaxy_slides: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/VNE0pF6Nqgw
Melissa Burke (melissa@biocommons.org.au)
Price, Gareth (orcid: 0000-0003-2439-8650)
Hiltemann, Saskia (orcid: 0000-0003-3803-468X)
Rasche, Helena (orcid: 0000-0001-9760-8992)
Bioinformatics, Galaxy, Training, Training infrastructure
WEBINAR: Effective, inclusive, and scalable training in the life sciences, clinical education and beyond
This record includes training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Effective, inclusive, and scalable training in the life sciences, clinical education and beyond’. This webinar took place on 4 November 2022.
Event description
Scientists and educators...
Keywords: Short-format training, Clinical education, Continuing education, Professional development, Training, Lifelong learning, Pedagogy
WEBINAR: Effective, inclusive, and scalable training in the life sciences, clinical education and beyond
https://zenodo.org/records/7281360
https://dresa.org.au/materials/webinar-effective-inclusive-and-scalable-training-in-the-life-sciences-clinical-education-and-beyond-52c113ff-573c-4ae8-a3f0-482c86f1818a
This record includes training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Effective, inclusive, and scalable training in the life sciences, clinical education and beyond’. This webinar took place on 4 November 2022.
Event description
Scientists and educators working in the life sciences must continuously acquire new knowledge and skills to stay up-to-date with the latest methods, technologies and research. Short-format training, such as webinars, workshops and bootcamps, are popular ways of quickly learning about new topics and gaining new skills.
As trainers and educators, how can we ensure that short-format training is effective and inclusive for all? How can we ensure that our learners are equipped to continue learning and applying their new skills once they return to their day jobs? And how can we do this in a way that is scalable and sustainable?
The Bicycle Principles assemble education theory and community experience into a framework for improving short-format training so that it is effective, inclusive and scalable. Over 30 international experts, including colleagues from the Australian BioCommons, Melbourne Genomics and other Australian and New Zealand organisations, helped develop the principles and an associated set of recommendations.
Jason Williams, Assistant Director, DNA Learning Center, Cold Spring Harbor Laboratory - a leading genomics and bioinformatics educator and project lead, joins us to discuss the Principles and how they can be applied to achieve scalable and sustainable training in a range of Australian settings.
This webinar is co-hosted by Australian BioCommons and Melbourne Genomics
Training Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
WILLIAMS-Jason_aus-biocommons_nov-2022 (PDF): A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/18dub7jGeQ8
Melissa Burke (melissa@biocommons.org.au)
Williams, Jason (orcid: 0000-0003-3049-2010)
Short-format training, Clinical education, Continuing education, Professional development, Training, Lifelong learning, Pedagogy
WEBINAR: Making sense of phosphoproteomics data with Phosphomatics
This 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.
Mass spectrometry-based phosphoproteomics is one of the most powerful tools available for investigating...
Keywords: Phosphoproteomics, Proteomics, Mass spectrometry
WEBINAR: Making sense of phosphoproteomics data with Phosphomatics
https://zenodo.org/records/5126083
https://dresa.org.au/materials/webinar-making-sense-of-phosphoproteomics-data-with-phosphomatics-a46784bd-7efe-4018-8893-761d1fcd32ba
This 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.
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 provides 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 users 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.
The webinar is followed by a short Q&A session.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Phosphomatics -slides (PDF and PPTX): Slides used in the presentation
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/_WpeL5t2DSI
Melissa Burke (melissa@biocommons.org.au)
Leeming, Michael (orcid: 0000-0001-8981-0701)
Phosphoproteomics, Proteomics, Mass spectrometry
WEBINAR:Genomic data - improving discovery and access management
This record includes training materials associated with the Australian BioCommons webinar ‘Genomic data - improving discovery and access management’. This webinar took place on 14 June 2023.
Event description
Australian human genome initiatives are generating vast amounts of human genome data...
Keywords: Bioinformatics, Data security, Genomics, Data access management
WEBINAR:Genomic data - improving discovery and access management
https://zenodo.org/records/8067584
https://dresa.org.au/materials/webinar-genomic-data-improving-discovery-and-access-management-1b7da2fd-54b0-49b9-bd13-b1f846a5c1c4
This record includes training materials associated with the Australian BioCommons webinar ‘Genomic data - improving discovery and access management’. This webinar took place on 14 June 2023.
Event description
Australian human genome initiatives are generating vast amounts of human genome data to understand the cause of complex diseases, improve diagnosis / early disease detection and identify tailored treatment options.
To achieve this, genomic data needs to be compared between multiple individuals and cohorts, often across efforts/jurisdictions, at national or global scales, and requires the genomic data to be findable, searchable, shareable, and linkable to analytical capabilities.
The Human Genome Platform Project aims to make it as easy as possible to securely and responsibly share human genome research data nationally and internationally. The project is building a ‘services toolbox’ that combines best practice technologies in human genome data sharing.
