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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
WEBINAR: AlphaFold: what's in it for me?

This record includes training materials associated with the Australian BioCommons webinar ‘WEBINAR: AlphaFold: what’s in it for me?’. This webinar took place on 18 April 2023.

Event description 

AlphaFold has taken the scientific world by storm with the ability to accurately predict the...

Keywords: Bioinformatics, Machine Learning, Structural Biology, Proteins, Drug discovery, AlphaFold, AI, Artificial Intelligence, Deep learning

WEBINAR: AlphaFold: what's in it for me? https://dresa.org.au/materials/webinar-alphafold-what-s-in-it-for-me This record includes training materials associated with the Australian BioCommons webinar ‘WEBINAR: AlphaFold: what’s in it for me?’. This webinar took place on 18 April 2023. Event description  AlphaFold has taken the scientific world by storm with the ability to accurately predict the structure of any protein in minutes using artificial intelligence (AI). From drug discovery to enzymes that degrade plastics, this promises to speed up and fundamentally change the way that protein structures are used in biological research.  Beyond the hype, what does this mean for structural biology as a field (and as a career)? Dr Craig Morton, Drug Discovery Lead at the CSIRO, is an early adopter of AlphaFold and has decades of expertise in protein structure / function, protein modelling, protein – ligand interactions and computational small molecule drug discovery, with particular interest in anti-infective agents for the treatment of bacterial and viral diseases. Craig joins this webinar to share his perspective on the implications of AlphaFold for science and structural biology. He will give an overview of how AlphaFold works, ways to access AlphaFold, and some examples of how it can be used for protein structure/function analysis. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/4ytn2_AiH8s Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Machine Learning, Structural Biology, Proteins, Drug discovery, AlphaFold, AI, Artificial Intelligence, Deep learning
WEBINAR AND PANEL DISCUSSION: Sustainability of biodata resources

This record includes training materials associated with the Australian BioCommons webinar and panel discussion ‘Sustainability of biodata resources’. This event took place on 8 March 2023.

Event description 

Environmental, agricultural and biomedical research is dependent on the availability of...

Keywords: Bioinformatics, Open science, Services and resources, Tools, Databases, Global Biodata Coalition

WEBINAR AND PANEL DISCUSSION: Sustainability of biodata resources https://dresa.org.au/materials/webinar-and-panel-discussion-sustainability-of-biodata-resources This record includes training materials associated with the Australian BioCommons webinar and panel discussion ‘Sustainability of biodata resources’. This event took place on 8 March 2023. Event description  Environmental, agricultural and biomedical research is dependent on the availability of high quality data that is made available through biodata resources and databases hosted locally, nationally and internationally. The reality is that funding for development, maintenance and sustainability of biodata resources is often short-term and piecemeal leaving the resources that life scientists depend on in a precarious position. The Global Biodata Coalition was formed in response to this challenge to provide a forum for research funders and others around the globe to better coordinate and share approaches for the efficient management and growth of biodata resources worldwide. In this extended webinar we discuss the theme of development and sustainability of biodata resources with a panel of guests. We’ll hear about the goals and activities of the Global Biodata Coalition and the challenges faced by well established and highly curated Australian and international data resources (Stemformatics, Community for Antimicrobial Drug Discovery (CO-ADD) Database and InnateDB) in sustaining these resources. The presentations and panel discussion will be followed by questions from the audience. 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/T5Z5prXkvEA Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Open science, Services and resources, Tools, Databases, Global Biodata Coalition
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
ARDC 2023 Skills Summit - Frameworks Panel Discussion (Day 2 - February 10, 2023)

Presentations to the ARDC Skills Summit 2023 (Panel Talks Day 2 - February 10th, 2023)

Dr Peter Derbyshire - Unpacking the ATSE report - Our STEM skilled future and the need for a national skills taxonomy
Anthony Beitz - Applying Skills Framework for the Information Age (SFIA) within DSTG
Kate...

Keywords: training material, research, training, skills, framework, sfia, eresearch, skills frameworks, skills taxonomies, skills classifications, skill shortages, transferrable skills, applying SFIA, training gaps, workforce requirements, job requirements, DReSA, digital literacy, applying skills frameworks, Australian Skills Classification framework, ASC

ARDC 2023 Skills Summit - Frameworks Panel Discussion (Day 2 - February 10, 2023) https://dresa.org.au/materials/ardc-2023-skills-summit-frameworks-panel-discussion-day-2-february-10-2023 Presentations to the ARDC Skills Summit 2023 (Panel Talks Day 2 - February 10th, 2023) Dr Peter Derbyshire - Unpacking the ATSE report - Our STEM skilled future and the need for a national skills taxonomy Anthony Beitz - Applying Skills Framework for the Information Age (SFIA) within DSTG Kate Morrison - A national skills taxonomy - Australian Skills Classification (ASC) Kathryn Unsworth - ARDC Digital Research Capabilities & Skills Framework Peter Embelton - Enhancing skills uplift for researchers through the alignment and implementation of skills frameworks These presentations cover skills frameworks/taxonomies/classifications, skill shortages, transferrable skills, applying SFIA (Skills Framework for the Information Age), Australian Skills Classification framework, training gaps, workforce/job requirements, Digital Research Skills Australasia (DReSA), digital literacy and applying skills frameworks. contact@ardc.edu.au training material, research, training, skills, framework, sfia, eresearch, skills frameworks, skills taxonomies, skills classifications, skill shortages, transferrable skills, applying SFIA, training gaps, workforce requirements, job requirements, DReSA, digital literacy, applying skills frameworks, Australian Skills Classification framework, ASC
Setting The Scene

Opening Address for the ARDC Skills Summit 2023

This presentation provides a welcome to the ARDC Skills Summit 2023, and includes an outline of the importance of digital research skills to data-enriched research, the value of skills training and highly skilled research workforce to the broader...

Keywords: research, training, skills, training material, ARDC, research data commons, digital research skills agenda

Setting The Scene https://dresa.org.au/materials/setting-the-scene Opening Address for the ARDC Skills Summit 2023 This presentation provides a welcome to the ARDC Skills Summit 2023, and includes an outline of the importance of digital research skills to data-enriched research, the value of skills training and highly skilled research workforce to the broader economy, and an overview of related ARDC activity. contact@ardc.edu.au research, training, skills, training material, ARDC, research data commons, digital research skills agenda
ARDC 2023 Skills Summit Lightning Talks (Day 2 - February 10, 2023)

Presentations to the ARDC Skills Summit 2023 (Lightning Talks Day 2 - February 10th, 2023)
Dr Nisha Ghatak - From local to the global: NeSI's efforts in building digital skills capabilities across Aotearoa
Dr Melissa Burke - No one has time for training. Is doing less the answer?
Dr Giorgia Mori...

Keywords: training material, digital skills capability, digital skills partnerships, The Carpentries, bioinformatics training, cooperative training approaches, industry partnered training, learner pathways, user guidance, new training approaches, innovative training approaches

ARDC 2023 Skills Summit Lightning Talks (Day 2 - February 10, 2023) https://dresa.org.au/materials/ardc-2023-skills-summit-lightning-talks-day-2-february-10-2023 Presentations to the ARDC Skills Summit 2023 (Lightning Talks Day 2 - February 10th, 2023) Dr Nisha Ghatak - From local to the global: NeSI's efforts in building digital skills capabilities across Aotearoa Dr Melissa Burke - No one has time for training. Is doing less the answer? Dr Giorgia Mori - Industry training collaborations. Is this the future? Ann Backhaus - Skills pathways for developing the research workforce - status quo or let's get creative? These presentations cover a national perspective of New Zealand's digital skills capability and partnerships, The Carpentries, bioinformatics training, innovative and cooperative training approaches, industry-partnered training, learner pathways, and the importance of user guidance. contact@ardc.edu.au training material, digital skills capability, digital skills partnerships, The Carpentries, bioinformatics training, cooperative training approaches, industry partnered training, learner pathways, user guidance, new training approaches, innovative training approaches
ARDC 2023 Skills Summit Lightning Talks (Day 1 - February 9, 2023)

Presentations to the ARDC Skills Summit 2023 (Lightning Talks Day 1 - February 9th, 2023)
Dr Pablo Franco - Assessing the effectiveness of training: Teaching digital skills to researchers
Aidan Wilson - Scaling training operations & succession planning
Dr Paula Martinez - Building...

