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  • WORKSHOP: RNASeq: reads to differential genes and pathways

    11 - 12 October 2023

    WORKSHOP: RNASeq: reads to differential genes and pathways https://dresa.org.au/events/workshop-rnaseq-reads-to-differential-genes-and-pathways RNA 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](https://nf-co.re/rnaseq/usage) 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 is being delivered as a part of the Australian BioCommons[ Bring Your Own Data Platforms Project](https://www.biocommons.org.au/byo-data-platform-expansion) 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](https://pawsey.org.au/systems/nimbus-cloud-service/) platform and be able to process your own RNAseq datasets and perform differential expression analysis on the command-line. **Lead Trainers:** Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub Dr Georgina Samaha, Bioinformatics Group Lead, Sydney Informatics Hub **Date/Time:** 11 & 12 October 2023, 2 - 5pm AEST/1:30 - 4:30pm ACST/12 - 3pm AWST **Location:** Online **Format:** This online workshop will take place over two three-hour sessions. You must attend both sessions to get the most out of the workshop. Expert trainers will introduce new topics and guide you through hands-on activities to help you put your new skills into action. **Learning outcomes:** By the end of the workshop you should be able to: - List the steps involved in RNAseq data processing and differential expression analysis - Understand key concepts and considerations for RNAseq experiments - Describe the benefits of using nf-core workflows - Run the nf-core/rnaseq workflow to perform: - Quality control - Read alignment - Read quantification to generate raw counts - Use R/RStudio on to perform: - Quality control - Identify differentially expressed genes - Perform functional enrichment/pathway analysis **Who the workshop is for:** This workshop is for Australian researchers or bioinformaticians who are new to working with RNAseq datasets on the command-line interface and have or will be using bulk RNAseq datasets to identify differentially expressed genes as part of their projects. You must be associated with an Australian organisation for your application to be considered. The workshop will be conducted in a Unix environment and will use R/RStudio. Basic command line knowledge is required. You must know how to navigate the directory structure and copy files between the computers. If you need a refresher on Unix/Linux try[ this online tutorial](https://linuxjourney.com/lesson/the-shell). Basic knowledge of R/RStudio is required. You must know how to set up directories, run commands, reading in and outputting files. If you need a refresher on R/RStudio try the[ Introduction to R and RStudio section](https://swcarpentry.github.io/r-novice-gapminder/01-rstudio-intro.html) of this online tutorial. It’s recommended that you watch the following webinars before joining the workshop: - [Getting started with RNAseq: Transforming raw reads into biological insights](https://www.biocommons.org.au/events/rnaseqwebinar) - [Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud](https://youtu.be/VnLX63yXbJU). **How to apply:** **[Apply here](https://www.eventbrite.com.au/e/rna-seq-reads-to-differential-genes-and-pathways-tickets-677905422367)** This workshop is free but participation is subject to application with selection. **_Applications close at 11:59pm AEST, Monday 25 September 2023._** 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) **[Apply here](https://www.eventbrite.com.au/e/rna-seq-reads-to-differential-genes-and-pathways-tickets-677905422367)** _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/),[ Sydney Informatics Hub](https://www.sydney.edu.au/research/facilities/sydney-informatics-hub.html) and[ Pawsey Supercomputing Research Centre](https://pawsey.org.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative)._ _This event is part of a series of[ bioinformatics training events](https://www.biocommons.org.au/events). If you'd like to hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to Australian BioCommons._ 2023-10-11 14:00:00 UTC 2023-10-12 17:00:00 UTC Australian BioCommons Australian BioCommons training@biocommons.org.au [] [] 50 [] expression_of_interest RNASeqRNA-SeqTranscriptomics

  • TechTalk23: Galaxy - Distributed Computing Through Total Perspective Vortex

    26 October 2023

    TechTalk23: Galaxy - Distributed Computing Through Total Perspective Vortex https://dresa.org.au/events/techtalk23-galaxy-distributed-computing-through-total-perspective-vortex . 2023-10-26 14:00:00 UTC 2023-10-26 15:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) contact@ardc.edu.au [] [] 25 [] open_to_all []

  • Introduction to HPC

    13 November 2023

    Introduction to HPC https://dresa.org.au/events/introduction-to-hpc-a3084e80-4009-4b80-b800-5c859a1b5130 High-Performance Computing, or HPC, is the use of computers orders of magnitude faster and more powerful than even the best desktop PC. As research becomes more and more data-intensive, an ever broader range of researchers are using HPC for their data analysis. This workshop will give you an introduction to using high-performance computing systems effectively (as well as their limitations), and will introduce the basics of how to access a HPC cluster, load and use software, and submit jobs to run. 2023-11-13 09:00:00 UTC 2023-11-13 13:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop host_institution []

  • 2023 Vocabulary Symposium: FAIR Vocabularies For All

    14 - 15 November 2023

    Acton, Australia

    2023 Vocabulary Symposium: FAIR Vocabularies For All https://dresa.org.au/events/2023-vocabulary-symposium-fair-vocabularies-for-all Spanning research, government & industry. Discussing approaches to using, developing, publishing, and maintaining vocabularies 2023-11-14 09:00:00 UTC 2023-11-15 17:00:00 UTC Australian Research Data Commons 146 Ellery Crescent, Acton, Australia 146 Ellery Crescent Acton Australia 2601 Australian Research Data Commons (ARDC) contact@ardc.edu.au [] [] 420 conference open_to_all Other