In this webinar the project team will discuss three important aspects of human genomic data sharing
i) discovery of genomic cohorts and the GA4GH Beacon protocol that enables this functionality across multiple sites
ii) streamlining of data access request management; the Garvan will share experience using the Resource Entitlement Management System (REMS) software package.
iii) community management functionality of CILogon and
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Genomic data - improving discovery and access managements - slides.pdf: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/9SD6gpjDGWE
Melissa Burke (melissa@biocommons.org.au)
Holliday, Jess (orcid: 0000-0003-2855-0066)
Patterson, Andrew (orcid: 0000-0002-1163-8558)
Syed, Mustafa
Kummerfeld, Sarah (orcid: 0000-0002-0089-2358)
Bioinformatics, Data security, Genomics, Data access management
WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset
This 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.
Hybridisation plays an important role in evolution, leading to the exchange of genes...
Keywords: Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing
WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset
https://zenodo.org/records/5105013
https://dresa.org.au/materials/webinar-detection-of-and-phasing-of-hybrid-accessions-in-a-target-capture-dataset-51cc7740-0da1-45f1-95de-f1a47f676053
This 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.
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 showcases a novel bioinformatic workflow, HybPhaser, that can be used to detect and phase hybrids in target capture datasets and will provide the theoretical background and concepts behind the workflow.
This webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focuses on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference.
The materials are shared under a Creative Commons 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Nauheimer_hybphaser_slides (PDF): Slides presented during the webinar
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/japXwTAhA5U
Melissa Burke (melissa@biocommons.org.au)
Nauheimer, Lars (orcid: 0000-0002-2847-0966)
Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing
WEBINAR: KBase - A knowledge base for systems biology
This record includes training materials associated with the Australian BioCommons webinar ‘KBase - A knowledge base for systems biology’. This webinar took place on 22 September 2021.
Event description
Developed for bench biologists and bioinformaticians, The Department of Energy Systems...
Keywords: Systems Biology, FAIR Research, Open Source Software, Metagenomics, Microbiology
WEBINAR: KBase - A knowledge base for systems biology
https://zenodo.org/records/5717580
https://dresa.org.au/materials/webinar-kbase-a-knowledge-base-for-systems-biology-653d9753-989d-4194-9230-6e2d90652955
This record includes training materials associated with the Australian BioCommons webinar ‘KBase - A knowledge base for systems biology’. This webinar took place on 22 September 2021.
Event description
Developed for bench biologists and bioinformaticians, The Department of Energy Systems Biology Knowledgebase (KBase) 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.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Q&A for Australian BioCommons KBase Webinar [PDF]: Document containing answers to questions asked during the webinar and links to additional resources
Introduction to KBase: Australian BioCommons Webinar [PDF]: Slides presented during the webinar
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/tJ94i9gOJfU
The slides are also available as Google slides:
https://tinyurl.com/KBase-webinar-slides
Melissa Burke (melissa@biocommons.org.au)
Dow, Ellen (orcid: 0000-0002-2079-0260)
Wood-Charlson, Elisha (orcid: 0000-0001-9557-7715)
Systems Biology, FAIR Research, Open Source Software, Metagenomics, Microbiology
WORKSHOP: Variant calling in humans, animals and plants with Galaxy
This 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.
Variant calling in polyploid organisms, including humans, plants and animals, can help determine single...
Keywords: Variant calling, Genetic Variation Analysis, SNP annotation
WORKSHOP: Variant calling in humans, animals and plants with Galaxy
https://zenodo.org/records/5076668
https://dresa.org.au/materials/workshop-variant-calling-in-humans-animals-and-plants-with-galaxy-767f1816-1c06-478c-adf4-90b3b2d32a9c
This 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.
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 focused on the tools and workflows available for variant calling in polyploid organisms in Galaxy Australia. The workshop provided opportunities for hands-on experience using Freebayes for variant calling and SnpEff and GEMINI for variant annotation. The workshop made 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 was via Galaxy Australia, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience.
The materials are shared under a Creative Commons 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Schedule (PDF): schedule for the workshop
Variant calling - humans, animals, plants - slides (PPTX and PDF): slides used in the workshop
Materials shared elsewhere:
The tutorial used in this workshop is available via the Galaxy Training Network.
Wolfgang Maier, Bérénice Batut, Torsten Houwaart, Anika Erxleben, Björn Grüning, 2021 Exome sequencing data analysis for diagnosing a genetic disease (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html Online; accessed 25 May 2021
Melissa Burke (melissa@biocommons.org.au)
Price, Gareth (orcid: 0000-0003-2439-8650)
Variant calling, Genetic Variation Analysis, SNP annotation
WEBINAR: Variant interpretation: from the clinic to the lab… and back again
This record collates training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Variant interpretation: from the clinic to the lab… and back again’. This webinar took place on 7 December 2022.
Event description
The use of genomic testing is increasing rapidly as...
Keywords: Clinical genomics, Variant interpretation, Variant curation, Continuing Professional Development, Professional Development, Bioinformatics, Genomics, Variant calling
WEBINAR: Variant interpretation: from the clinic to the lab… and back again
https://zenodo.org/records/7425920
https://dresa.org.au/materials/webinar-variant-interpretation-from-the-clinic-to-the-lab-and-back-again-5c6aed91-24cd-4314-9638-5e60d51e1af1
This record collates training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Variant interpretation: from the clinic to the lab… and back again’. This webinar took place on 7 December 2022.
