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Authors: Coddington, Paul (orcid: 00...  or Price, Gareth (orcid: 0000-...  or Chew, Tracy (orcid: 0000-00... 

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
WEBINAR: High performance bioinformatics: submitting your best NCMAS application

This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021.

Bioinformaticians are increasingly turning to specialised compute infrastructure and...

Keywords: Computational Biology, Bioinformatics, High Performance Computing, HPC, NCMAS

WEBINAR: High performance bioinformatics: submitting your best NCMAS application https://dresa.org.au/materials/webinar-high-performance-bioinformatics-submitting-your-best-ncmas-application-ee80822f-74ac-41af-a5a4-e162c10e6d78 This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021. Bioinformaticians are increasingly turning to specialised compute infrastructure and efficient, scalable workflows as their research becomes more data intensive. Australian researchers that require extensive compute resources to process large datasets can apply for access to national high performance computing facilities (e.g. Pawsey and NCI) to power their research through the National Computational Merit Allocation Scheme (NCMAS). NCMAS is a competitive, merit-based scheme and requires applicants to carefully consider how the compute infrastructure and workflows will be applied.  This webinar provides life science researchers with insights into what makes a strong NCMAS application, with a focus on the technical assessment, and how to design and present effective and efficient bioinformatic workflows for the various national compute facilities. It will be followed by a short Q&A session. 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. High performance bioinformatics: submitting your best NCMAS application - slides (PDF and PPTX): Slides presented during the webinar   Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/HeFGjguwS0Y Melissa Burke (melissa@biocommons.org.au) Computational Biology, Bioinformatics, High Performance Computing, HPC, NCMAS
WORKSHOP: Variant calling in humans, animals and plants with Galaxy

This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021.

Variant calling in polyploid organisms, including humans, plants and animals, can help determine single...

Keywords: Variant calling, Genetic Variation Analysis, SNP annotation

WORKSHOP: Variant calling in humans, animals and plants with Galaxy https://dresa.org.au/materials/workshop-variant-calling-in-humans-animals-and-plants-with-galaxy-767f1816-1c06-478c-adf4-90b3b2d32a9c This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021. Variant calling in polyploid organisms, including humans, plants and animals, can help determine single or multi-variant contributors to a phenotype. Further, sexual reproduction (as compared to asexual) combines variants in a novel manner; this can be used to determine previously unknown variant - phenotype combinations but also to track lineage and lineage associated traits (GWAS studies), that all rely on highly accurate variant calling. The ability to confidently call variants in polyploid organisms is highly dependent on the balance between the frequency of variant observations against the background of non-variant observations, and even further compounded when one considers multi-variant positions within the genome. These are some of the challenges that will be explored in the workshop. In this online workshop we focused on the tools and workflows available for variant calling in polyploid organisms in Galaxy Australia. The workshop provided opportunities for hands-on experience using Freebayes for variant calling and SnpEff and GEMINI for variant annotation. The workshop made use of data from a case study on diagnosing a genetic disease however the tools and workflows are equally applicable to other polyploid organisms and biological questions. Access to all of the tools covered in this workshop was via Galaxy Australia, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. The materials are shared under a Creative Commons 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): schedule for the workshop Variant calling - humans, animals, plants - slides (PPTX and PDF): slides used in the workshop   Materials shared elsewhere: The tutorial used in this workshop is available via the Galaxy Training Network. Wolfgang Maier, Bérénice Batut, Torsten Houwaart, Anika Erxleben, Björn Grüning, 2021 Exome sequencing data analysis for diagnosing a genetic disease (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html Online; accessed 25 May 2021 Melissa Burke (melissa@biocommons.org.au) Variant calling, Genetic Variation Analysis, SNP annotation
WEBINAR: Managing hands-on data analysis training with Galaxy

This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023.

Event description 

Looking for flexible, scalable, real-world solutions that enable data analysis skills to...

Keywords: Bioinformatics, Galaxy, Training, Training infrastructure

WEBINAR: Managing hands-on data analysis training with Galaxy https://dresa.org.au/materials/webinar-managing-hands-on-data-analysis-training-with-galaxy-6d3e8b36-69f2-4fec-9290-d5acd068624a This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023. Event description  Looking for flexible, scalable, real-world solutions that enable data analysis skills to be taught to anyone and anywhere?  Galaxy Australia, a national web service supporting 1000s of bioinformatics tools and workflows is a fantastic solution for training on bioinformatics concepts. Their "Training Infrastructure as a Service”, or TIaaS provides free compute and back-end support for data analysis training. It is paired with 100’s of easy-to-follow tutorials developed and maintained by the worldwide community on the Galaxy Training Network (GTN). TIaaS frees trainers from setting up and maintaining computational resources for their training events so that they can focus on student needs and learning outcomes This webinar will show you how to make the most of Galaxy Australia, TIaaS and the Galaxy Training Network for bioinformatics training. We’ll highlight all the nifty features you can use to plan, manage and deliver training to any size audience efficiently. Materials 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. Managing data analysis training with Galaxy_slides: A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/VNE0pF6Nqgw Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Galaxy, Training, Training infrastructure
WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia

This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022.

Event description 

Have you discovered a brilliant...

Keywords: Bioinformatics, Workflows, FAIR, Galaxy Australia

WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia https://dresa.org.au/materials/webinar-here-s-one-we-prepared-earlier-re-creating-bioinformatics-methods-and-workflows-with-galaxy-australia-134a8bf5-3801-421f-a454-e0f9020f4871 This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022. Event description  Have you discovered a brilliant bioinformatics workflow but you’re not quite sure how to use it? In this webinar we will introduce the power of Galaxy for construction and (re)use of reproducible workflows, whether building workflows from scratch, recreating them from published descriptions and/or extracting from Galaxy histories. Using an established bioinformatics method, we’ll show you how to: Use the workflows creator in Galaxy Australia  Build a workflow based on a published method Annotate workflows so that you (and others) can understand them  Make workflows finable and citable (important and very easy to do!) 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. GalaxyWorkflows_Slides (PDF): A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/IMkl6p7hkho Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, FAIR, Galaxy Australia
WORKSHOP: RNA-Seq: reads to differential genes and pathways

This record includes training materials associated with the Australian BioCommons workshop ‘RNA-Seq: reads to differential genes and pathways’. This workshop took place over two, 3.5 hour sessions on 27 and 28 September 2022.

Event description

RNA sequencing (RNA-seq) is a common method used to...

Keywords: Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re

WORKSHOP: RNA-Seq: reads to differential genes and pathways https://dresa.org.au/materials/workshop-rna-seq-reads-to-differential-genes-and-pathways-5a384156-d3de-4d5d-9797-e689bf6592f8 This record includes training materials associated with the Australian BioCommons workshop ‘RNA-Seq: reads to differential genes and pathways’. This workshop took place over two, 3.5 hour sessions on 27 and 28 September 2022. Event description 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 - a portable, scalable, reproducible and publicly available workflow on Pawsey Nimbus Cloud. 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! This workshop is presented by the Australian BioCommons and Sydney Informatics Hub with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. 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. RNAseq reads to differential genes and pathways - Additional Resources (PDF): Additional resources compiled by the Sydney Informatics Hub rnaseq_DE_analysis_Day2.html: HTML version of code used on day 2 of the workshop rnaseq_DE_analysis_Day2.Rmd: R Markdown version of code used on day 2 of the workshop RNAseq reads to differential genes and pathways_Q_and_A (PDF): Archive of questions and their answers from the workshop Slack Channel. Materials shared elsewhere: This workshop follows the tutorial ‘RNA-seq: reads to differential gene expression workshop series’ developed by the Sydney Informatics Hub. https://sydney-informatics-hub.github.io/training.RNAseq.series-quarto/ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re
WEBINAR: Managing hands-on data analysis training with Galaxy

This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023.

Event description 

Looking for flexible, scalable, real-world solutions that enable data analysis skills to...

Keywords: Bioinformatics, Galaxy, Training, Training infrastructure

WEBINAR: Managing hands-on data analysis training with Galaxy https://dresa.org.au/materials/webinar-managing-hands-on-data-analysis-training-with-galaxy This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023. Event description  Looking for flexible, scalable, real-world solutions that enable data analysis skills to be taught to anyone and anywhere?  Galaxy Australia, a national web service supporting 1000s of bioinformatics tools and workflows is a fantastic solution for training on bioinformatics concepts. Their "Training Infrastructure as a Service”, or TIaaS provides free compute and back-end support for data analysis training. It is paired with 100’s of easy-to-follow tutorials developed and maintained by the worldwide community on the Galaxy Training Network (GTN). TIaaS frees trainers from setting up and maintaining computational resources for their training events so that they can focus on student needs and learning outcomes This webinar will show you how to make the most of Galaxy Australia, TIaaS and the Galaxy Training Network for bioinformatics training. We’ll highlight all the nifty features you can use to plan, manage and deliver training to any size audience efficiently. Materials 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. Managing data analysis training with Galaxy_slides: A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/VNE0pF6Nqgw Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Galaxy, Training, Training infrastructure
WORKSHOP: RNA-Seq: reads to differential genes and pathways

This record includes training materials associated with the Australian BioCommons workshop ‘RNA-Seq: reads to differential genes and pathways’. This workshop took place over two, 3.5 hour sessions on 27 and 28 September 2022.

Event description

RNA sequencing (RNA-seq) is a common method...

Keywords: Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re

WORKSHOP: RNA-Seq: reads to differential genes and pathways https://dresa.org.au/materials/workshop-rna-seq-reads-to-differential-genes-and-pathways This record includes training materials associated with the Australian BioCommons workshop ‘RNA-Seq: reads to differential genes and pathways’. This workshop took place over two, 3.5 hour sessions on 27 and 28 September 2022. **Event description** 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 - a portable, scalable, reproducible and publicly available workflow on Pawsey Nimbus Cloud. 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! This workshop is presented by the Australian BioCommons and Sydney Informatics Hub with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. 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. * RNAseq reads to differential genes and pathways - Additional Resources (PDF): Additional resources compiled by the Sydney Informatics Hub * rnaseq_DE_analysis_Day2.html: HTML version of code used on day 2 of the workshop * rnaseq_DE_analysis_Day2.Rmd: R Markdown version of code used on day 2 of the workshop * RNAseq reads to differential genes and pathways_Q_and_A (PDF): Archive of questions and their answers from the workshop Slack Channel. **Materials shared elsewhere:** This workshop follows the tutorial ‘RNA-seq: reads to differential gene expression workshop series’ developed by the Sydney Informatics Hub. https://sydney-informatics-hub.github.io/training.RNAseq.series-quarto/ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re
WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia

This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022.

