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32 materials found

Keywords: FAIR  or HPC 


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
WEBINAR: Pro tips for scaling bioinformatics workflows to HPC

This record includes training materials associated with the Australian BioCommons webinar ‘Pro tips for scaling bioinformatics workflows to HPC’. This webinar took place on 31 May 2023.

Event description 

High Performance Computing (HPC) infrastructures offer the computational scale and...

Keywords: Bioinformatics, Workflows, HPC, High Performance Computing

WEBINAR: Pro tips for scaling bioinformatics workflows to HPC https://dresa.org.au/materials/webinar-pro-tips-for-scaling-bioinformatics-workflows-to-hpc-9f2a8b90-88da-433b-83b2-b1ab262dd9df This record includes training materials associated with the Australian BioCommons webinar ‘Pro tips for scaling bioinformatics workflows to HPC’. This webinar took place on 31 May 2023. Event description  High Performance Computing (HPC) infrastructures offer the computational scale and efficiency that life scientists need to handle complex biological datasets and multi-step computational workflows. But scaling workflows to HPC from smaller, more familiar computational infrastructures brings with it new jargon, expectations, and processes to learn. To make the most of HPC resources, bioinformatics workflows need to be designed for distributed computing environments and carefully manage varying resource requirements, and data scale related to biology.   In this webinar, Dr Georgina Samaha from the Sydney Informatics Hub, Dr Matthew Downton from the National Computational Infrastructure (NCI) and Dr Sarah Beecroft from the Pawsey Supercomputing Research Centre help you navigate the world of HPC for running and developing bioinformatics workflows. They explain when you should take your workflows to HPC and highlight the architectural features you should make the most of to scale your analyses once you’re there. You’ll hear pro-tips for dealing with common pain points like software installation, optimising for parallel computing and resource management, and will find out how to get access to Australia’s National HPC infrastructures at NCI and Pawsey.  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. Pro-tips_HPC_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/YKJDRXCmGMo Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, HPC, High Performance Computing
WORKSHOP: Make your bioinformatics workflows findable and citable

This record includes training materials associated with the Australian BioCommons workshop ‘Make your bioinformatics workflows findable and citable’. This workshop took place on 21 March 2023.

Event description

Computational workflows are invaluable resources for research communities. They help...

Keywords: Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science

WORKSHOP: Make your bioinformatics workflows findable and citable https://dresa.org.au/materials/workshop-make-your-bioinformatics-workflows-findable-and-citable-74e85d1c-d869-429e-b942-8391f4bab23d This record includes training materials associated with the Australian BioCommons workshop ‘Make your bioinformatics workflows findable and citable’. This workshop took place on 21 March 2023. Event description Computational workflows are invaluable resources for research communities. They help us  standardise common analyses, collaborate with other researchers, and support reproducibility. Bioinformatics workflow developers invest significant time and expertise to create, share, and maintain these resources for the benefit of the wider community and being able to easily find and access workflows is an essential factor in their uptake by the community. Increasingly, the research community is turning to workflow registries to find and access public workflows that can be applied to their research. Workflow registries support workflow findability and citation by providing a central repository and allowing users to search for and discover them easily. This workshop will introduce you to workflow registries and support attendees to register their workflows on the popular workflow registry, WorkflowHub. We’ll kick off the workshop with an introduction to the concepts underlying workflow findability, how it can benefit workflow developers, and how you can make the most of workflow registries to share your computational workflows with the research community. You will then have the opportunity to register your own workflows in WorkflowHub with support from our trainers.  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. 2023-03-21_Workflows_slides (PDF): A copy of the slides presented during the workshop Materials shared elsewhere: A recording of the first part of this workshop is available on the Australian BioCommons YouTube Channel: https://youtu.be/2kGKxaPuQN8 Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science
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
WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software

This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.

Event description 

bio.tools provides easy access to essential scientific...

