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2 events found
Organiser: Australian BioCommons
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WEBINAR: BioSamples: supporting multi-omics data integration with FAIR sample records
4 October 2023
WEBINAR: BioSamples: supporting multi-omics data integration with FAIR sample records https://www.biocommons.org.au/events/biosamples https://dresa.org.au/events/webinar-biosamples-supporting-multi-omics-data-integration-with-fair-sample-records The [BioSamples database](https://www.ebi.ac.uk/biosamples/) 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. **Speaker:** Tony Burdett, Technical Team Leader - Archival Infrastructure and Technology, EMBL-EBI **Date/Time:** Wednesday 4 October 2023, 4pm AEDT/ 3pm AEST/ 3:30pm ACDT/ 1pm AWST ([Check in your timezone](https://www.timeanddate.com/worldclock/fixedtime.html?ah=1&iso=20231004T16&msg=BioSamples%3A%20Supporting%20multi-omics%20data%20integration%20with%20FAIR%20sample%20records&p1=152)) **Who the webinar is for:** This webinar is for biologists and bioinformaticians who search, submit and/or curate samples across multiple projects and contexts. It’s particularly relevant to anyone interested in linking datasets to support the FAIR principles. **How to join:** This webinar is free to join but you must register for a place in advance. **[Register here](https://unimelb.zoom.us/webinar/register/WN_ndRqEPcWSvqGnbkSl5EqUg)** 2023-10-04 16:00:00 UTC 2023-10-04 17:00:00 UTC Australian BioCommons Australian BioCommons training@biocommons.org.au [] [] [] open_to_all BioSamplesData IntegrationMetadataMultiomicsData submissionData curation -
WORKSHOP: RNASeq: reads to differential genes and pathways
11 - 12 October 2023
WORKSHOP: RNASeq: reads to differential genes and pathways https://www.biocommons.org.au/events/rnaseq2023 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
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WEBINAR: BioSamples: supporting multi-omics data integration with FAIR sample records
4 October 2023
WEBINAR: BioSamples: supporting multi-omics data integration with FAIR sample records https://www.biocommons.org.au/events/biosamples https://dresa.org.au/events/webinar-biosamples-supporting-multi-omics-data-integration-with-fair-sample-records The [BioSamples database](https://www.ebi.ac.uk/biosamples/) 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. **Speaker:** Tony Burdett, Technical Team Leader - Archival Infrastructure and Technology, EMBL-EBI **Date/Time:** Wednesday 4 October 2023, 4pm AEDT/ 3pm AEST/ 3:30pm ACDT/ 1pm AWST ([Check in your timezone](https://www.timeanddate.com/worldclock/fixedtime.html?ah=1&iso=20231004T16&msg=BioSamples%3A%20Supporting%20multi-omics%20data%20integration%20with%20FAIR%20sample%20records&p1=152)) **Who the webinar is for:** This webinar is for biologists and bioinformaticians who search, submit and/or curate samples across multiple projects and contexts. It’s particularly relevant to anyone interested in linking datasets to support the FAIR principles. **How to join:** This webinar is free to join but you must register for a place in advance. **[Register here](https://unimelb.zoom.us/webinar/register/WN_ndRqEPcWSvqGnbkSl5EqUg)** 2023-10-04 16:00:00 UTC 2023-10-04 17:00:00 UTC Australian BioCommons Australian BioCommons training@biocommons.org.au [] [] [] open_to_all BioSamplesData IntegrationMetadataMultiomicsData submissionData curation -
WORKSHOP: RNASeq: reads to differential genes and pathways
11 - 12 October 2023
WORKSHOP: RNASeq: reads to differential genes and pathways https://www.biocommons.org.au/events/rnaseq2023 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
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