Keywords: training material, research, training, Kirkpatrick framework, RezBaz, impact, skills, impact assessment, training at scale, succession planning, automated training organisation systems, trainer workforce, research software community, participation models, community building, visible research software interest group, carpentries, social infrastructure

ARDC 2023 Skills Summit Lightning Talks (Day 1 - February 9, 2023) https://dresa.org.au/materials/ardc-2023-skills-summit-lightning-talks-day-1-february-9-2023 Presentations to the ARDC Skills Summit 2023 (Lightning Talks Day 1 - February 9th, 2023) Dr Pablo Franco - Assessing the effectiveness of training: Teaching digital skills to researchers Aidan Wilson - Scaling training operations & succession planning Dr Paula Martinez - Building community Dr Mark Crowe - Bringing training to research communities - ResBaz Liz Stokes - The Carpentries Partnership These presentations cover theoretical frameworks for assessing training, The Kirkpatrick Model of Training Evaluation, outreach, RezBaz, impact assessment, training at scale, succession planning, automated training organisation systems, trainer workforce, research software community, participation models, community building ideas, visible research software interest group, The Carpentries and social infrastructure. contact@ardc.edu.au training material, research, training, Kirkpatrick framework, RezBaz, impact, skills, impact assessment, training at scale, succession planning, automated training organisation systems, trainer workforce, research software community, participation models, community building, visible research software interest group, carpentries, social infrastructure
Professionalizing Training - Origin Stories for the Modern Researcher

Keynote Presentation for the ARDC Skills Summit 2023

This keynote presentation provides a brief outline of Jason William’s experience and an overview of the training initiatives he has been involved in. His presentation looks at what makes a good researcher and provokes thinking about modern...

Keywords: research, training, skills, superheroes, formal, career, change, workshops, milestones, community, principles, bicycle principles, professionalizing, training material

Professionalizing Training - Origin Stories for the Modern Researcher https://dresa.org.au/materials/professionalizing-training-origin-stories-for-the-modern-researcher Keynote Presentation for the ARDC Skills Summit 2023 This keynote presentation provides a brief outline of Jason William’s experience and an overview of the training initiatives he has been involved in. His presentation looks at what makes a good researcher and provokes thinking about modern researchers and the need for them to get serious bout career-spanning training. Jason also provides an overview of the Bike Principles and focuses on the first Bike Principles recommendation - Professionalize the training of short-format training instructors and instructional designers. contact@ardc.edu.au research, training, skills, superheroes, formal, career, change, workshops, milestones, community, principles, bicycle principles, professionalizing, training material
Introduction to REDCap at Griffith University

This site is designed as a companion to Griffith Library’s Research Data Capture workshops. It can also be treated as a standalone, self-paced tutorial for learning to use REDCap (Research Electronic Data Capture) a secure web application for building and managing online surveys and databases.

Keywords: REDCap, survey instruments

Resource type: tutorial

Introduction to REDCap at Griffith University https://dresa.org.au/materials/introduction-to-redcap-at-griffith-university This site is designed as a companion to Griffith Library’s Research Data Capture workshops. It can also be treated as a standalone, self-paced tutorial for learning to use REDCap (Research Electronic Data Capture) a secure web application for building and managing online surveys and databases. y.banens@griffith.edu.au REDCap, survey instruments mbr phd ecr researcher support
Introduction to text mining and analysis

In this self-paced workshop you will learn steps to: 
- Build data sets: find where and how to gather textual data for your corpus or data set.  
- Prepare data for analysis: explore useful processes and tools to prepare and clean textual data for analysis
- Analyse data: identify different...

Keywords: textual training materials

Resource type: tutorial

Introduction to text mining and analysis https://dresa.org.au/materials/introduction-to-text-mining-and-analysis In this self-paced workshop you will learn steps to:  - Build data sets: find where and how to gather textual data for your corpus or data set.   - Prepare data for analysis: explore useful processes and tools to prepare and clean textual data for analysis - Analyse data: identify different types of analysis used to interrogate content and uncover new insights s.stapleton@griffith.edu.au; y.banens@griffith.edu.au; textual training materials mbr phd ecr researcher support
Introducing Computational Thinking

This workshop is for researchers at all career stages who want to understand the uses and the building blocks of computational thinking. This skill is useful for all kinds of problem solving, whether in real life or in computing.

The workshop will not teach computer programming per se. Instead...

Keywords: computational skills, data skills

Resource type: tutorial

Introducing Computational Thinking https://dresa.org.au/materials/introducing-computational-thinking This workshop is for researchers at all career stages who want to understand the uses and the building blocks of computational thinking. This skill is useful for all kinds of problem solving, whether in real life or in computing. The workshop will not teach computer programming per se. Instead it will cover the thought processes involved should you want to learn to program. s.stapleton@griffith.edu.au computational skills, data skills
Advanced Data Wrangling with OpenRefine

This online self-paced workshop teaches advanced data wrangling skills including combining datasets, geolocating data, and “what if” exploration using OpenRefine.

