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://zenodo.org/records/5240578
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)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Chew, Tracy (orcid: 0000-0001-9529-7705)
Sadsad, Rosemarie (orcid: 0000-0003-2488-953X)
Coddington, Paul (orcid: 0000-0003-1336-9686)
Gladman, Simon (orcid: 0000-0002-6100-4385)
Edberg, Roger
Shaikh, Javed
Cytowski, Maciej (orcid: 0000-0002-0007-0979)
Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
WEBINAR: Conservation genomics in the age of extinction
This record includes training materials associated with the Australian BioCommons webinar ‘Conservation genomics in the age of extinction’. This webinar took place on 8 March 2022.
Event description
Biodiversity is crashing and millions of plant and animal species are at the edge of...
Keywords: Conservation genomics, Genomics, Bioinformatics, Sequencing, Threatened Species Initiative, Galaxy Australia
WEBINAR: Conservation genomics in the age of extinction
https://zenodo.org/records/6350785
https://dresa.org.au/materials/webinar-conservation-genomics-in-the-age-of-extinction-c7718a53-68ee-4c69-adf4-cd0550710d3f
This record includes training materials associated with the Australian BioCommons webinar ‘Conservation genomics in the age of extinction’. This webinar took place on 8 March 2022.
Event description
Biodiversity is crashing and millions of plant and animal species are at the edge of extinction. Understanding the genetic diversity of these species is an important tool for conservation biology but obtaining high quality genomes for threatened species is not always straightforward.
In this webinar Dr Carolyn Hogg speaks about the work she has been doing with the Threatened Species Initiative to build genomic resources to understand and protect Australia’s threatened species. Using examples such as the Kroombit Tinker Frog and the Greater Bilby, Carolyn describes some of the complexities and challenges of generating genomes from short reads and HiFi reads for critically endangered species. She outlines the technologies and resources being used and how these are bridging the gap between genomicists, bioinformaticians and conservation experts to help save Australian species.
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.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/Bl7CaiGQ91s
Melissa Burke (melissa@biocommons.org.au)
Hogg, Carolyn (orcid: 0000-0002-6328-398X)
Conservation genomics, Genomics, Bioinformatics, Sequencing, Threatened Species Initiative, Galaxy Australia
WORKSHOP: Hybrid de novo genome assembly
This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021.
Workshop description
It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches...
Keywords: Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly
WORKSHOP: Hybrid de novo genome assembly
https://zenodo.org/records/5781781
https://dresa.org.au/materials/workshop-hybrid-de-novo-genome-assembly-714004ba-0348-47c8-a68f-038a1f8ccfb1
This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021.
Workshop description
It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches which enable research on organisms for which reference genomes were not previously available. These approaches combine the strengths of short (Illumina) and long (PacBio or Nanopore) read technologies, resulting in improved assembly quality.
In this workshop we will learn how to create and assess genome assemblies from Illumina and Nanopore reads using data from a Bacillus Subtilis strain. We will demonstrate two hybrid-assembly methods using the tools Flye, Pilon, and Unicycler to perform assembly and subsequent error correction. You will learn how to visualise input read sets and the assemblies produced at each stage and assess the quality of the final assembly.
All analyses will be performed using 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.
This workshop is presented by the Australian BioCommons and Melbourne Bioinformatics 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.
Schedule (PDF): A breakdown of the topics and timings for the workshop
Materials shared elsewhere:
This workshop follows the tutorial ‘Hybrid genome assembly - Nanopore and Illumina’ developed by Melbourne Bioinformatics.
https://www.melbournebioinformatics.org.au/tutorials/tutorials/hybrid_assembly/nanopore_assembly/
Melissa Burke (melissa@biocommons.org.au)
Hall, Grace (orcid: 0000-0002-5105-8347)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Makunin, Igor
Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly