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9 events found

Keywords: Setonix  or nf-core 

  • P’Con – Exascale Data Management with ADIOS

    7 December 2021

    P’Con – Exascale Data Management with ADIOS https://dresa.org.au/events/p-con-exascale-data-management-with-adios Speakers: Speaker: Scott Klasky, Norbert Podhorszki (Oak Ridge National Laboratories) ADIOS is a high performance publish/subscribe I/O framework which has been designed and developed for the exascale computing era. In a snapshot, ADIOS: - Is integrated into most of the popular analysis and visualization packages. - Has strict continuous integration practices, providing stable, portable and efficient I/O services. - Has a programming interface designed for easy switching from files to streams (on-HPC machines) to streams over the Wide Area Network. In this presentation, the speaker will introduce the ADIOS I/O framework and describe how it is being used, including: - In data intensive supercomputing simulations, using it for data storage and retrieval moving petabytes of data in a single job, - In coupled simulations using it for data movement between the simulation codes and to in situ analysis and in situ visualization services, - In AI applications, for collecting training data from ensembles of computations on the fly, and - In collaborations between experimental facilities and HPC centers to stream experimental data for near-real-time decision making. We will present how ADIOS was used in the 2020 Gordon Bell finalist paper from Pawsey and ORNL about the workflow for simulating and processing the full-scale low-frequency telescope data of SKA Phase 1 on the Summit supercomputer at ORNL. ADIOS is also a research framework for new I/O technologies, pushing the boundaries beyond current use cases. Our research focuses on data reduction with trusted lossy compression techniques, data refactoring for easier on-demand retrieval, hierarchical storage to speed up access to the most important data, asynchronous I/O techniques and others. The techniques in ADIOS have been developed for over 15 years through collaborations with science applications, and we are always seeking new collaborations and new challenges that will define the I/O landscape of the future. We hope this presentation will allow the audience to learn about how others are using extreme I/O in their fields and also stimulate the audience to bring new challenges to us. Exascale Data Management with ADIOS session, is part of the first PaCER Conference – P’con: A week where Pawsey continues setting the pace for exascale. 2021-12-07 09:30:00 UTC 2021-12-07 11:30:00 UTC Pawsey Supercomputing Research Centre Pawsey Supercomputing Research Centre training@pawsey.org.au [] [] webinarconference open_to_all ADIOSsupercomputersupercomputingPawseyPaCERSetonix
  • P’Con – Porting multi-GPU SELF-Fluids code to HIPFort

    8 December 2021

    P’Con – Porting multi-GPU SELF-Fluids code to HIPFort https://dresa.org.au/events/p-con-porting-multi-gpu-self-fluids-code-to-hipfort Speaker: By Dr Joseph Schoonover, Fluid Numerics LLC During this talk, we will share our experience with porting process for SELF-Fluids from multi-GPU CUDA-Fortran to multi-GPU HIPFort. The talk will cover the design principles and roadmap for SELF and the strategy to port from Nvidia-only platforms to AMD & Nvidia GPUs. We’ll discuss hurdles encountered along the way and considerations for developing multi-GPU accelerated applications in Fortran. SELF is an object-oriented Fortran library that supports the implementation of Spectral Element Methods for solving partial differential equations. SELF-Fluids is an implementation of SELF that solves the compressible Navier Stokes equations on CPU only and GPU accelerated compute platforms using the Discontinuous Galerkin Spectral Element Method. The SELF API is designed based on the assumption that SEM developers and researchers need to be able to implement derivatives in 1-D and divergence, gradient, and curl in 2-D and 3-D on scalar, vector, and tensor functions using spectral collocation, continuous Galerkin, and discontinuous Galerkin spectral element methods. Additionally, as we enter the Exascale era, we are currently faced with a zoo of compute hardware that is available. Because of this, SELF routines provide support for GPU acceleration through AMD’s HIP and support for multi-core, multi-node, and multi-GPU platforms with MPI. SELF and SELF-Fluids are publicly available online at https://github.com/fluidnumerics/self Porting multi-GPU SELF-Fluids code to HIPFort, is part of the first PaCER Conference – P’con: A week where Pawsey continues setting the pace for exascale. 2021-12-08 09:30:00 UTC 2021-12-08 11:30:00 UTC Pawsey Supercomputing Research Centre Pawsey Supercomputing Research Centre training@pawsey.org.au [] [] webinarconference open_to_all GPUsHipFortsupercomputersupercomputingSetonix
  • Using Supercomputers: Parts 1 and 2