Keywords: data skills, data

Resource type: tutorial

Advanced Data Wrangling with OpenRefine https://dresa.org.au/materials/advanced-data-wrangling-with-openrefine This online self-paced workshop teaches advanced data wrangling skills including combining datasets, geolocating data, and “what if” exploration using OpenRefine. s.stapleton@griffith.edu.au data skills, data mbr phd ecr researcher support professional
Introduction to Data Cleaning with OpenRefine

Learn basic data cleaning techniques in this self-paced online workshop using open data from data.qld.gov.au and open source tool OpenRefine openrefine.org. Learn techniques to prepare messy tabular data for comupational analysis. Of most relevance to HASS disciplines, working with textual data...

Keywords: data skills, Data analysis

Resource type: tutorial

Introduction to Data Cleaning with OpenRefine https://dresa.org.au/materials/introduction-to-data-cleaning-with-openrefine Learn basic data cleaning techniques in this self-paced online workshop using open data from data.qld.gov.au and open source tool OpenRefine openrefine.org. Learn techniques to prepare messy tabular data for comupational analysis. Of most relevance to HASS disciplines, working with textual data in a structured or semi-structured format. s.stapleton@griffith.edu.au; Sharron Stapleton data skills, Data analysis mbr phd ecr researcher support professional
Digital research skills trainer certification guide

This guide to certification is for those who currently design, develop and deliver training as full-time trainers or where training is part of their role, and for those who are considering becoming a skills trainer.

Keywords: digital research skills training, trainer certification, training material

Digital research skills trainer certification guide https://dresa.org.au/materials/digital-research-skills-trainer-certification-guide This guide to certification is for those who currently design, develop and deliver training as full-time trainers or where training is part of their role, and for those who are considering becoming a skills trainer. contact@ardc.edu.au digital research skills training, trainer certification, training material
Guide to designing digital research skills training materials: presentations and videos

The Australian Research Data Commons (ARDC) Guide to Designing Digital Research Skills Training Materials: Presentations and Videos aims to support training materials creators, trainers and national training infrastructure providers in the design and delivery of presentations and videos while...

Keywords: digital research skills training, learning design, training presentations, training videos, training material

Guide to designing digital research skills training materials: presentations and videos https://dresa.org.au/materials/guide-to-designing-digital-research-skills-training-materials-presentations-and-videos The Australian Research Data Commons (ARDC) Guide to Designing Digital Research Skills Training Materials: Presentations and Videos aims to support training materials creators, trainers and national training infrastructure providers in the design and delivery of presentations and videos while also encouraging the sharing and reuse of their training materials. It aims to facilitate the design, development and delivery of digital research and data skills videos and presentations in alignment with best practices for learning and training.  This tool is informed by the Universal Design for Learning framework, which aims to eliminate barriers in the design of learning materials and make content accessible to all. contact@ardc.edu.au digital research skills training, learning design, training presentations, training videos, training material
Guide to designing digital research skills training materials: textual materials

The Australian Research Data Commons (ARDC) Guide to Designing Digital Research Skills Training Materials: Textual Materials aims to support training materials creators, trainers and national training infrastructure providers in the creation of textual guides while also encouraging the sharing...

Keywords: digital research skills training, learning design, textual training materials, training material

Guide to designing digital research skills training materials: textual materials https://dresa.org.au/materials/guide-to-designing-digital-research-skills-training-materials-textual-materials The Australian Research Data Commons (ARDC) Guide to Designing Digital Research Skills Training Materials: Textual Materials aims to support training materials creators, trainers and national training infrastructure providers in the creation of textual guides while also encouraging the sharing and reuse of their training materials. It aims to facilitate the design, development and delivery of textual guides on digital research and data skills in alignment with best practices in learning and training. This tool is informed by the Universal Design for Learning principles which aims to eliminate barriers in the design of learning materials to make content accessible to all. contact@ardc.edu.au digital research skills training, learning design, textual training materials, training material
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
Exploring Chi-Square and Correlation in SPSS

This hands-on training is designed to familiarize you further with the SPSS data analysis environment. In this session, we will traverse into the realm of inferential statistics, beginning with linear correlation and reliability. We will present a brief conceptual overview and the SPSS procedures...