Event description 

Have you discovered a...

Keywords: Bioinformatics, Workflows, FAIR, Galaxy Australia

WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia https://dresa.org.au/materials/webinar-here-s-one-we-prepared-earlier-re-creating-bioinformatics-methods-and-workflows-with-galaxy-australia This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022. **Event description**  Have you discovered a brilliant bioinformatics workflow but you’re not quite sure how to use it? In this webinar we will introduce the power of Galaxy for construction and (re)use of reproducible workflows, whether building workflows from scratch, recreating them from published descriptions and/or extracting from Galaxy histories. Using an established bioinformatics method, we’ll show you how to: * Use the workflows creator in Galaxy Australia  * Build a workflow based on a published method * Annotate workflows so that you (and others) can understand them  * Make workflows finable and citable (important and very easy to do!) 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. * GalaxyWorkflows_Slides (PDF): A PDF copy of the slides presented during the webinar. **Materials shared elsewhere:** A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/IMkl6p7hkho Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, FAIR, Galaxy Australia
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
WEBINAR: High performance bioinformatics: submitting your best NCMAS application

This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021.

Bioinformaticians are increasingly turning to specialised compute infrastructure and...

Keywords: Computational Biology, Bioinformatics, High Performance Computing, HPC, NCMAS

WEBINAR: High performance bioinformatics: submitting your best NCMAS application https://dresa.org.au/materials/webinar-high-performance-bioinformatics-submitting-your-best-ncmas-application This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021. Bioinformaticians are increasingly turning to specialised compute infrastructure and efficient, scalable workflows as their research becomes more data intensive. Australian researchers that require extensive compute resources to process large datasets can apply for access to national high performance computing facilities (e.g. Pawsey and NCI) to power their research through the National Computational Merit Allocation Scheme (NCMAS). NCMAS is a competitive, merit-based scheme and requires applicants to carefully consider how the compute infrastructure and workflows will be applied.  This webinar provides life science researchers with insights into what makes a strong NCMAS application, with a focus on the technical assessment, and how to design and present effective and efficient bioinformatic workflows for the various national compute facilities. It will be followed by a short Q&A session. 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. - High performance bioinformatics: submitting your best NCMAS application - slides (PDF and PPTX): Slides presented during the webinar **Materials shared elsewhere:** A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/HeFGjguwS0Y Melissa Burke (melissa@biocommons.org.au) Computational Biology, Bioinformatics, High Performance Computing, HPC, NCMAS
WORKSHOP: Variant calling in humans, animals and plants with Galaxy

This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021.

Variant calling in polyploid organisms, including humans, plants and animals, can help determine...

Keywords: Variant calling, Genetic Variation Analysis, SNP annotation

WORKSHOP: Variant calling in humans, animals and plants with Galaxy https://dresa.org.au/materials/workshop-variant-calling-in-humans-animals-and-plants-with-galaxy This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021. Variant calling in polyploid organisms, including humans, plants and animals, can help determine single or multi-variant contributors to a phenotype. Further, sexual reproduction (as compared to asexual) combines variants in a novel manner; this can be used to determine previously unknown variant - phenotype combinations but also to track lineage and lineage associated traits (GWAS studies), that all rely on highly accurate variant calling. The ability to confidently call variants in polyploid organisms is highly dependent on the balance between the frequency of variant observations against the background of non-variant observations, and even further compounded when one considers multi-variant positions within the genome. These are some of the challenges that will be explored in the workshop. In this online workshop we focused on the tools and workflows available for variant calling in polyploid organisms in Galaxy Australia. The workshop provided opportunities for hands-on experience using Freebayes for variant calling and SnpEff and GEMINI for variant annotation. The workshop made use of data from a case study on diagnosing a genetic disease however the tools and workflows are equally applicable to other polyploid organisms and biological questions. Access to all of the tools covered in this workshop was via Galaxy Australia, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. The materials are shared under a Creative Commons 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): schedule for the workshop - Variant calling - humans, animals, plants - slides (PPTX and PDF): slides used in the workshop **Materials shared elsewhere:** The tutorial used in this workshop is available via the Galaxy Training Network. Wolfgang Maier, Bérénice Batut, Torsten Houwaart, Anika Erxleben, Björn Grüning, 2021 Exome sequencing data analysis for diagnosing a genetic disease (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html Online; accessed 25 May 2021 Melissa Burke (melissa@biocommons.org.au) Variant calling, Genetic Variation Analysis, SNP annotation