Keywords: Bioinformatics, Research software, EDAM, Workflows, FAIR

WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software https://dresa.org.au/materials/webinar-bio-tools-making-it-easier-to-find-understand-and-cite-biological-tools-and-software-aea38c9e-0b40-4308-bafd-f7580563f520 This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022. Event description  bio.tools provides easy access to essential scientific and technical information about software, command-line tools, databases and services. It’s backed by ELIXIR, the European Infrastructure for Biological Information, and is being used in Australia to register software (e.g. Galaxy Australia, prokka). It underpins the information provided in the Australian BioCommons discovery service ToolFinder. Hans Ienasescu and Matúš Kalaš join us to explain how bio.tools uses a community driven, open science model to create this collection of resources and how it makes it easier to find, understand, utilise and cite them. They’ll delve into how bio.tools is using standard semantics (e.g. the EDAM ontology) and syntax (e.g. biotoolsSchema) to enrich the annotation and description of tools and resources. Finally, we’ll see how the community can contribute to bio.tools and take advantage of its key features to share and promote their own research software.   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. biotools_EDAM_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/K0J4_bAUG3Y Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Research software, EDAM, Workflows, FAIR
Research Data Governance

This video contains key information for those who make research data-related decisions. It will help project leaders to start investigating ways to develop their own data governance policy, roles and responsibilities and procedures with the input of appropriate stakeholders.

If you want to share...

Keywords: data governance, data, research, FAIR, data management, authority, share, reuse, access, provenance, policy, responsibilities, ARDC_AU, training material

Research Data Governance https://dresa.org.au/materials/research-data-governance-6ad9ab90-1a29-41db-b4aa-f1988501530d This video contains key information for those who make research data-related decisions. It will help project leaders to start investigating ways to develop their own data governance policy, roles and responsibilities and procedures with the input of appropriate stakeholders. If you want to share the video please use this: Australian Research Data Commons, 2021. Research Data Governance. [video] Available at: https://youtu.be/K_xVQRdgCIc  DOI: http://doi.org/10.5281/zenodo.5044585 [Accessed dd Month YYYY]. contact@ardc.edu.au Martinez, Paula Andrea (type: ProjectLeader) Wilkinson, Max (type: Editor) Callaghan,Shannon (type: Editor) Savill, Jo (type: Editor) Kang, Kristan (type: Editor) Levett, Kerry (type: Editor) Russell, Keith (type: Editor) Simons, Natasha (type: Editor) data governance, data, research, FAIR, data management, authority, share, reuse, access, provenance, policy, responsibilities, ARDC_AU, training material
ARDC Skills Landscape

The Australian Research Data Commons is driving transformational change in the research data ecosystem, enabling researchers to conduct world class data-intensive research. One interconnected component of this ecosystem is skills development/uplift, which is critical to the Commons and its...

Keywords: skills, data skills, eresearch skills, community, skilled workforce, FAIR, research data management, data stewardship, data governance, data use, data generation, training material

ARDC Skills Landscape https://dresa.org.au/materials/ardc-skills-landscape-56b224ca-9e30-4771-8615-d028c7be86a6 The Australian Research Data Commons is driving transformational change in the research data ecosystem, enabling researchers to conduct world class data-intensive research. One interconnected component of this ecosystem is skills development/uplift, which is critical to the Commons and its purpose of providing Australian researchers with a competitive advantage through data.   In this presentation, Kathryn Unsworth introduces the ARDC Skills Landscape. The Landscape is a first step in developing a national skills framework to enable a coordinated and cohesive approach to skills development across the Australian eResearch sector. It is also a first step towards helping to analyse current approaches in data training to identify: - Siloed skills initiatives, and finding ways to build partnerships and improve collaboration - Skills deficits, and working to address the gaps in data skills - Areas of skills development for investment by skills stakeholders like universities, research organisations, skills and training service providers, ARDC, etc.   contact@ardc.edu.au skills, data skills, eresearch skills, community, skilled workforce, FAIR, research data management, data stewardship, data governance, data use, data generation, training material
ARDC Your first step to FAIR

This workshop gives a brief overview of the FAIR principles, including a method to make a one-file dataset FAIR.