Keywords: Data Analysis, SPSS

Exploring Chi-Square and Correlation in SPSS https://dresa.org.au/materials/exploring-chi-square-and-correlation-in-spss-d38c2067-302a-4194-80a2-71f2311f8756 This hands-on training is designed to familiarize you further with the SPSS data analysis environment. In this session, we will traverse into the realm of inferential statistics, beginning with linear correlation and reliability. We will present a brief conceptual overview and the SPSS procedures for computing Pearson's r and Spearman's Rho, followed by a short session on reliability . In the remainder of the session, we will explore the Chi-Square Goodness-of-Fit test and Chi-Square Test of Association for analysing categorical data. #### You'll learn: - Perform Pearson’s Correlation (r) Test - Perform Spearman’s Rho Correlation (⍴) Test - Carry out basic reliability analysis on survey items - Perform Chi-Square Goodness-of-Fit test - Perform Chi-Square Test of Association #### Prerequisites: In order to participate, attendees must have a licensed copy of SPSS installed on their computer. Speak to your local university IT or Research Office for assistance in obtaining a license and installing the software. This workshop is recommended for researchers and postgraduate students who have previously attended the Intersect’s [Data Entry and Processing in SPSS](https://intersect.org.au/training/course/spss101/) workshop. **For more information, please click [here](https://intersect.org.au/training/course/spss102).** training@intersect.org.au Data Analysis, SPSS
WEBINAR: Variant interpretation: from the clinic to the lab… and back again

This record collates training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Variant interpretation: from the clinic to the lab… and back again’. This webinar took place on 7 December 2022.

Event description

The use of genomic testing is increasing...

Keywords: Clinical genomics, Variant interpretation, Variant curation, Continuing Professional Development, Professional Development, Bioinformatics, Genomics, Variant calling

WEBINAR: Variant interpretation: from the clinic to the lab… and back again https://dresa.org.au/materials/webinar-variant-interpretation-from-the-clinic-to-the-lab-and-back-again This record collates training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Variant interpretation: from the clinic to the lab… and back again’. This webinar took place on 7 December 2022. **Event description** The use of genomic testing is increasing rapidly as the cost of genome sequencing decreases. Many areas of the health workforce are upskilling in genomics to help meet the increased demand. From clinicians learning how to use the right test, for the right patient, at the right time, to medical scientists learning how to interpret and classify variants, and data scientists to learning how to better create and continuously refine the pipelines and software to handle and curate big data. In this webinar, we’ll hear from two people working at the coalface of variant interpretation – one in a diagnostic laboratory and the other in a cancer research laboratory. Naomi Baker is Medical Scientist at Victorian Clinical Genetics Services. She helps process hundreds of genomic tests per year to find the variants that cause rare diseases. She’ll explain the clinical variant interpretation processes she uses, the pipelines, professions and people involved. Joep Vissers is a Curation Team Leader, at the University of Melbourne Centre for Cancer Research, Department of Clinical Pathology. Joep, who also teaches cancer biology at the University, will describe how he uses variant interpretation in his work at the research/clinical interface, and the shift in mindset required when working with data for these different purposes. Amy Nisselle, Genomics Workforce Lead at Melbourne Genomics, will then briefly outline some of the education programs available in clinical variant interpretation. This webinar is co-presented by Australian BioCommons and Melbourne Genomics 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. * Variant interpretation from the clinic to the lab and back again.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/wLMhwIiK8Lw Melissa Burke (melissa@biocommons.org.au) Clinical genomics, Variant interpretation, Variant curation, Continuing Professional Development, Professional Development, Bioinformatics, Genomics, Variant calling
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
Introduction to Unix

A hands-on workshop covering the basics of the Unix command line interface.

Knowledge of the Unix operating system is fundamental to the use of many popular bioinformatics command-line tools. Whether you choose to run your analyses locally or on a high-performance computing system, knowing...