  • WORKSHOP: RNASeq: reads to differential genes and pathways

    11 - 12 October 2023

    WORKSHOP: RNASeq: reads to differential genes and pathways https://dresa.org.au/events/workshop-rnaseq-reads-to-differential-genes-and-pathways RNA 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](https://nf-co.re/rnaseq/usage) 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 is being delivered as a part of the Australian BioCommons[ Bring Your Own Data Platforms Project](https://www.biocommons.org.au/byo-data-platform-expansion) 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](https://pawsey.org.au/systems/nimbus-cloud-service/) platform and be able to process your own RNAseq datasets and perform differential expression analysis on the command-line. **Lead Trainers:** Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub Dr Georgina Samaha, Bioinformatics Group Lead, Sydney Informatics Hub **Date/Time:** 11 & 12 October 2023, 2 - 5pm AEST/1:30 - 4:30pm ACST/12 - 3pm AWST **Location:** Online **Format:** This online workshop will take place over two three-hour sessions. You must attend both sessions to get the most out of the workshop. Expert trainers will introduce new topics and guide you through hands-on activities to help you put your new skills into action. **Learning outcomes:** By the end of the workshop you should be able to: - List the steps involved in RNAseq data processing and differential expression analysis - Understand key concepts and considerations for RNAseq experiments - Describe the benefits of using nf-core workflows - Run the nf-core/rnaseq workflow to perform: - Quality control - Read alignment - Read quantification to generate raw counts - Use R/RStudio on to perform: - Quality control - Identify differentially expressed genes - Perform functional enrichment/pathway analysis **Who the workshop is for:** This workshop is for Australian researchers or bioinformaticians who are new to working with RNAseq datasets on the command-line interface and have or will be using bulk RNAseq datasets to identify differentially expressed genes as part of their projects. You must be associated with an Australian organisation for your application to be considered. The workshop will be conducted in a Unix environment and will use R/RStudio. Basic command line knowledge is required. You must know how to navigate the directory structure and copy files between the computers. If you need a refresher on Unix/Linux try[ this online tutorial](https://linuxjourney.com/lesson/the-shell). Basic knowledge of R/RStudio is required. You must know how to set up directories, run commands, reading in and outputting files. If you need a refresher on R/RStudio try the[ Introduction to R and RStudio section](https://swcarpentry.github.io/r-novice-gapminder/01-rstudio-intro.html) of this online tutorial. It’s recommended that you watch the following webinars before joining the workshop: - [Getting started with RNAseq: Transforming raw reads into biological insights](https://www.biocommons.org.au/events/rnaseqwebinar) - [Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud](https://youtu.be/VnLX63yXbJU). **How to apply:** **[Apply here](https://www.eventbrite.com.au/e/rna-seq-reads-to-differential-genes-and-pathways-tickets-677905422367)** This workshop is free but participation is subject to application with selection. **_Applications close at 11:59pm AEST, Monday 25 September 2023._** 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) **[Apply here](https://www.eventbrite.com.au/e/rna-seq-reads-to-differential-genes-and-pathways-tickets-677905422367)** _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/),[ Sydney Informatics Hub](https://www.sydney.edu.au/research/facilities/sydney-informatics-hub.html) and[ Pawsey Supercomputing Research Centre](https://pawsey.org.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative)._ _This event is part of a series of[ bioinformatics training events](https://www.biocommons.org.au/events). If you'd like to hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to Australian BioCommons._ 2023-10-11 14:00:00 UTC 2023-10-12 17:00:00 UTC Australian BioCommons Australian BioCommons training@biocommons.org.au [] [] 50 [] expression_of_interest RNASeqRNA-SeqTranscriptomics

  • TechTalk23: Galaxy - Distributed Computing Through Total Perspective Vortex

    26 October 2023

    TechTalk23: Galaxy - Distributed Computing Through Total Perspective Vortex https://dresa.org.au/events/techtalk23-galaxy-distributed-computing-through-total-perspective-vortex . 2023-10-26 14:00:00 UTC 2023-10-26 15:00:00 UTC Australian Research Data Commons Australian Research Data Commons (ARDC) contact@ardc.edu.au [] [] 25 [] open_to_all []

  • Introduction to HPC

    13 November 2023

    Introduction to HPC https://dresa.org.au/events/introduction-to-hpc-a3084e80-4009-4b80-b800-5c859a1b5130 High-Performance Computing, or HPC, is the use of computers orders of magnitude faster and more powerful than even the best desktop PC. As research becomes more and more data-intensive, an ever broader range of researchers are using HPC for their data analysis. This workshop will give you an introduction to using high-performance computing systems effectively (as well as their limitations), and will introduce the basics of how to access a HPC cluster, load and use software, and submit jobs to run. 2023-11-13 09:00:00 UTC 2023-11-13 13:00:00 UTC QCIF QCIF training@qcif.edu.au [] [] workshop host_institution []

  • 2023 Vocabulary Symposium: FAIR Vocabularies For All

    14 - 15 November 2023

    Acton, Australia

    2023 Vocabulary Symposium: FAIR Vocabularies For All https://dresa.org.au/events/2023-vocabulary-symposium-fair-vocabularies-for-all Spanning research, government & industry. Discussing approaches to using, developing, publishing, and maintaining vocabularies 2023-11-14 09:00:00 UTC 2023-11-15 17:00:00 UTC Australian Research Data Commons 146 Ellery Crescent, Acton, Australia 146 Ellery Crescent Acton Australia 2601 Australian Research Data Commons (ARDC) contact@ardc.edu.au [] [] 420 conference open_to_all Other

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