    22 - 23 August 2022

    Using Supercomputers: Parts 1 and 2 https://dresa.org.au/events/using-supercomputers-parts-1-and-2 In this course, students will be introduced to supercomputers and what makes them different to other computers. A typical supercomputing architecture, parallelism, compute resource sharing, command line interfaces and other key concepts and practices will be discussed. Students will practice what they learn using Pawsey's new supercomputer Setonix. 2022-08-22 10:00:00 UTC 2022-08-23 13:00:00 UTC Pawsey Supercomputing Research Centre Pawsey Supercomputing Research Centre training@pawsey.org.au [] [] workshopwebinar open_to_all supercomputingsupercomputersUnixSetonix
  • 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
  • WORKSHOP: Unlocking nf-core - customising workflows for your research

    18 - 19 May 2023

    WORKSHOP: Unlocking nf-core - customising workflows for your research https://dresa.org.au/events/workshop-unlocking-nf-core-customising-workflows-for-your-research 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](https://nf-co.re/) 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](https://nf-co.re/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. **Lead Trainers** Dr Georgina Samaha, Senior Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Cali Willet, Senior Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Chris Hakkaart, Developer Advocate, Sequera Labs. **Date/Time** 18 and 19 May 2023, 1-4pm AEST/12:30-3:30pm ACST/11am -2pm AWST **Format** This online workshop will take place over two sessions. You must attend both sessions to get the most out of the workshop. Expert trainers will introduce the 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: * Recognise how Nextflow and nf-core enable reproducible and portable bioinformatics * Write and run a basic nf-core run command * Describe nf-core code/directory structure (config, modules, submodules, workflow, main.nf) * Adjust the run command to customise the workflow * Describe Nextflow configuration hierarchy * Create and use a params file to customise workflow parameters * Create and use a custom config file to adjust resource usage * Apply external arguments not available as a workflow parameter to a process **Who the workshop is for** This workshop is for researchers and bioinformaticians who are already (or soon will) be using and customising nf-core workflows. The workshop will be conducted in a Unix environment. Command line experience is required. Prior experience running Nextflow and nf-core workflows is recommended. You must be associated with an Australian organisation for your application to be considered. If you’re looking for an introduction to the fundamentals of Nextflow and nf-core you can watch our webinar[ Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud](https://youtu.be/VnLX63yXbJU) or recordings of recent[ nf-core training](https://www.youtube.com/c/nf-core). **How to apply** **[Apply here](https://custom-nfcore.eventbrite.com.au/)** This workshop is free but participation is subject to application with selection. Applications close at **11:59pm AEST, Thursday 4 May 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) _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/), Sydney Informatics Hub and Sequera 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_ 2023-05-18 13:00:00 UTC 2023-05-19 16:00:00 UTC Australian BioCommons Online Online Australian BioCommonsSydney Informatics HubSequera training@biocommons.org.au [] [] 50 workshop expression_of_interest WorkflowsNextflownf-corePipelines
  • OpenCL workshop

    21 - 29 June 2023

    OpenCL workshop https://dresa.org.au/events/opencl-workshop Supercomputers make use of accelerators from a variety of different hardware vendors, using devices such as multi-core CPU’s, GPU’s and even FPGA’s. OpenCL is a way for your HPC application to make effective use of heterogeneous computing devices, and to avoid code refactoring for new HPC infrastructure. 2023-06-21 09:00:00 UTC 2023-06-29 17:00:00 UTC Pawsey Supercomputing Centre Online, Perth, Australia Online Perth Australia 6100 Pawsey Supercomputing Research Centre Ann Backhaus [] technical staffstudentsprofessionalresearcher 10 webinarworkshop open_to_all supercomputingOpenCLSkills upliftPawsey Supercomputing CentreCPUsGPUs HPCSetonix
  • Using PennyLane on Pawsey’s Setonix Supercomputer