Keywords: training material, FAIR, data, workshop

ARDC Your first step to FAIR https://dresa.org.au/materials/ardc-your-first-step-to-fair-1ee3dc3c-23b0-4287-b96c-c120c5697932 This workshop gives a brief overview of the FAIR principles, including a method to make a one-file dataset FAIR. contact@ardc.edu.au Stokes, Liz (type: Editor) Martinez, Paula Andrea (type: Editor) Russell, Keith (type: Editor) training material, FAIR, data, workshop
ARDC Training Materials Metadata Checklist v1.1

The ARDC Training Materials Metadata Checklist aims to support learning designers, training materials creators, trainers and national training infrastructure providers to capture key information and apply appropriate mechanisms to enable sharing and reuse of their training materials

Keywords: checklist, Training material, FAIR, standard, requirements, metadata

ARDC Training Materials Metadata Checklist v1.1 https://dresa.org.au/materials/ardc-training-materials-metadata-checklist-v1-1 The ARDC Training Materials Metadata Checklist aims to support learning designers, training materials creators, trainers and national training infrastructure providers to capture key information and apply appropriate mechanisms to enable sharing and reuse of their training materials contact@ardc.edu.au checklist, Training material, FAIR, standard, requirements, metadata
Locking the front door without leaving the windows open: positioning authentication technologies within the "Five Safes" framework for effective use of sensitive research data

This project explores the options for access to sensitive data sets; what authentication technologies (e.g. multi-factor authentication) are needed to access sensitive data and secure compute environments.  This project seeks to position choices around authentication technologies within the Five...

Keywords: ARDC, Storage and Compute Summit, FAIR, Infrastructure, NCRIS, eResearch, training material

Locking the front door without leaving the windows open: positioning authentication technologies within the "Five Safes" framework for effective use of sensitive research data https://dresa.org.au/materials/locking-the-front-door-without-leaving-the-windows-open-positioning-authentication-technologies-within-the-five-safes-framework-for-effective-use-of-sensitive-research-data-b83124f8-2add-41c6-b194-d5dd50d098f6 This project explores the options for access to sensitive data sets; what authentication technologies (e.g. multi-factor authentication) are needed to access sensitive data and secure compute environments.  This project seeks to position choices around authentication technologies within the Five Safes framework for research use of sensitive data, proposed in 2003 by Felix Ritchie of the UK Office of National Statistics: • Safe Projects: is the proposed research use of the data appropriate?  • Safe People: can the users be trusted to use the data in an appropriate manner?  • Safe Settings: does the access facility limit unauthorised use? • Safe Data: is there a disclosure risk in the data itself? • Safe Outputs: are the research results non-disclosive i.e. they do not compromise privacy or breach confidentiality? contact@ardc.edu.au ARDC, Storage and Compute Summit, FAIR, Infrastructure, NCRIS, eResearch, training material
ARDC FAIR Data 101 self-guided

FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles

The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course.

The course structure was based on 'FAIR Data in the...

Keywords: training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management

ARDC FAIR Data 101 self-guided https://dresa.org.au/materials/ardc-fair-data-101-self-guided-2d794a84-f0ff-4e11-a39c-fa8ea481e097 FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course. The course structure was based on 'FAIR Data in the Scholarly Communications Lifecycle', run by Natasha Simons at the FORCE11 Scholarly Communications Institute. These training materials are hosted on GitHub. contact@ardc.edu.au training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management
Pawsey: AWS Quantum 101 Using Amazon Braket

Join us as AWS Quantum Specialists introduce quantum simulators and gate-based quantum computers, before turning to more advanced topics.

Keywords: Pawsey Supercomputing Centre, AWS, quantum, HPC

Pawsey: AWS Quantum 101 Using Amazon Braket https://dresa.org.au/materials/pawsey-aws-quantum-101-using-amazon-braket Join us as AWS Quantum Specialists introduce quantum simulators and gate-based quantum computers, before turning to more advanced topics. training@pawsey.org.au Pawsey Supercomputing Centre, AWS, quantum, HPC
OpenCL

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...

