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Content provider: Australian BioCommons 

and

Authors: Dow, Ellen (orcid: 0000-000...  or Lu, Ching-Yu 

WORKSHOP: Genetic Outlier Analysis

This record includes training materials associated with the Australian BioCommons workshop ‘Genetic Outlier Analysis’. 
These workshops took place on:

27 - 28 February 2024: Online via Zoom
10 - 11 April 2024: In person in Melbourne
4 - 5 July 2024: In person in Sydney 

Event description
There...

Keywords: Bioinformatics, Genetics

WORKSHOP: Genetic Outlier Analysis https://dresa.org.au/materials/workshop-genetic-outlier-analysis This record includes training materials associated with the Australian BioCommons workshop ‘Genetic Outlier Analysis’.  These workshops took place on: 27 - 28 February 2024: Online via Zoom 10 - 11 April 2024: In person in Melbourne 4 - 5 July 2024: In person in Sydney  Event description There are many interesting patterns that you can extract from genetic variant data. This can include patterns of linkage, balancing selection, or even inbreeding signals. One of the most common approaches is to find sites on the genome that are under selection.  This workshop introduces the basics of genetic selection analysis. It will step you through the process of identifying signals of selection using your own data (or an example genomic dataset) using the outlier analysis method.  Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. This workshop is presented by the Australian BioCommons and the Genetics Society of AustralAsia Lead trainer:  Dr Katarina Stuart, Research Fellow, University of Auckland.  Facilitators: Adele Barugahare, Monash Genomics and Bioinformatics Platform  Dr Georgina Samaha, Sydney Informatics Hub, University of Sydney  Dr Ching-Yu Lu, Sydney Informatics Hub, University of Sydney Soleille Miller, University of NSW Dr Nandan Deshpande, Sydney Informatics Hub, University of Sydney   Infrastructure provision: Audrey Stott, Pawsey Supercomputing Research Centre 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. Schedules describing the timing of sessions for the in person and online events Materials shared elsewhere: These workshops followed the materials developed by Dr Katarina Stuart https://github.com/katarinastuart/Ev1_SelectionMetaAnalysis   Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Genetics
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://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) Systems Biology, FAIR Research, Open Source Software, Metagenomics, Microbiology
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://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) bioinformatics, transcriptomics, RNA-seq, RNAseq