    28 November 2023

    Using PennyLane on Pawsey’s Setonix Supercomputer https://dresa.org.au/events/using-pennylane-on-pawsey-s-setonix-supercomputer Join this free, online training, where Xanadu’s Quantum Community Manager Catalina Albornoz introduces quantum computing using the Python-based PennyLane software library. During this training, you’ll have the opportunity to work hands-on with PennyLane on Pawsey’s Setonix supercomputer. Xanadu is a Canadian quantum computing company with the mission to build quantum computers that are useful and available to people everywhere. Xanadu is one of the world’s leading quantum hardware and software companies and also leads the development of PennyLane, an open-source software library for quantum computing and application development. This training consists of 2 days: 1 training day (this session) and a follow-up Q&A session. 2023-11-28 09:00:00 UTC 2023-11-28 13:00:00 UTC Pawsey Supercomputing Centre Perth, Australia Perth Australia Pawsey Supercomputing Research CentreXanadu training@pawsey.org.au [] Researchers and research students, or anyone who wants to learn intermediate statistical concepts to apply in R.Data scientistsProfessional/support staff [] open_to_all online learningsupercomputingPawsey Supercomputing CentrePennyLaneSetonix
  • Q&A Using PennyLane on Pawsey’s Setonix Supercomputer

    1 December 2023

    Q&A Using PennyLane on Pawsey’s Setonix Supercomputer https://dresa.org.au/events/q-a-using-pennylane-on-pawsey-s-setonix-supercomputer This is a Question and Answer (Q&A) session following up the 28 November Using PennyLane on Pawsey’s Setonix Supercomputer training. Join this session if you have questions that have come from your use of PennyLane, or come to learn more from your colleagues about their use. 2023-12-01 09:00:00 UTC 2023-12-01 10:00:00 UTC Pawsey Supercomputing Research Centre Perth, Australia Perth Australia Pawsey Supercomputing Research Centre training@pawsey.org.au [] Researchers and research students, or anyone who wants to learn intermediate statistical concepts to apply in R.Professional/support staff Data scientists webinar open_to_all Pawsey Supercomputing CentrePennyLaneSetonixsupercomputing
  • P’Con – Exascale Data Management with ADIOS

    7 December 2021

    P’Con – Exascale Data Management with ADIOS https://dresa.org.au/events/p-con-exascale-data-management-with-adios Speakers: Speaker: Scott Klasky, Norbert Podhorszki (Oak Ridge National Laboratories) ADIOS is a high performance publish/subscribe I/O framework which has been designed and developed for the exascale computing era. In a snapshot, ADIOS: - Is integrated into most of the popular analysis and visualization packages. - Has strict continuous integration practices, providing stable, portable and efficient I/O services. - Has a programming interface designed for easy switching from files to streams (on-HPC machines) to streams over the Wide Area Network. In this presentation, the speaker will introduce the ADIOS I/O framework and describe how it is being used, including: - In data intensive supercomputing simulations, using it for data storage and retrieval moving petabytes of data in a single job, - In coupled simulations using it for data movement between the simulation codes and to in situ analysis and in situ visualization services, - In AI applications, for collecting training data from ensembles of computations on the fly, and - In collaborations between experimental facilities and HPC centers to stream experimental data for near-real-time decision making. We will present how ADIOS was used in the 2020 Gordon Bell finalist paper from Pawsey and ORNL about the workflow for simulating and processing the full-scale low-frequency telescope data of SKA Phase 1 on the Summit supercomputer at ORNL. ADIOS is also a research framework for new I/O technologies, pushing the boundaries beyond current use cases. Our research focuses on data reduction with trusted lossy compression techniques, data refactoring for easier on-demand retrieval, hierarchical storage to speed up access to the most important data, asynchronous I/O techniques and others. The techniques in ADIOS have been developed for over 15 years through collaborations with science applications, and we are always seeking new collaborations and new challenges that will define the I/O landscape of the future. We hope this presentation will allow the audience to learn about how others are using extreme I/O in their fields and also stimulate the audience to bring new challenges to us. Exascale Data Management with ADIOS session, is part of the first PaCER Conference – P’con: A week where Pawsey continues setting the pace for exascale. 2021-12-07 09:30:00 UTC 2021-12-07 11:30:00 UTC Pawsey Supercomputing Research Centre Pawsey Supercomputing Research Centre training@pawsey.org.au [] [] webinarconference open_to_all ADIOSsupercomputersupercomputingPawseyPaCERSetonix
  • P’Con – Porting multi-GPU SELF-Fluids code to HIPFort