Event description
The use of genomic testing is increasing rapidly as the cost of genome sequencing decreases. Many areas of the health workforce are upskilling in genomics to help meet the increased demand. From clinicians learning how to use the right test, for the right patient, at the right time, to medical scientists learning how to interpret and classify variants, and data scientists to learning how to better create and continuously refine the pipelines and software to handle and curate big data.
In this webinar, we’ll hear from two people working at the coalface of variant interpretation – one in a diagnostic laboratory and the other in a cancer research laboratory.
Naomi Baker is Medical Scientist at Victorian Clinical Genetics Services. She helps process hundreds of genomic tests per year to find the variants that cause rare diseases. She’ll explain the clinical variant interpretation processes she uses, the pipelines, professions and people involved.
Joep Vissers is a Curation Team Leader, at the University of Melbourne Centre for Cancer Research, Department of Clinical Pathology. Joep, who also teaches cancer biology at the University, will describe how he uses variant interpretation in his work at the research/clinical interface, and the shift in mindset required when working with data for these different purposes.
Amy Nisselle, Genomics Workforce Lead at Melbourne Genomics, will then briefly outline some of the education programs available in clinical variant interpretation.
This webinar is co-presented by Australian BioCommons and Melbourne Genomics
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Variant interpretation from the clinic to the lab and back again.pdf: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/wLMhwIiK8Lw
Melissa Burke (melissa@biocommons.org.au)
Baker, Naomi
Vissers, Joep (orcid: 0000-0003-0435-6824)
Nisselle, Amy (orcid: 0000-0002-8908-5906)
Clinical genomics, Variant interpretation, Variant curation, Continuing Professional Development, Professional Development, Bioinformatics, Genomics, Variant calling
WORKSHOP: Working with genomics sequences and features in R with Bioconductor
This record includes training materials associated with the Australian BioCommons workshop ‘Working with genomics sequences and features in R with Bioconductor’. This workshop took place on 23 September 2021.
Workshop description
Explore the many useful functions that the Bioconductor...
Keywords: R software, Bioconductor, Bioinformatics, Analysis, Genomics, Sequence analysis
WORKSHOP: Working with genomics sequences and features in R with Bioconductor
https://zenodo.org/records/5781776
https://dresa.org.au/materials/workshop-working-with-genomics-sequences-and-features-in-r-with-bioconductor-8399bf0d-1e9e-48f3-a840-3f70f23254bb
This record includes training materials associated with the Australian BioCommons workshop ‘Working with genomics sequences and features in R with Bioconductor’. This workshop took place on 23 September 2021.
Workshop description
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.
This workshop is presented by the Australian BioCommons and Monash Bioinformatics Platform with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Schedule (PDF): schedule for the workshop providing a breakdown of topics and timings
Materials shared elsewhere:
This workshop follows the tutorial ‘Working with DNA sequences and features in R with Bioconductor - version 2’ developed for Monash Bioinformatics Platform and Monash Data Fluency by Paul Harrison.
https://monashdatafluency.github.io/r-bioc-2/
Melissa Burke (melissa@biocommons.org.au)
Harrison, Paul (orcid: 0000-0002-3980-268X)
Deshpande, Nandan (orcid: 0000-0002-0324-8728)
Barugahare, Adele (orcid: 0000-0002-8976-0094)
Perry, Andrew (orcid: 0000-0001-9256-6068)
Wong, Nick (orcid: 0000-0003-4393-7541)
Reames, Benjamin
R software, Bioconductor, Bioinformatics, Analysis, Genomics, Sequence analysis
WORKSHOP: RNASeq: reads to differential genes and pathways
This record includes training materials associated with the Australian BioCommons workshop 'RNASeq: reads to differential genes and pathways'. This workshop took place over two, 3 hour sessions on 11 and 12 October 2023.Event descriptionRNA sequencing (RNAseq) is a popular and powerful technique...
