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3 event found

Content provider: Australian BioCommons 

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Event types: Workshop  or Webinar 

  • WEBINAR: Getting started with whole genome mapping and variant calling on the command line

    24 August 2022

    WEBINAR: Getting started with whole genome mapping and variant calling on the command line https://dresa.org.au/events/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line 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. **Who the webinar is for** This webinar is intended for life scientists who are using and building whole genome sequencing mapping and variant calling pipelines. Some familiarity with the concepts of whole genome sequencing is recommended. **Presenter:** Dr Georgina Samaha, Sydney Informatics Hub, University of Sydney **Date/time:** 24 August 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST **How to join:** This webinar is free to join but you must register for a place in advance. **[Register here] (https://unimelb.zoom.us/webinar/register/WN_ekHib2_2QYazaH06VFMPgQ)** 2022-08-24 12:00:00 UTC 2022-08-24 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] 500 webinar open_to_all BioinformaticsworkflowsWhole genome sequencingVariant callingSequence mapping
  • WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud

    20 September 2022

    WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud https://dresa.org.au/events/webinar-portable-reproducible-and-scalable-bioinformatics-workflows-using-nextflow-and-pawsey-nimbus-cloud 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](https://nf-co.re/). So far, [39 workflows for omics data](https://nf-co.re/pipelines) 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 show you how you can use Nextflow to build your own workflows that 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. **Speakers:** Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Sarah Beecroft, Bioinformatics Applications Specialist, Pawsey Supercomputing Research Centre. **Who the webinar is for:** This webinar is for biologists who are new to bioinformatics on the command-line and bioinformaticians and would like to use existing best practice workflows available through nf.co-re. **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_P54j05SaQ6qbQz8h0Su_Zw)** 2022-09-20 12:00:00 UTC 2022-09-20 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] webinar open_to_all Nextflownf-coreWorkflowsBioinformaticsReproducibility
  • WORKSHOP: RNA-Seq: reads to differential genes and pathways

    27 - 28 September 2022

    WORKSHOP: RNA-Seq: reads to differential genes and pathways https://dresa.org.au/events/workshop-rna-seq-reads-to-differential-genes-and-pathways 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](https://nf-co.re/rnaseq/usage) - a portable, scalable, reproducible and publicly available workflow on[ Pawsey Nimbus Cloud](https://pawsey.org.au/systems/nimbus-cloud-service/). 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! **Lead Trainers:** Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub **Date/Time**: 27 & 28 September 2022, 2-5pm AEST/1:30-4:30pm ACST/12-3pm AWST **Format:** This online workshop will take place over two three-hour sessions. You must attend both sessions in order 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: 1. List the steps involved in analysis of RNA-seq data 2. Describe key concepts and considerations for RNA-seq experiments 3. Describe the benefits of using nf-core workflows 4. Deploy an RNA-seq nf-core workflow on Pawsey’s Nimbus Cloud to perform: 1. Quality control 2. Alignment 3. Quantification to generate raw counts 5. Use R/RStudio on Pawsey’s Nimbus Cloud to perform 4. Quality control 5. Identify differentially expressed genes using DESeq2 6. Perform functional enrichment/pathway analysis **Who the workshop is for:** This workshop is for Australian researchers who have or will work on RNAseq data 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/index.html) of this online tutorial. It’s recommended that you watch the webinar[ Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud](http://biocommons.org.au/events/nextflow-nimbus) in advance. You may join this webinar live on 20 September 2022. A recording will be posted on the[ Australian BioCommons YouTube Channel](https://www.youtube.com/c/AustralianBioCommonsChannel). **How to apply:** This workshop is free but participation is subject to application with selection. Applications close at **11:59pm AEST, Sunday 11 September 2022**. 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. **[Apply here](https://biocommons-rnaseq-2022.eventbrite.com.au/)** _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/), Sydney Informatics Hub and Pawsey Supercomputing Research Centre 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_ 2022-09-27 14:00:00 UTC 2022-09-28 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] workshop expression_of_interest BioinformaticsRNA-seqGene ExpressionPathway analysisNextflownf-coreWorkflowsFunctional analysis
  • WEBINAR: Getting started with whole genome mapping and variant calling on the command line

    24 August 2022

    WEBINAR: Getting started with whole genome mapping and variant calling on the command line https://dresa.org.au/events/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line 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. **Who the webinar is for** This webinar is intended for life scientists who are using and building whole genome sequencing mapping and variant calling pipelines. Some familiarity with the concepts of whole genome sequencing is recommended. **Presenter:** Dr Georgina Samaha, Sydney Informatics Hub, University of Sydney **Date/time:** 24 August 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST **How to join:** This webinar is free to join but you must register for a place in advance. **[Register here] (https://unimelb.zoom.us/webinar/register/WN_ekHib2_2QYazaH06VFMPgQ)** 2022-08-24 12:00:00 UTC 2022-08-24 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] 500 webinar open_to_all BioinformaticsworkflowsWhole genome sequencingVariant callingSequence mapping
  • WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud

    20 September 2022

    WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud https://dresa.org.au/events/webinar-portable-reproducible-and-scalable-bioinformatics-workflows-using-nextflow-and-pawsey-nimbus-cloud 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](https://nf-co.re/). So far, [39 workflows for omics data](https://nf-co.re/pipelines) 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 show you how you can use Nextflow to build your own workflows that 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. **Speakers:** Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Sarah Beecroft, Bioinformatics Applications Specialist, Pawsey Supercomputing Research Centre. **Who the webinar is for:** This webinar is for biologists who are new to bioinformatics on the command-line and bioinformaticians and would like to use existing best practice workflows available through nf.co-re. **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_P54j05SaQ6qbQz8h0Su_Zw)** 2022-09-20 12:00:00 UTC 2022-09-20 13:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] webinar open_to_all Nextflownf-coreWorkflowsBioinformaticsReproducibility
  • WORKSHOP: RNA-Seq: reads to differential genes and pathways

    27 - 28 September 2022

    WORKSHOP: RNA-Seq: reads to differential genes and pathways https://dresa.org.au/events/workshop-rna-seq-reads-to-differential-genes-and-pathways 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](https://nf-co.re/rnaseq/usage) - a portable, scalable, reproducible and publicly available workflow on[ Pawsey Nimbus Cloud](https://pawsey.org.au/systems/nimbus-cloud-service/). 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! **Lead Trainers:** Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub **Date/Time**: 27 & 28 September 2022, 2-5pm AEST/1:30-4:30pm ACST/12-3pm AWST **Format:** This online workshop will take place over two three-hour sessions. You must attend both sessions in order 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: 1. List the steps involved in analysis of RNA-seq data 2. Describe key concepts and considerations for RNA-seq experiments 3. Describe the benefits of using nf-core workflows 4. Deploy an RNA-seq nf-core workflow on Pawsey’s Nimbus Cloud to perform: 1. Quality control 2. Alignment 3. Quantification to generate raw counts 5. Use R/RStudio on Pawsey’s Nimbus Cloud to perform 4. Quality control 5. Identify differentially expressed genes using DESeq2 6. Perform functional enrichment/pathway analysis **Who the workshop is for:** This workshop is for Australian researchers who have or will work on RNAseq data 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/index.html) of this online tutorial. It’s recommended that you watch the webinar[ Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud](http://biocommons.org.au/events/nextflow-nimbus) in advance. You may join this webinar live on 20 September 2022. A recording will be posted on the[ Australian BioCommons YouTube Channel](https://www.youtube.com/c/AustralianBioCommonsChannel). **How to apply:** This workshop is free but participation is subject to application with selection. Applications close at **11:59pm AEST, Sunday 11 September 2022**. 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. **[Apply here](https://biocommons-rnaseq-2022.eventbrite.com.au/)** _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/), Sydney Informatics Hub and Pawsey Supercomputing Research Centre 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_ 2022-09-27 14:00:00 UTC 2022-09-28 17:00:00 UTC Australian BioCommons Online, Australia Online Australia Australian Biocommons training@biocommons.org.au [] [] workshop expression_of_interest BioinformaticsRNA-seqGene ExpressionPathway analysisNextflownf-coreWorkflowsFunctional analysis

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