    8 December 2021

    P’Con – Porting multi-GPU SELF-Fluids code to HIPFort https://dresa.org.au/events/p-con-porting-multi-gpu-self-fluids-code-to-hipfort Speaker: By Dr Joseph Schoonover, Fluid Numerics LLC During this talk, we will share our experience with porting process for SELF-Fluids from multi-GPU CUDA-Fortran to multi-GPU HIPFort. The talk will cover the design principles and roadmap for SELF and the strategy to port from Nvidia-only platforms to AMD & Nvidia GPUs. We’ll discuss hurdles encountered along the way and considerations for developing multi-GPU accelerated applications in Fortran. SELF is an object-oriented Fortran library that supports the implementation of Spectral Element Methods for solving partial differential equations. SELF-Fluids is an implementation of SELF that solves the compressible Navier Stokes equations on CPU only and GPU accelerated compute platforms using the Discontinuous Galerkin Spectral Element Method. The SELF API is designed based on the assumption that SEM developers and researchers need to be able to implement derivatives in 1-D and divergence, gradient, and curl in 2-D and 3-D on scalar, vector, and tensor functions using spectral collocation, continuous Galerkin, and discontinuous Galerkin spectral element methods. Additionally, as we enter the Exascale era, we are currently faced with a zoo of compute hardware that is available. Because of this, SELF routines provide support for GPU acceleration through AMD’s HIP and support for multi-core, multi-node, and multi-GPU platforms with MPI. SELF and SELF-Fluids are publicly available online at https://github.com/fluidnumerics/self Porting multi-GPU SELF-Fluids code to HIPFort, is part of the first PaCER Conference – P’con: A week where Pawsey continues setting the pace for exascale. 2021-12-08 09:30:00 UTC 2021-12-08 11:30:00 UTC Pawsey Supercomputing Research Centre Pawsey Supercomputing Research Centre training@pawsey.org.au [] [] webinarconference open_to_all GPUsHipFortsupercomputersupercomputingSetonix
  • Using Supercomputers: Parts 1 and 2

    22 - 23 August 2022

    Using Supercomputers: Parts 1 and 2 https://dresa.org.au/events/using-supercomputers-parts-1-and-2 In this course, students will be introduced to supercomputers and what makes them different to other computers. A typical supercomputing architecture, parallelism, compute resource sharing, command line interfaces and other key concepts and practices will be discussed. Students will practice what they learn using Pawsey's new supercomputer Setonix. 2022-08-22 10:00:00 UTC 2022-08-23 13:00:00 UTC Pawsey Supercomputing Research Centre Pawsey Supercomputing Research Centre training@pawsey.org.au [] [] workshopwebinar open_to_all supercomputingsupercomputersUnixSetonix
  • 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
  • WORKSHOP: Unlocking nf-core - customising workflows for your research