Keywords: bioinformatics, transcriptomics, RNA-seq, RNAseq
WORKSHOP: RNASeq: reads to differential genes and pathways
https://zenodo.org/records/10045628
https://dresa.org.au/materials/workshop-rnaseq-reads-to-differential-genes-and-pathways
This record includes training materials associated with the Australian BioCommons workshop 'RNASeq: reads to differential genes and pathways'. This workshop took place over two, 3 hour sessions on 11 and 12 October 2023.Event descriptionRNA sequencing (RNAseq) is a popular and powerful technique used to understand the activity of genes. Using differential gene profiling methods, we can use RNAseq data to gain valuable insights into gene activity and identify variability in gene expression between samples to understand the molecular pathways underpinning many different traits. In this hands-on workshop, you will learn RNAseq fundamentals as you process, analyse, and interpret the results from a real RNAseq experiment on the command-line. In session one, you will convert raw sequence reads to analysis-ready count data with the nf-core/rnaseq workflow. In session two, you'll work interactively in RStudio to identify differentially expressed genes,perform functional enrichment analysis, and visualise and interpret your results using popular and best practice R packages. This workshop was delivered as a part of the Australian BioCommons Bring Your Own Data Platforms Project and will provide you with an opportunity to explore services and infrastructure built specifically for life scientists working at the command line. By the end of the workshop, you will be familiar with Pawsey's Nimbus cloud platform and be able to process your own RNAseq datasets and perform differential expression analysis on the command-line. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.Lead trainers: Dr Georgina Samaha (Sydney Informatics Hub), Dr Nandan Deshpande (Sydney Informatics Hub)Facilitators: Ching-Yu Lu and Jessica Chung.Infrastructure provision: Audrey Stott (Pawsey Supercomputing Research Centre), Alex Ip (AARNet)Host: Melissa Burke, Australian BioCommons Training materialsFiles and materials included in this record:Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.Materials shared elsewhere:This workshop follows the tutorial 'Introduction to RNAseq workshop: reads to differential gene expression' developed by the Sydney Informatics Hub.https://sydney-informatics-hub.github.io/rnaseq-workshop-2023/Additional supporting materials are available via GitHubRstudio rnaseq container: https://github.com/Sydney-Informatics-Hub/Rstudio-rnaseq-contained/tree/mainRNAseq differential expression R notebook: https://github.com/Sydney-Informatics-Hub/rna-differential-expression-Rnotebook
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Deshpande, Nandan (orcid: 0000-0002-0324-8728)
Lu, Ching-Yu
Chung, Jessica (orcid: 0000-0002-0627-0955)
Stott, Audrey
Ip, Alex (orcid: 0000-0001-8937-8904)
bioinformatics, transcriptomics, RNA-seq, RNAseq
WEBINAR: Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share
This record includes training materials associated with the Australian BioCommons webinar ‘Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share’. This webinar took place on 12 March 2024.
Event description
The Australian BioCommons Leadership Share (ABLeS) supports...
Keywords: Bioinformatics, Computational biology, Computational infrastructure
WEBINAR: Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share
https://zenodo.org/records/10866820
https://dresa.org.au/materials/webinar-scaling-up-bioinformatics-with-ables-the-australian-biocommons-leadership-share
This record includes training materials associated with the Australian BioCommons webinar ‘Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share’. This webinar took place on 12 March 2024.
Event description
The Australian BioCommons Leadership Share (ABLeS) supports access to, and efficient use of, national computational systems for big-data bioinformatics. Designed for established life sciences projects, groups, institutes and consortia, ABLeS can be used to facilitate software optimisation and scaling, implementation of optimised software for production analyses, and creation of reference data.
This webinar highlights how ABLeS is being used by life science communities across Australia to access and leverage bioinformatics at scale. We’ll explain the structure of the ABLeS program and how your life science community can get involved, as well as providing a breakdown of the program expectations and the support available from the BioCommons and our partners. Community members making use of ABLeS will share their perspective on the program, and the research outcomes that have resulted.
ABLeS is supported by the Australian BioCommons in partnership with Bioplatforms Australia, the National Computational Infrastructure, and the Pawsey Supercomputing Centre.
Speakers:
Australian BioCommons:
Dr Steven Manos
Dr Johan Gustafsson
Dr Ziad Al Bkhetan
ABLeS users:
Dr Hardip Patel, National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University
Chelsea Mayoh, Zero Childhood Cancer, Children's Cancer Institute
Theodore Allnutt, Royal Botanic Gardens Victoria
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
BioCommons_ABLeS: A PDF copy of the slides presented by the BioCommons team during the webinar.
Mayoh_ABLeS: A PDF copy of the slides presented by Chelsea Mayoh
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/Eb0z2-yaJbY
Melissa Burke (melissa@biocommons.org.au)
Al Bkhetan, Ziad
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Manos, Steven (orcid: 0000-0002-3461-1307)
Patel, Hardip (orcid: 0000-0003-3169-049X)
Mayoh, Chelsea (orcid: 0000-0002-6398-3046)
Allnutt, Theodore (orcid: 0000-0002-8258-0058)
Bioinformatics, Computational biology, Computational infrastructure
WEBINAR: Pro tips for scaling bioinformatics workflows to HPC
This record includes training materials associated with the Australian BioCommons webinar ‘Pro tips for scaling bioinformatics workflows to HPC’. This webinar took place on 31 May 2023.
Event description
High Performance Computing (HPC) infrastructures offer the computational scale and...
Keywords: Bioinformatics, Workflows, HPC, High Performance Computing
WEBINAR: Pro tips for scaling bioinformatics workflows to HPC
https://zenodo.org/records/8008227
https://dresa.org.au/materials/webinar-pro-tips-for-scaling-bioinformatics-workflows-to-hpc-9f2a8b90-88da-433b-83b2-b1ab262dd9df
This record includes training materials associated with the Australian BioCommons webinar ‘Pro tips for scaling bioinformatics workflows to HPC’. This webinar took place on 31 May 2023.
Event description
High Performance Computing (HPC) infrastructures offer the computational scale and efficiency that life scientists need to handle complex biological datasets and multi-step computational workflows. But scaling workflows to HPC from smaller, more familiar computational infrastructures brings with it new jargon, expectations, and processes to learn. To make the most of HPC resources, bioinformatics workflows need to be designed for distributed computing environments and carefully manage varying resource requirements, and data scale related to biology.
