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Authors: Coddington, Paul (orcid: 00...  or AMD  or Geissler, Laura 


WEBINAR: Where to go when your bioinformatics outgrows your compute

This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.

Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute...

Keywords: Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing

WEBINAR: Where to go when your bioinformatics outgrows your compute https://dresa.org.au/materials/webinar-where-to-go-when-your-bioinformatics-outgrows-your-compute-7a5a0ff8-8f4f-4fd0-af20-a88d515a6554 This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021. Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute resources. “I don’t know what compute resources I will need”, “My analysis won’t run and I don’t know why” and "Just getting it to work" are common pain points for researchers. In this webinar, you will learn how to understand the compute requirements for your bioinformatics workflows. You will also hear about ways of accessing compute that suits your needs as an Australian researcher, including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey.  We also describe bioinformatics and computing support services available to Australian researchers.  This webinar was jointly organised with the Sydney Informatics Hub at the University of Sydney. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Where to go when your bioinformatics outgrows your compute - slides (PDF and PPTX): Slides presented during the webinar Australian research computing resources cheat sheet (PDF): A list of resources and useful links mentioned during the webinar. Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/hNTbngSc-W0 Melissa Burke (melissa@biocommons.org.au) Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
WORKSHOP: Introduction to Metabarcoding using QIIME2

This record includes training materials associated with the Australian BioCommons workshop ‘Introduction to Metabarcoding using QIIME2’. This workshop took place on 22 February 2022.

Event description

Metabarcoding has revolutionised the study of biodiversity science. By combining DNA taxonomy...

Keywords: Bioinformatics, Analysis, Workflows, Microbial ecology, Metabarcoding, Microbiome

WORKSHOP: Introduction to Metabarcoding using QIIME2 https://dresa.org.au/materials/workshop-introduction-to-metabarcoding-using-qiime2-d3a7ac82-63aa-47e6-9d8e-5126419f9982 This record includes training materials associated with the Australian BioCommons workshop ‘Introduction to Metabarcoding using QIIME2’. This workshop took place on 22 February 2022. Event description Metabarcoding has revolutionised the study of biodiversity science. By combining DNA taxonomy with high-throughput DNA sequencing, it offers the potential to observe a larger diversity in the taxa within a single sample, rapidly expanding the scope of microbial analysis and generating high-quality biodiversity data.  This workshop will introduce the topic of metabarcoding and how you can use Qiime2 to analyse 16S data and gain simultaneous identification of all taxa within a sample. Qiime2 is a popular tool used to perform powerful microbiome analysis that can transform your raw data into publication quality visuals and statistics. In this workshop, using example 16S data from the shallow-water marine anemone E. diaphana, you will learn how to use this pipeline to run essential steps in microbial analysis including generating taxonomic assignments and phylogenic trees, and performing both alpha- and beta- diversity analysis.  Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schedule (PDF): A breakdown of the topics and timings for the workshop Materials shared elsewhere: This workshop follows the tutorial ‘Introduction to metabarcoding with QIIME2’ which has been made publicly available by Melbourne Bioinformatics. https://www.melbournebioinformatics.org.au/tutorials/tutorials/qiime2/qiime2/ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Workflows, Microbial ecology, Metabarcoding, Microbiome
AMD Profiling

The AMD profiling workshop covers the AMD suite of tools for development of HPC applications on AMD GPUs.

You will learn how to use the rocprof profiler and trace visualization tool that has long been available as part of the ROCm software suite.

You will also learn how to use the new...

Keywords: supercomputing, performance, GPUs, CPUs, AMD, HPC, ROCm

Resource type: activity

AMD Profiling https://dresa.org.au/materials/amd-profiling The AMD profiling workshop covers the AMD suite of tools for development of HPC applications on AMD GPUs. You will learn how to use the rocprof profiler and trace visualization tool that has long been available as part of the ROCm software suite. You will also learn how to use the new Omnitools - Omnitrace and Omniperf - that were introduced at the end of 2022. Omnitrace is a powerful tracing profiler for both CPU and GPU. It can collect data from a much wider range of sources and includes hardware counters and sampling approaches. Omniperf is a performance analysis tool that can help you pinpoint how your application is performing with a visual view of the memory hierarchy on the GPU as well as reporting the percentage of peak for many different measurements. training@pawsey.org.au supercomputing, performance, GPUs, CPUs, AMD, HPC, ROCm
WORKSHOP: Introduction to Metabarcoding using QIIME2

This record includes training materials associated with the Australian BioCommons workshop ‘Introduction to Metabarcoding using QIIME2’. This workshop took place on 22 February 2022.

Event description

Metabarcoding has revolutionised the study of biodiversity science. By combining DNA...

Keywords: Bioinformatics, Analysis, Workflows, Microbial ecology, Metabarcoding, Microbiome

WORKSHOP: Introduction to Metabarcoding using QIIME2 https://dresa.org.au/materials/workshop-introduction-to-metabarcoding-using-qiime2 This record includes training materials associated with the Australian BioCommons workshop ‘Introduction to Metabarcoding using QIIME2’. This workshop took place on 22 February 2022. **Event description** Metabarcoding has revolutionised the study of biodiversity science. By combining DNA taxonomy with high-throughput DNA sequencing, it offers the potential to observe a larger diversity in the taxa within a single sample, rapidly expanding the scope of microbial analysis and generating high-quality biodiversity data.  This workshop will introduce the topic of metabarcoding and how you can use Qiime2 to analyse 16S data and gain simultaneous identification of all taxa within a sample. Qiime2 is a popular tool used to perform powerful microbiome analysis that can transform your raw data into publication quality visuals and statistics. In this workshop, using example 16S data from the shallow-water marine anemone E. diaphana, you will learn how to use this pipeline to run essential steps in microbial analysis including generating taxonomic assignments and phylogenic trees, and performing both alpha- and beta- diversity analysis.  Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. **Files and materials included in this record:** - Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. - Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. - Schedule (PDF): A breakdown of the topics and timings for the workshop **Materials shared elsewhere:** This workshop follows the tutorial ‘Introduction to metabarcoding with QIIME2’ which has been made publicly available by Melbourne Bioinformatics. https://www.melbournebioinformatics.org.au/tutorials/tutorials/qiime2/qiime2/ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Workflows, Microbial ecology, Metabarcoding, Microbiome
WEBINAR: Where to go when your bioinformatics outgrows your compute

This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.

Bioinformatics analyses are often complex, requiring multiple software tools and specialised...

Keywords: Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing

WEBINAR: Where to go when your bioinformatics outgrows your compute https://dresa.org.au/materials/webinar-where-to-go-when-your-bioinformatics-outgrows-your-compute This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021. Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute resources. “I don’t know what compute resources I will need”, “My analysis won’t run and I don’t know why” and "Just getting it to work" are common pain points for researchers. In this webinar, you will learn how to understand the compute requirements for your bioinformatics workflows. You will also hear about ways of accessing compute that suits your needs as an Australian researcher, including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey.  We also describe bioinformatics and computing support services available to Australian researchers.  This webinar was jointly organised with the Sydney Informatics Hub at the University of Sydney. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. **Files and materials included in this record:** - Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. - Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. - Where to go when your bioinformatics outgrows your compute - slides (PDF and PPTX): Slides presented during the webinar - Australian research computing resources cheat sheet (PDF): A list of resources and useful links mentioned during the webinar. **Materials shared elsewhere:** A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/hNTbngSc-W0 Melissa Burke (melissa@biocommons.org.au) Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing