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Authors: Coddington, Paul (orcid: 00...  or AMD  or Dr Henry Lydecker  or Brian Ballsun-Stanton 

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
Unlocking the potential of ChatGPT for your research

In this 1 hr masterclass, Dr. Henry Lydecker and Dr. Gordon McDonald from the University of Sydney's Sydney Informatics Hub discuss:

  • What ChatGPT is,
  • A breif history of how we got here,
  • Some ideas on how you can use it to accelerate your research
  • Some pitfalls to beware of
  • Some...

Keywords: ChatGPT, training material

Unlocking the potential of ChatGPT for your research https://dresa.org.au/materials/unlocking-the-potential-of-chatgpt-for-your-research In this 1 hr masterclass, Dr. Henry Lydecker and Dr. Gordon McDonald from the University of Sydney's Sydney Informatics Hub discuss: - What ChatGPT is, - A breif history of how we got here, - Some ideas on how you can use it to accelerate your research - Some pitfalls to beware of - Some ethical/legal/moral and IP considerations for use of the tool. Slides for the presentation are available [here](https://github.com/Sydney-Informatics-Hub/ChatGPT-Masterclass/blob/main/chatgpt_masterclass.pdf). Presented by Dr. Henry Lydecker and Dr. Gordon McDonald from the University of Sydney's Sydney Informatics Hub. [https://sydney.edu.au/sydney-informatics-hub](https://sydney.edu.au/sydney-informatics-hub) sih.training@sydney.edu.au ChatGPT, training material
Generative AI in Research

Slides available here.

Presented by Dr. Henry Lydecker and Dr. Gordon McDonald of the Sydney Informatics Hub, on the 30th November 2023, as part of CSIRO's National AI Month.

Everyone is using ChatGPT these...

Keywords: Artificial Intelligence, training material

Generative AI in Research https://dresa.org.au/materials/generative-ai-in-research Slides available [here](https://github.com/Sydney-Informatics-Hub/Generative-AI-in-Research-Masterclass/). Presented by Dr. Henry Lydecker and Dr. Gordon McDonald of the Sydney Informatics Hub, on the 30th November 2023, as part of CSIRO's National AI Month. Everyone is using ChatGPT these days, but how exactly can you get the most out of generative AI tools for your research? In this Sydney Informatics Hub Masterclass we'll show you three killer ways you can take advantage of these new AI magic tricks so you can use them like a research wizard. We'll briefly overview the traps to avoid, and then show you a glimpse of the future where AI does the boring parts of your job for you! *The Sydney Informatics Hub is a Core Research Facility at The University of Sydney, enabling excellence in research.* [https://sydney.edu.au/informatics-hub](https://sydney.edu.au/informatics-hub) sih.training@sydney.edu.au Artificial Intelligence, training material
AMD Profiling

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

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

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

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

Resource type: activity

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

Event run 7 June at the MQ Incubator. Event description:

A two-hour hands-on workshop giving a brief history of the last 4 months of development of "Generative AI."

These tools, these Large Language Models, offer present promise and peril -- disruption -- to ways of working and of...

Keywords: Large Language Model, ChatGPT

A hands on introduction to Large Language Models like Bing Chat and ChatGPT https://dresa.org.au/materials/a-hands-on-introduction-to-large-language-models-like-bing-chat-and-chatgpt Event run 7 June at the MQ Incubator. Event description: A two-hour hands-on workshop giving a brief history of the last 4 months of development of "Generative AI." These tools, these Large Language Models, offer present promise and peril -- disruption -- to ways of working and of learning. Outside the "hype," these tools are "calculators for words" and allow the same manipulation and reflection of a user's words as a calculator offers for a user's numbers. The workshop will guide users into using various free and paid tools, and the effective use of Large Language Models through chain of thought prompting. Remember: a LLM is "Always confident and usually correct." OSF Description (LLM generated): This two-hour workshop provides a comprehensive introduction to the world of Large Language Models (LLMs), focusing on the recent advancements in Generative AI. Participants will gain insights into the development and functionality of prominent LLMs such as Bing Chat and ChatGPT. The workshop will delve into the concept of LLMs as "calculators for words," highlighting their potential to revolutionize ways of working and learning. The session will explore the principles of Prompt Engineering and Transactional Prompting, demonstrating how consistent prompts can yield reliable and reproducible results. Participants will also learn about the practical applications of LLMs, including editing and proofreading papers, generating technical documentation, recipe ideation, and more. The workshop emphasizes the importance of understanding the terms of use and the responsibilities that come with using these powerful AI tools. By the end of the session, participants will be equipped with the knowledge and skills to effectively use LLMs in various contexts, guided by the mantra that a LLM is "Always confident and usually correct." Brian Ballsun-Stanton (brian.ballsun-stanton@mq.edu.au) Large Language Model, ChatGPT researcher
Managing Active Research Data

In this train-the-trainer workshop, we will be exploring and discussing methods for active data management.

Participants will become familiar with cloud storage and associated tools and services for managing active research data. Learn how to organise, maintain, store and analyse active data,...

Keywords: RDM Training, CloudStor, cloud

Resource type: lesson

Managing Active Research Data https://dresa.org.au/materials/managing-active-research-data In this train-the-trainer workshop, we will be exploring and discussing methods for active data management. Participants will become familiar with cloud storage and associated tools and services for managing active research data. Learn how to organise, maintain, store and analyse active data, and understand safe and secure ways of sharing and storing data. Topics such as cloud storage, collaborative editing, versioning and data sharing will be discussed and demonstrated. Sara King RDM Training, CloudStor, cloud phd support masters ecr researcher
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
Research Data Management (RDM) Online Orientation Module (Macquarie University)

This is a self-paced, guided orientation to the essential elements of Research Data Management. It is available for others to use and modify.
The course introduces the following topics: data policies, data sensitivity, data management planning, storage and security, organisation and metadata,...

Keywords: research data, data management, FAIR data, training

Resource type: quiz, activity, other

Research Data Management (RDM) Online Orientation Module (Macquarie University) https://dresa.org.au/materials/macquarie-university-research-data-management-rdm-online This is a self-paced, guided orientation to the essential elements of Research Data Management. It is available for others to use and modify. The course introduces the following topics: data policies, data sensitivity, data management planning, storage and security, organisation and metadata, benefits of data sharing, licensing, repositories, and best practice including the FAIR principles. Embedded activities and examples help extend learner experience and awareness. The course was designed to assist research students and early career researchers in complying with policies and legislative requirements, understand safe data practices, raise awareness of the benefits of data curation and data sharing (efficiency and impact) and equip them with the required knowledge to plan their data management early in their projects. This course is divided into four sections 1. Crawl - What is Research Data and why care for it? Policy and legislative requirements. The Research Data Life-cycle. Data Management Planning (~30 mins) 2. Walk - Data sensitivity, identifiability, storage, and security (~60 mins) 3. Run - Record keeping, data retention, file naming, folder structures, version control, metadata, data sharing, open data, licences, data repositories, data citation, and ethics (~75 mins) 4. Jump - Best practice FAIR data principles (~45 mins) 5. Fight - Review - a quiz designed to review and reinforce knowledge (~15 mins) https://rise.articulate.com/share/-AWqSPaEI_jTbHwzQHdmQ43R50edrCl0 * *Password: "FAIR" *Password: "FAIR" Any queries or suggestions for course improvement can be directed to the Macquarie University Research Integrity Team: Dr Paul Sou (paul.sou@mq.edu.au) or Dr Shannon Smith (shannon.smith@mq.edu.au). Scorm files can be made available upon request. research data, data management, FAIR data, training