In this webinar, Dr Georgina Samaha from the Sydney Informatics Hub, Dr Matthew Downton from the National Computational Infrastructure (NCI) and Dr Sarah Beecroft from the Pawsey Supercomputing Research Centre help you navigate the world of HPC for running and developing bioinformatics workflows. They explain when you should take your workflows to HPC and highlight the architectural features you should make the most of to scale your analyses once you’re there. You’ll hear pro-tips for dealing with common pain points like software installation, optimising for parallel computing and resource management, and will find out how to get access to Australia’s National HPC infrastructures at NCI and Pawsey.
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Pro-tips_HPC_Slides: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/YKJDRXCmGMo
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
Downton, Matthew (orcid: 0000-0002-4693-1965)
Bioinformatics, Workflows, HPC, High Performance Computing
WEBINAR: AlphaFold: what's in it for me?
This record includes training materials associated with the Australian BioCommons webinar ‘WEBINAR: AlphaFold: what’s in it for me?’. This webinar took place on 18 April 2023.
Event description
AlphaFold has taken the scientific world by storm with the ability to accurately predict the...
Keywords: Bioinformatics, Machine Learning, Structural Biology, Proteins, Drug discovery, AlphaFold, AI, Artificial Intelligence, Deep learning
WEBINAR: AlphaFold: what's in it for me?
https://zenodo.org/records/7865494
https://dresa.org.au/materials/webinar-alphafold-what-s-in-it-for-me-4d1ea222-4240-4b68-b9ae-7769ac664ee0
This record includes training materials associated with the Australian BioCommons webinar ‘WEBINAR: AlphaFold: what’s in it for me?’. This webinar took place on 18 April 2023.
Event description
AlphaFold has taken the scientific world by storm with the ability to accurately predict the structure of any protein in minutes using artificial intelligence (AI). From drug discovery to enzymes that degrade plastics, this promises to speed up and fundamentally change the way that protein structures are used in biological research.
Beyond the hype, what does this mean for structural biology as a field (and as a career)?
Dr Craig Morton, Drug Discovery Lead at the CSIRO, is an early adopter of AlphaFold and has decades of expertise in protein structure / function, protein modelling, protein – ligand interactions and computational small molecule drug discovery, with particular interest in anti-infective agents for the treatment of bacterial and viral diseases.
Craig joins this webinar to share his perspective on the implications of AlphaFold for science and structural biology. He will give an overview of how AlphaFold works, ways to access AlphaFold, and some examples of how it can be used for protein structure/function analysis.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/4ytn2_AiH8s
Melissa Burke (melissa@biocommons.org.au)
Morton, Craig (orcid: 0000-0001-5452-5193)
Bioinformatics, Machine Learning, Structural Biology, Proteins, Drug discovery, AlphaFold, AI, Artificial Intelligence, Deep learning
WEBINAR: Getting started with RNAseq: Transforming raw reads into biological insights
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with RNAseq: Transforming raw reads into biological insights’. This webinar took place on 6 September 2023.
Event description
RNA sequencing (RNAseq) is a powerful technique for...
Keywords: Bioinformatics, Transcriptomics, RNA-seq, RNAseq, Gene expression
WEBINAR: Getting started with RNAseq: Transforming raw reads into biological insights
https://zenodo.org/records/8323208
https://dresa.org.au/materials/webinar-getting-started-with-rnaseq-transforming-raw-reads-into-biological-insights-1f7db385-e282-4332-a1c4-d1d73a769b1b
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with RNAseq: Transforming raw reads into biological insights’. This webinar took place on 6 September 2023.
Event description
RNA sequencing (RNAseq) is a powerful technique for investigating gene expression in biological samples. Processing and analysing RNAseq data involves multiple steps to align raw sequence reads to a reference genome, count the number of reads mapped to each gene, and perform statistical analyses to identify differentially expressed genes and functionally annotate them. RNAseq experiments have many different applications as we apply them to a variety of research questions and organisms. This diversity of applications can make it challenging to appreciate all the design considerations, processing requirements, and limitations of RNAseq experiments as they apply to you.
In this webinar, you will gain an understanding of the key considerations for designing and performing your own successful experiments with bulk RNA. We’ll start at the lab bench with RNA extraction, quality control, and library preparation, then move to the sequencing machine where you will make essential decisions about sequencing platforms, optimal sequencing depth, and the importance of replicates. We’ll talk about bioinformatics workflows for RNAseq data processing and the computational requirements of transforming raw sequencing reads to analysis-ready count data. Finally, we’ll discuss how to apply differential expression and functional enrichment analyses to gain biological insights from differentially expressed genes.
This webinar was developed by the Sydney Informatics Hub in collaboration with the Australian BioCommons.
Training materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Getting started with RNAseq: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/tITR3WR_jWI
Melissa Burke (melissa@biocommons.org.au)
Deshpande, Nandan (orcid: 0000-0002-0324-8728)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Bioinformatics, Transcriptomics, RNA-seq, RNAseq, Gene expression
WORKSHOP: Translating workflows into Nextflow with Janis
This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023.