    18 - 19 May 2023

    WORKSHOP: Unlocking nf-core - customising workflows for your research https://dresa.org.au/events/workshop-unlocking-nf-core-customising-workflows-for-your-research 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](https://nf-co.re/) 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](https://nf-co.re/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. **Lead Trainers** Dr Georgina Samaha, Senior Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Cali Willet, Senior Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Chris Hakkaart, Developer Advocate, Sequera Labs. **Date/Time** 18 and 19 May 2023, 1-4pm AEST/12:30-3:30pm ACST/11am -2pm AWST **Format** This online workshop will take place over two sessions. You must attend both sessions to get the most out of the workshop. Expert trainers will introduce the 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: * Recognise how Nextflow and nf-core enable reproducible and portable bioinformatics * Write and run a basic nf-core run command * Describe nf-core code/directory structure (config, modules, submodules, workflow, main.nf) * Adjust the run command to customise the workflow * Describe Nextflow configuration hierarchy * Create and use a params file to customise workflow parameters * Create and use a custom config file to adjust resource usage * Apply external arguments not available as a workflow parameter to a process **Who the workshop is for** This workshop is for researchers and bioinformaticians who are already (or soon will) be using and customising nf-core workflows. The workshop will be conducted in a Unix environment. Command line experience is required. Prior experience running Nextflow and nf-core workflows is recommended. You must be associated with an Australian organisation for your application to be considered. If you’re looking for an introduction to the fundamentals of Nextflow and nf-core you can watch our webinar[ Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud](https://youtu.be/VnLX63yXbJU) or recordings of recent[ nf-core training](https://www.youtube.com/c/nf-core). **How to apply** **[Apply here](https://custom-nfcore.eventbrite.com.au/)** This workshop is free but participation is subject to application with selection. Applications close at **11:59pm AEST, Thursday 4 May 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) _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/), Sydney Informatics Hub and Sequera 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_ 2023-05-18 13:00:00 UTC 2023-05-19 16:00:00 UTC Australian BioCommons Online Online Australian BioCommonsSydney Informatics HubSequera training@biocommons.org.au [] [] 50 workshop expression_of_interest WorkflowsNextflownf-corePipelines
  • OpenCL workshop

    21 - 29 June 2023

    OpenCL workshop https://dresa.org.au/events/opencl-workshop Supercomputers make use of accelerators from a variety of different hardware vendors, using devices such as multi-core CPU’s, GPU’s and even FPGA’s. OpenCL is a way for your HPC application to make effective use of heterogeneous computing devices, and to avoid code refactoring for new HPC infrastructure. 2023-06-21 09:00:00 UTC 2023-06-29 17:00:00 UTC Pawsey Supercomputing Centre Online, Perth, Australia Online Perth Australia 6100 Pawsey Supercomputing Research Centre Ann Backhaus [] technical staffstudentsprofessionalresearcher 10 webinarworkshop open_to_all supercomputingOpenCLSkills upliftPawsey Supercomputing CentreCPUsGPUs HPCSetonix
  • Using PennyLane on Pawsey’s Setonix Supercomputer

    28 November 2023

    Using PennyLane on Pawsey’s Setonix Supercomputer https://dresa.org.au/events/using-pennylane-on-pawsey-s-setonix-supercomputer Join this free, online training, where Xanadu’s Quantum Community Manager Catalina Albornoz introduces quantum computing using the Python-based PennyLane software library. During this training, you’ll have the opportunity to work hands-on with PennyLane on Pawsey’s Setonix supercomputer. Xanadu is a Canadian quantum computing company with the mission to build quantum computers that are useful and available to people everywhere. Xanadu is one of the world’s leading quantum hardware and software companies and also leads the development of PennyLane, an open-source software library for quantum computing and application development. This training consists of 2 days: 1 training day (this session) and a follow-up Q&A session. 2023-11-28 09:00:00 UTC 2023-11-28 13:00:00 UTC Pawsey Supercomputing Centre Perth, Australia Perth Australia Pawsey Supercomputing Research CentreXanadu training@pawsey.org.au [] Researchers and research students, or anyone who wants to learn intermediate statistical concepts to apply in R.Data scientistsProfessional/support staff [] open_to_all online learningsupercomputingPawsey Supercomputing CentrePennyLaneSetonix
  • Q&A Using PennyLane on Pawsey’s Setonix Supercomputer

    1 December 2023

    Q&A Using PennyLane on Pawsey’s Setonix Supercomputer https://dresa.org.au/events/q-a-using-pennylane-on-pawsey-s-setonix-supercomputer This is a Question and Answer (Q&A) session following up the 28 November Using PennyLane on Pawsey’s Setonix Supercomputer training. Join this session if you have questions that have come from your use of PennyLane, or come to learn more from your colleagues about their use. 2023-12-01 09:00:00 UTC 2023-12-01 10:00:00 UTC Pawsey Supercomputing Research Centre Perth, Australia Perth Australia Pawsey Supercomputing Research Centre training@pawsey.org.au [] Researchers and research students, or anyone who wants to learn intermediate statistical concepts to apply in R.Professional/support staff Data scientists webinar open_to_all Pawsey Supercomputing CentrePennyLaneSetonixsupercomputing

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