Keywords: OpenCL, supercomputing, CPUs, GPUs, FPGAs, HPC

OpenCL https://dresa.org.au/materials/opencl-3eabb316-794d-4f46-959a-725be3ae1bde 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. Topics covered in this course are : - Introduction to OpenCL - How to build and run applications on Setonix with OpenCL and MPI - Matrix multiplication with OpenCL – fully explained line by line - How to debug OpenCL applications and kernels - Measure performance with OpenCL Events and open source tools - Memory management - Coarse and fine-grained shared memory - Strategies for building optimised OpenCL kernels - Optimise IO performance with asynchronous operations training@pawsey.org.au OpenCL, supercomputing, CPUs, GPUs, FPGAs, HPC
PCon Preparing applications for El Capitan and beyond

As Lawrence Livermore National Laboratories (LLNL) prepares to stand up its next supercomputer, El Capitan, application teams prepare to pivot to another GPU architecture.

This talk presents how the LLNL application teams made the transition from distributed-memory, CPU-only architectures to...

Keywords: GPUs, supercomputing, HPC, PaCER

PCon Preparing applications for El Capitan and beyond https://dresa.org.au/materials/pcon-preparing-applications-for-el-capitan-and-beyond As Lawrence Livermore National Laboratories (LLNL) prepares to stand up its next supercomputer, El Capitan, application teams prepare to pivot to another GPU architecture. This talk presents how the LLNL application teams made the transition from distributed-memory, CPU-only architectures to GPUs. They share institutional best practices. They discuss new open-source software products as tools for porting and profiling applications and as avenues for collaboration across the computational science community. Join LLNL's Erik Draeger and Jane Herriman, who presented this talk at Pawsey's PaCER Conference in September 2023. training@pawsey.org.au Pawsey Supercomputing Research Centre GPUs, supercomputing, HPC, PaCER masters phd researcher ecr support professional ugrad
WEBINAR: Pro tips for scaling bioinformatics workflows to HPC

This record includes training materials associated with the Australian BioCommons webinar ‘Pro tips for scaling bioinformatics workflows to HPC’. This webinar took place on 31 May 2023.

Event description 

High Performance Computing (HPC) infrastructures offer the computational scale and...

Keywords: Bioinformatics, Workflows, HPC, High Performance Computing

WEBINAR: Pro tips for scaling bioinformatics workflows to HPC https://dresa.org.au/materials/webinar-pro-tips-for-scaling-bioinformatics-workflows-to-hpc This record includes training materials associated with the Australian BioCommons webinar ‘Pro tips for scaling bioinformatics workflows to HPC’. This webinar took place on 31 May 2023. Event description  High Performance Computing (HPC) infrastructures offer the computational scale and efficiency that life scientists need to handle complex biological datasets and multi-step computational workflows. But scaling workflows to HPC from smaller, more familiar computational infrastructures brings with it new jargon, expectations, and processes to learn. To make the most of HPC resources, bioinformatics workflows need to be designed for distributed computing environments and carefully manage varying resource requirements, and data scale related to biology.   In this webinar, Dr Georgina Samaha from the Sydney Informatics Hub, Dr Matthew Downton from the National Computational Infrastructure (NCI) and Dr Sarah Beecroft from the Pawsey Supercomputing Research Centre help you navigate the world of HPC for running and developing bioinformatics workflows. They explain when you should take your workflows to HPC and highlight the architectural features you should make the most of to scale your analyses once you’re there. You’ll hear pro-tips for dealing with common pain points like software installation, optimising for parallel computing and resource management, and will find out how to get access to Australia’s National HPC infrastructures at NCI and Pawsey.  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. Pro-tips_HPC_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/YKJDRXCmGMo Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, HPC, High Performance Computing
WORKSHOP: Make your bioinformatics workflows findable and citable

This record includes training materials associated with the Australian BioCommons workshop ‘Make your bioinformatics workflows findable and citable’. This workshop took place on 21 March 2023.

Event description

Computational workflows are invaluable resources for research communities. They help...

Keywords: Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science

WORKSHOP: Make your bioinformatics workflows findable and citable https://dresa.org.au/materials/workshop-make-your-bioinformatics-workflows-findable-and-citable This record includes training materials associated with the Australian BioCommons workshop ‘Make your bioinformatics workflows findable and citable’. This workshop took place on 21 March 2023. Event description Computational workflows are invaluable resources for research communities. They help us  standardise common analyses, collaborate with other researchers, and support reproducibility. Bioinformatics workflow developers invest significant time and expertise to create, share, and maintain these resources for the benefit of the wider community and being able to easily find and access workflows is an essential factor in their uptake by the community. Increasingly, the research community is turning to workflow registries to find and access public workflows that can be applied to their research. Workflow registries support workflow findability and citation by providing a central repository and allowing users to search for and discover them easily. This workshop will introduce you to workflow registries and support attendees to register their workflows on the popular workflow registry, WorkflowHub. We’ll kick off the workshop with an introduction to the concepts underlying workflow findability, how it can benefit workflow developers, and how you can make the most of workflow registries to share your computational workflows with the research community. You will then have the opportunity to register your own workflows in WorkflowHub with support from our trainers.  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. 2023-03-21_Workflows_slides (PDF): A copy of the slides presented during the workshop Materials shared elsewhere: A recording of the first part of this workshop is available on the Australian BioCommons YouTube Channel: https://youtu.be/2kGKxaPuQN8 Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science
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: bio.tools - making it easier to find, understand and cite biological tools and software

This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.

Event description

bio.tools provides easy access to essential...

Keywords: Bioinformatics, Research software, EDAM, Workflows, FAIR

WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software https://dresa.org.au/materials/webinar-bio-tools-making-it-easier-to-find-understand-and-cite-biological-tools-and-software-9180e32a-f4f5-4993-a90a-a9bfcfafd4f3 This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022. **Event description** bio.tools provides easy access to essential scientific and technical information about software, command-line tools, databases and services. It’s backed by ELIXIR, the European Infrastructure for Biological Information, and is being used in Australia to register software (e.g. Galaxy Australia, prokka). It underpins the information provided in the Australian BioCommons discovery service ToolFinder. Hans Ienasescu and Matúš Kalaš join us to explain how bio.tools uses a community driven, open science model to create this collection of resources and how it makes it easier to find, understand, utilise and cite them. They’ll delve into how bio.tools is using standard semantics (e.g. the EDAM ontology) and syntax (e.g. biotoolsSchema) to enrich the annotation and description of tools and resources. Finally, we’ll see how the community can contribute to bio.tools and take advantage of its key features to share and promote their own research software.   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. * biotools_EDAM_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/K0J4_bAUG3Y Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Research software, EDAM, Workflows, FAIR
WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software

This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.

Event description

bio.tools provides easy access to essential...

Keywords: Bioinformatics, Research software, EDAM, Workflows, FAIR

WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software https://dresa.org.au/materials/webinar-bio-tools-making-it-easier-to-find-understand-and-cite-biological-tools-and-software This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022. **Event description** bio.tools provides easy access to essential scientific and technical information about software, command-line tools, databases and services. It’s backed by ELIXIR, the European Infrastructure for Biological Information, and is being used in Australia to register software (e.g. Galaxy Australia, prokka). It underpins the information provided in the Australian BioCommons discovery service ToolFinder. Hans Ienasescu and Matúš Kalaš join us to explain how bio.tools uses a community driven, open science model to create this collection of resources and how it makes it easier to find, understand, utilise and cite them. They’ll delve into how bio.tools is using standard semantics (e.g. the EDAM ontology) and syntax (e.g. biotoolsSchema) to enrich the annotation and description of tools and resources. Finally, we’ll see how the community can contribute to bio.tools and take advantage of its key features to share and promote their own research software.   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. - biotools_EDAM_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/K0J4_bAUG3Y Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Research software, EDAM, Workflows, FAIR
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
Research Data Governance

This video contains key information for those who make research data-related decisions. It will help project leaders to start investigating ways to develop their own data governance policy, roles and responsibilities and procedures with the input of appropriate stakeholders.

If you want to share...