Event description
Bioinformatics workflows are critical for reproducibly transferring methodologies...
Keywords: Bioinformatics, Workflows, Nextflow, CWL, Galaxy
WORKSHOP: Translating workflows into Nextflow with Janis
https://zenodo.org/records/8072678
https://dresa.org.au/materials/workshop-translating-workflows-into-nextflow-with-janis-36386c6d-f9a2-4b4d-afa9-062ce3b8ac5d
This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023.
Event description
Bioinformatics workflows are critical for reproducibly transferring methodologies between research groups and for scaling between computational infrastructures. Research groups currently invest a lot of time and effort in creating and updating workflows; the ability to translate from one workflow language into another can make them easier to share, and maintain with minimal effort. For example, research groups that would like to run an existing Galaxy workflow on HPC, or extend it for their use, might find translating the workflow to Nextflow more suitable for their ongoing use-cases.
Janis is a framework that provides an abstraction layer for describing workflows, and a tool that can translate workflows between existing languages such as CWL, WDL, Galaxy and Nextflow. Janis aims to translate as much as it can, leaving the user to validate the workflow and make small manual adjustments where direct translations are not possible. Originating from the Portable Pipelines Project between Melbourne Bioinformatics, the Peter MacCallum Cancer Centre, and the Walter and Eliza Hall Institute of Medical Research, this tool is now available for everyone to use.
This workshop provides an introduction to Janis and how it can be used to translate Galaxy and CWL based tools and workflows into Nextflow. Using hands-on examples we’ll step you through the process and demonstrate how to optimise, troubleshoot and test the translated workflows.
This workshop event and accompanying materials were developed by the Melbourne Bioinformatics and the Peter MacCallum Cancer Centre. The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project funded by the Australian Research Data Commons and NCRIS via Bioplatforms Australia.
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Intro to Galaxy (PDF): Slides presented during the workshop
Intro to CWL (PDF): Slides presented during the workshop
Intro to the session & Janis (PDF): Slides presented during the workshop
Janis_Schedule (PDF): Schedule for the workshop providing a breakdown of topics and timings
Materials shared elsewhere:
This workshop follows the accompanying training materials: https://www.melbournebioinformatics.org.au/tutorials/tutorials/janis_translate/janis_translate
A recording of the workshop is available on the Australian BioCommons YouTube channel: https://youtu.be/0IiY1GEx_BY
Melissa Burke (melissa@biocommons.org.au)
Hall, Grace (orcid: 0000-0002-5105-8347)
Lupat, Richard (orcid: 0000-0002-6435-7100)
Bioinformatics, Workflows, Nextflow, CWL, Galaxy
WORKSHOP: Single cell RNAseq analysis in R
This record includes training materials associated with the Australian BioCommons workshop ‘Single cell RNAseq analysis in R’. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022.
Event description
Analysis and interpretation of single cell RNAseq (scRNAseq) data...
Keywords: Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq
WORKSHOP: Single cell RNAseq analysis in R
https://zenodo.org/records/7072910
https://dresa.org.au/materials/workshop-single-cell-rnaseq-analysis-in-r-4f60b82d-2f1e-4021-9569-6955878dd945
This record includes training materials associated with the Australian BioCommons workshop ‘Single cell RNAseq analysis in R’. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022.
Event description
Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using Seurat - an R package for QC, analysis, and exploration of single-cell RNAseq data.
We will discuss the ‘why’ behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data.
This workshop is presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
scRNAseq_Slides (PDF): Slides used to introduce topics
scRNAseq_Schedule (PDF): A breakdown of the topics and timings for the workshop
scRNAseq_Resources (PDF): A list of resources recommended by trainers and participants
scRNAseq_QandA(PDF): Archive of questions and their answers from the workshop Slack Channel.
Materials shared elsewhere:
This workshop follows the tutorial ‘scRNAseq Analysis in R with Seurat’
https://swbioinf.github.io/scRNAseqInR_Doco/index.html
This material is based on the introductory Guided Clustering Tutorial tutorial from Seurat.
It is also drawing from a similar workshop held by Monash Bioinformatics Platform Single-Cell-Workshop, with material here.
Melissa Burke (melissa@biocommons.org.au)
Williams, Sarah
Mehdi, Ahmed (orcid: 0000-0002-9300-2341)
Matigan, Nick
Barugahare, Adele (orcid: 0000-0002-8976-0094)
Harrison, Paul (orcid: 0000-0002-3980-268X)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Whitfield, Holly (orcid: 0000-0002-7282-387X)
Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq
WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation
This 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.
Multi-gene datasets used in phylogenetic...
Keywords: Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing
WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation
https://zenodo.org/records/5104998
https://dresa.org.au/materials/webinar-conflict-in-multi-gene-datasets-why-it-happens-and-what-to-do-about-it-deep-coalescence-paralogy-and-reticulation-a6743550-b904-45e1-9635-4e481ee8f739
This 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.
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 explores three different forms of discordance: deep coalescence, paralogy, and reticulation. In each case, it considers underlying biological processes, how discordance presents in the data, and what bioinformatic or phylogenetic approaches and tools are available to address these challenges. It covers Yang and Smith paralogy resolution and general information on options for phylogenetic analysis.
This webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focused on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference.
The materials are shared under a Creative Commons 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Schmidt-Lebuhn - paralogy lineage sorting reticulation - slides (PDF): Slides presented during the webinar
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/1bw81q898z8
Melissa Burke (melissa@biocommons.org.au)
Schmidt-Lebuhn, Alexander (orcid: 0000-0002-7402-8941)
Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing
WEBINAR: MaveDB: discovery and interpretation of high-throughput functional assay data
This record includes training materials associated with the Australian BioCommons webinar ‘MaveDB: discovery and interpretation of high-throughput functional assay data’. This webinar took place on 26 March 2024.
Event description
Multiplexed assays of variant effect (MAVEs) are a family of...
Keywords: Bioinformatics, Genetic variation, Functional annotation, Clinical genetics
WEBINAR: MaveDB: discovery and interpretation of high-throughput functional assay data
https://zenodo.org/records/10929633
https://dresa.org.au/materials/webinar-mavedb-discovery-and-interpretation-of-high-throughput-functional-assay-data
This record includes training materials associated with the Australian BioCommons webinar ‘MaveDB: discovery and interpretation of high-throughput functional assay data’. This webinar took place on 26 March 2024.
Event description
Multiplexed assays of variant effect (MAVEs) are a family of experimental techniques that measure all single amino acid or single nucleotide changes in a gene or other functional element. MaveDB is an international community database that enables discovery and reuse of data from these experiments. It provides a platform for integrating large-scale measurements of sequence variant impact with applications that can be used to interpret the data for basic and clinical research.
In this webinar we consider:
What are MAVEs and how are the experiments performed?
How much MAVE data is available in MaveDB and how is it organised?
Who can submit datasets to MaveDB?
What are some of the clinical applications for MAVEs and how is the data being used to understand patient variants?
Speaker: Dr Alan Rubin, Senior Research Officer, WEHI
Host: Dr Melissa Burke, Australian BioCommons
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
MAVEDB_slides: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/BXGQ2IuDnGE
Melissa Burke (melissa@biocommons.org.au)
Rubin, Alan (orcid: 0000-0003-1474-605X)
Bioinformatics, Genetic variation, Functional annotation, Clinical genetics
WEBINAR: MetaboLights: the home for metabolomics experiments and derived information
This record includes training materials associated with the Australian BioCommons webinar ‘MetaboLights: the home for metabolomics experiments and derived information’. This webinar took place on 9 April 2024.
Event description
MetaboLights is an open-access database for metabolomics studies,...
Keywords: Bioinformatics, Metabolomics, Metabolites, Data sharing
WEBINAR: MetaboLights: the home for metabolomics experiments and derived information
https://zenodo.org/records/10963462
https://dresa.org.au/materials/webinar-metabolights-the-home-for-metabolomics-experiments-and-derived-information
This record includes training materials associated with the Australian BioCommons webinar ‘MetaboLights: the home for metabolomics experiments and derived information’. This webinar took place on 9 April 2024.
Event description
MetaboLights is an open-access database for metabolomics studies, their raw experimental data and associated metadata. It is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles and locations where available. MetaboLights is the recommended metabolomics repository for a number of leading journals and ELIXIR, the European infrastructure for life science information.
This webinar will provide an introduction to MetaboLights and how it can be used as:
A repository, enabling the metabolomics community to share findings, data and protocols from metabolomics studies.
A compound library of curated knowledge about metabolite structures, their reference spectra, as well as their biological roles, locations, concentrations, and raw data from metabolic experiments.
The webinar will provide details about data availability, standards and re-use, as well as guidance on submitting your own metabolomics data.
Speaker: Dr Thomas Payne, Scientific Database Curator - MetaboLights, EMBL-EBI
Host: Dr Patrick Capon, Australian BioCommons
Training materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
2024_MetaboLights_Webinar_TP: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/aCALHhqxOiM
Melissa Burke (melissa@biocommons.org.au)
Payne, Thomas (orcid: 0000-0001-7522-981X)
Bioinformatics, Metabolomics, Metabolites, Data sharing
WEBINAR: Conservation genomics in the age of extinction
This record includes training materials associated with the Australian BioCommons webinar ‘Conservation genomics in the age of extinction’. This webinar took place on 8 March 2022.
Event description
Biodiversity is crashing and millions of plant and animal species are at the edge of...
Keywords: Conservation genomics, Genomics, Bioinformatics, Sequencing, Threatened Species Initiative, Galaxy Australia
WEBINAR: Conservation genomics in the age of extinction
https://zenodo.org/records/6350785
https://dresa.org.au/materials/webinar-conservation-genomics-in-the-age-of-extinction-c7718a53-68ee-4c69-adf4-cd0550710d3f
This record includes training materials associated with the Australian BioCommons webinar ‘Conservation genomics in the age of extinction’. This webinar took place on 8 March 2022.