Keywords: data governance, data, research, FAIR, data management, authority, share, reuse, access, provenance, policy, responsibilities, ARDC_AU, training material

Research Data Governance https://dresa.org.au/materials/research-data-governance-cab2ebba-4e56-418d-b52f-197619e542f8 This video contains key information for those who make research data-related decisions. It will help project leaders to start investigating ways to develop their own data governance policy, roles and responsibilities and procedures with the input of appropriate stakeholders. If you want to share the video please use this: Australian Research Data Commons, 2021. Research Data Governance. [video] Available at: https://youtu.be/K_xVQRdgCIc  DOI: http://doi.org/10.5281/zenodo.5044585 [Accessed dd Month YYYY]. contact@ardc.edu.au Martinez, Paula Andrea (type: ProjectLeader) Wilkinson, Max (type: Editor) Callaghan,Shannon (type: Editor) Savill, Jo (type: Editor) Kang, Kristan (type: Editor) Levett, Kerry (type: Editor) Russell, Keith (type: Editor) Simons, Natasha (type: Editor) data governance, data, research, FAIR, data management, authority, share, reuse, access, provenance, policy, responsibilities, ARDC_AU, training material
ARDC Your first step to FAIR

This workshop gives a brief overview of the FAIR principles, including a method to make a one-file dataset FAIR.

Keywords: training material, FAIR, data, workshop

ARDC Your first step to FAIR https://dresa.org.au/materials/ardc-your-first-step-to-fair This workshop gives a brief overview of the FAIR principles, including a method to make a one-file dataset FAIR. contact@ardc.edu.au Stokes, Liz (type: Editor) Martinez, Paula Andrea (type: Editor) Russell, Keith (type: Editor) training material, FAIR, data, workshop
Locking the front door without leaving the windows open: positioning authentication technologies within the "Five Safes" framework for effective use of sensitive research data

This project explores the options for access to sensitive data sets; what authentication technologies (e.g. multi-factor authentication) are needed to access sensitive data and secure compute environments.  This project seeks to position choices around authentication technologies within the Five...

Keywords: ARDC, Storage and Compute Summit, FAIR, Infrastructure, NCRIS, eResearch, training material

Locking the front door without leaving the windows open: positioning authentication technologies within the "Five Safes" framework for effective use of sensitive research data https://dresa.org.au/materials/locking-the-front-door-without-leaving-the-windows-open-positioning-authentication-technologies-within-the-five-safes-framework-for-effective-use-of-sensitive-research-data This project explores the options for access to sensitive data sets; what authentication technologies (e.g. multi-factor authentication) are needed to access sensitive data and secure compute environments.  This project seeks to position choices around authentication technologies within the Five Safes framework for research use of sensitive data, proposed in 2003 by Felix Ritchie of the UK Office of National Statistics: • Safe Projects: is the proposed research use of the data appropriate?  • Safe People: can the users be trusted to use the data in an appropriate manner?  • Safe Settings: does the access facility limit unauthorised use? • Safe Data: is there a disclosure risk in the data itself? • Safe Outputs: are the research results non-disclosive i.e. they do not compromise privacy or breach confidentiality? contact@ardc.edu.au ARDC, Storage and Compute Summit, FAIR, Infrastructure, NCRIS, eResearch, training material
ARDC Skills Landscape

The Australian Research Data Commons is driving transformational change in the research data ecosystem, enabling researchers to conduct world class data-intensive research. One interconnected component of this ecosystem is skills development/uplift, which is critical to the Commons and its...

Keywords: skills, data skills, eresearch skills, community, skilled workforce, FAIR, research data management, data stewardship, data governance, data use, data generation, training material

ARDC Skills Landscape https://dresa.org.au/materials/ardc-skills-landscape The Australian Research Data Commons is driving transformational change in the research data ecosystem, enabling researchers to conduct world class data-intensive research. One interconnected component of this ecosystem is skills development/uplift, which is critical to the Commons and its purpose of providing Australian researchers with a competitive advantage through data.   In this presentation, Kathryn Unsworth introduces the ARDC Skills Landscape. The Landscape is a first step in developing a national skills framework to enable a coordinated and cohesive approach to skills development across the Australian eResearch sector. It is also a first step towards helping to analyse current approaches in data training to identify: - Siloed skills initiatives, and finding ways to build partnerships and improve collaboration - Skills deficits, and working to address the gaps in data skills - Areas of skills development for investment by skills stakeholders like universities, research organisations, skills and training service providers, ARDC, etc.   contact@ardc.edu.au skills, data skills, eresearch skills, community, skilled workforce, FAIR, research data management, data stewardship, data governance, data use, data generation, training material
ARDC FAIR Data 101 self-guided

FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles

The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course.

The course structure was based on 'FAIR Data in the...

Keywords: training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management

ARDC FAIR Data 101 self-guided https://dresa.org.au/materials/ardc-fair-data-101-self-guided-bba41a59-8479-4f4f-b9ee-337b9eb294bf FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course. The course structure was based on 'FAIR Data in the Scholarly Communications Lifecycle', run by Natasha Simons at the FORCE11 Scholarly Communications Institute. These training materials are hosted on GitHub. contact@ardc.edu.au training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management
HPC file systems and what users need to consider for appropriate and efficient usage

Three videos on miscellaneous aspects of HPC usage - useful reference for new users of HPC systems.

1 – General overview of different file systems that might be available on HPC. The video goes through shared file systems such as /home and /scratch, local compute node file systems (local...

Keywords: HPC, high performance computer, File systems

Resource type: video, presentation

HPC file systems and what users need to consider for appropriate and efficient usage https://dresa.org.au/materials/hpc-file-systems-and-what-users-need-to-consider-for-appropriate-and-efficient-usage Three videos on miscellaneous aspects of HPC usage - useful reference for new users of HPC systems. 1 – General overview of different file systems that might be available on HPC. The video goes through shared file systems such as /home and /scratch, local compute node file systems (local scratch or $TMPDIR) and storage file system. It outlines what users need to consider if they wish to use any of these in their workflows. 2 – Overview of the different directories that might be present on HPC. These could include /home, /scratch, /opt, /lib and lib64, /sw and others. 3 – Overview of the Message-of-the-day file and the message that is displayed to users every time they log in. This displays info about general help and often current problems or upcoming outages. QCIF Training (training@qcif.edu.au) HPC, high performance computer, File systems
Basic Linux/Unix commands

A series of eight videos (each between 5 and 10 minutes long) following the content of the Software Carpentry workshop "The Unix Shell".

Sessions 1, 2 and 3 provide instructions on the minimal level of Linux/Unix commands recommended for new...

Keywords: HPC, high performance computer, Unix, Linux, Software Carpentry

Resource type: video, guide

Basic Linux/Unix commands https://dresa.org.au/materials/basic-linux-unix-commands A series of eight videos (each between 5 and 10 minutes long) following the content of the Software Carpentry workshop ["The Unix Shell"](https://swcarpentry.github.io/shell-novice/). Sessions 1, 2 and 3 provide instructions on the minimal level of Linux/Unix commands recommended for new users of HPC. 1 – An overview of how to find out where a user is in the filesystem, list the files there, and how to get help on Unix commands 2 – How to move around the file system and change into other directories 3 – Explains the difference between an absolute and relative path 4 – Overview of how to create new directories, and to create and edit new files with nano 5 – How to use the vi editor to edit files 6 – Overview of file viewers available 7 – How to copy and move files and directories 8 – How to remove files and directories Further details and exercises with solutions can be found on the Software Carpentry "The Unix Shell" page (https://swcarpentry.github.io/shell-novice/) QCIF Training (training@qcif.edu.au) HPC, high performance computer, Unix, Linux, Software Carpentry
Transferring files and data

A short video outlining the basics on how to use FileZilla to establish a secure file transfer protocol (sftp) connection to HPC to use a drag and drop interface to transfer files between the HPC and a desktop computer.

Keywords: sftp, file transfer, HPC, high performance computer

Resource type: video, guide

Transferring files and data https://dresa.org.au/materials/transferring-files-and-data A short video outlining the basics on how to use FileZilla to establish a secure file transfer protocol (sftp) connection to HPC to use a drag and drop interface to transfer files between the HPC and a desktop computer. QCIF Training (training@qcif.edu.au) sftp, file transfer, HPC, high performance computer