Event description
Biodiversity is crashing and millions of plant and animal species are at the edge of extinction. Understanding the genetic diversity of these species is an important tool for conservation biology but obtaining high quality genomes for threatened species is not always straightforward.
In this webinar Dr Carolyn Hogg speaks about the work she has been doing with the Threatened Species Initiative to build genomic resources to understand and protect Australia’s threatened species. Using examples such as the Kroombit Tinker Frog and the Greater Bilby, Carolyn describes some of the complexities and challenges of generating genomes from short reads and HiFi reads for critically endangered species. She outlines the technologies and resources being used and how these are bridging the gap between genomicists, bioinformaticians and conservation experts to help save Australian species.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/Bl7CaiGQ91s
Melissa Burke (melissa@biocommons.org.au)
Hogg, Carolyn (orcid: 0000-0002-6328-398X)
Conservation genomics, Genomics, Bioinformatics, Sequencing, Threatened Species Initiative, Galaxy Australia
WEBINAR: Getting started with R
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with R’. This webinar took place on 16 August 2021.
Data analysis skills are now central to most biological experiments. While Excel can cover some of your data analysis needs, it is not...
Keywords: R statistical software, R studio, Tidyverse, Bioinformatics, Data analysis
WEBINAR: Getting started with R
https://zenodo.org/records/5214277
https://dresa.org.au/materials/webinar-getting-started-with-r-1c8f2b21-bc4b-4b42-9a5d-d6096a2afbe6
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with R’. This webinar took place on 16 August 2021.
Data analysis skills are now central to most biological experiments. While Excel can cover some of your data analysis needs, it is not always the best choice, particularly for large and complex datasets.
R is an open-source software and programming language that enables data exploration, statistical analysis visualisation and more. While it is the tool of choice for data analysis, getting started can be a little daunting for those without a background in statistics.
In this webinar Saskia Freytag, an R user with over a decade of experience and member of the Bioconductor Community Advisory Board, will walk you through their hints and tips for getting started with R and data analysis. She’ll cover topics like R Studio and why you need it, where to get help, basic data manipulation, visualisations and extending R with libraries. The webinar will be followed by a short Q&A session
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Getting started with R - slides (PDF): Slides used in the presentation
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/JS7yZw7bnX8
Melissa Burke (melissa@biocommons.org.au)
Freytag, Saskia (orcid: 0000-0002-2185-7068)
R statistical software, R studio, Tidyverse, Bioinformatics, Data analysis
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WORKSHOP: Introduction to Machine Learning in R - from data to knowledge
9 December 2024
WORKSHOP: Introduction to Machine Learning in R - from data to knowledge https://www.biocommons.org.au/events/dome-mlr https://dresa.org.au/events/workshop-introduction-to-machine-learning-in-r-from-data-to-knowledge With the rise in high-throughput sequencing technologies, the volume of omics data has grown exponentially. A major issue is to mine useful knowledge from these heterogeneous collections of data. The analysis of complex high-volume data is not trivial and classical tools cannot be used to explore their full potential. Machine Learning (ML), a discipline in which computers perform automated learning without being programmed explicitly and assist humans to make sense of large and complex data sets, can thus be very useful in mining large omics datasets to uncover new insights that can advance the field of bioinformatics. This hands-on workshop will introduce participants to the ML taxonomy and the applications of common ML algorithms to health data. The workshop will cover the foundational concepts and common methods being used to analyse omics data sets by providing a practical context through the use of basic but widely used R libraries. Participants will acquire an understanding of the standard ML processes, as well as the practical skills in applying them on familiar problems and publicly available real-world data sets. **Lead Trainer:** Dr Fotis Psomopoulos, Senior Researcher, Institute of Applied Biosciences (INAB), Center for Research and Technology Hellas (CERTH) **Date/Time:** 9 December 2024, 1 - 5 pm AEDT / 12 - 4 pm AEST / 12:30 - 4:30 pm ACDT / 10 am - 2 pm AWST [Check in your timezone](https://www.timeanddate.com/worldclock/fixedtime.html?ah=4&iso=20241209T13&msg=Introduction%20to%20Machine%20Learning%20in%20R%20-%20from%20data%20to%20knowledge&p1=152) **Location**: Online **Format**: This online workshop will take place over a single 4 hour session. The workshop is delivered in Carpentries style where expert trainers introduce the topic and guide you through hands-on activities to help you put your new skills into action. **Who the workshop is for:** This workshop is for Australian researchers who are or will apply ML to the analysis of omics data as part of their projects. It is suitable for beginners in ML. You must be associated with an Australian organisation for your application to be considered. **How to apply:** This workshop is free but participation is subject to application with selection. Applications close at 11:59pm AEST, 24 November 2024. [Apply here](https://www.eventbrite.com.au/e/workshop-introduction-to-machine-learning-in-r-from-data-to-knowledge-tickets-1066494576989) Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. More information on the selection process is provided in our [advice on applying for Australian BioCommons workshops](https://www.biocommons.org.au/workshop-applications). 2024-12-09 13:00:00 UTC 2024-12-09 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian BioCommons training@biocommons.org.au [] [] [] expression_of_interest BioinformaticsMachine Learning and Artificial Intelligence CourseR Programming