Keywords: Unix, Command line, Command-line, CLI

Resource type: tutorial

Introduction to Unix https://dresa.org.au/materials/introduction-to-unix A hands-on workshop covering the basics of the Unix command line interface. Knowledge of the Unix operating system is fundamental to the use of many popular bioinformatics command-line tools. Whether you choose to run your analyses locally or on a high-performance computing system, knowing your way around a command-line interface is highly valuable. This workshop will introduce you to Unix concepts by way of a series of hands-on exercises. This workshop is designed for participants with little or no command-line knowledge. Tools: Standard Unix commands, FileZilla Topic overview: Section 1: Getting started Section 2: Exploring your current directory Section 3: Making and changing directories Section 4: Viewing and manipulating files Section 5: Removing files and directories Section 6: Searching files Section 7: Putting it all together Section 8: Transferring files Tutorial instructions available here: https://www.melbournebioinformatics.org.au/tutorials/tutorials/unix/unix/ For queries relating to this workshop, contact Melbourne Bioinformatics (bioinformatics-training@unimelb.edu.au). Find out when we are next running this training as an in-person workshop, by visiting the Melbourne Bioinformaitcs Eventbrite page: https://www.eventbrite.com.au/o/melbourne-bioinformatics-13058846490 For queries relating to this workshop, contact Melbourne Bioinformatics (bioinformatics-training@unimelb.edu.au). Unix, Command line, Command-line, CLI ugrad masters mbr phd ecr researcher support professional
WEBINAR: Effective, inclusive, and scalable training in the life sciences, clinical education and beyond

This record includes training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Effective, inclusive, and scalable training in the life sciences, clinical education and beyond’. This webinar took place on 4 November 2022.

Event description 

Scientists and...

Keywords: Short-format training, Clinical education, Continuing education, Professional development, Training, Lifelong learning, Pedagogy

WEBINAR: Effective, inclusive, and scalable training in the life sciences, clinical education and beyond https://dresa.org.au/materials/webinar-effective-inclusive-and-scalable-training-in-the-life-sciences-clinical-education-and-beyond This record includes training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Effective, inclusive, and scalable training in the life sciences, clinical education and beyond’. This webinar took place on 4 November 2022. **Event description**  Scientists and educators working in the life sciences must continuously acquire new knowledge and skills to stay up-to-date with the latest methods, technologies and research. Short-format training, such as webinars, workshops and bootcamps, are popular ways of quickly learning about new topics and gaining new skills. As trainers and educators, how can we ensure that short-format training is effective and inclusive for all? How can we ensure that our learners are equipped to continue learning and applying their new skills once they return to their day jobs? And how can we do this in a way that is scalable and sustainable? The Bicycle Principles assemble education theory and community experience into a framework for improving short-format training so that it is effective, inclusive and scalable. Over 30 international experts, including colleagues from the Australian BioCommons, Melbourne Genomics and other Australian and New Zealand organisations, helped develop the principles and an associated set of recommendations. Jason Williams, Assistant Director, DNA Learning Center, Cold Spring Harbor Laboratory - a leading genomics and bioinformatics educator and project lead, joins us to discuss the Principles and how they can be applied to achieve scalable and sustainable training in a range of Australian settings. This webinar is co-hosted by Australian BioCommons and Melbourne Genomics Training 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. * WILLIAMS-Jason_aus-biocommons_nov-2022 (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/18dub7jGeQ8 Melissa Burke (melissa@biocommons.org.au) Short-format training, Clinical education, Continuing education, Professional development, Training, Lifelong learning, Pedagogy
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
Learn R or Python, generate Species Distribution Models (SDM) or SDM Climate Projections

EcoCommons has a variety of videos, R scripts, and support articles that introduce users to learning how to code in R or Python, how to generate Species Distribution Models (SDMs) or generate SDM climate projections.

We also have a growing number of use cases where users can see and work...

Keywords: Species Distribution Modelling, Beginner R coding, Beginer ecological modelling, Climate projections

Learn R or Python, generate Species Distribution Models (SDM) or SDM Climate Projections https://dresa.org.au/materials/learn-r-or-python-generate-species-distribution-models-sdm-or-sdm-climate-projections EcoCommons has a variety of videos, R scripts, and support articles that introduce users to learning how to code in R or Python, how to generate Species Distribution Models (SDMs) or generate SDM climate projections. We also have a growing number of use cases where users can see and work through examples that highlight the power of bringing data together. support@ecocommons.org.au EcoCommons Species Distribution Modelling, Beginner R coding, Beginer ecological modelling, Climate projections ugrad mbr phd ecr professional
Principles Aligned Institutionally-Contextualised (PAI-C) RDM Training

This GitHub repository contains resources for an institution to contextualise a principles-based RDM training with its institution's research data management policies, processes and systems.

The adoption of PAI-C across institutions will contribute to a common baseline understanding of RDM...

Keywords: PAI-C, Training, Data Management

Principles Aligned Institutionally-Contextualised (PAI-C) RDM Training https://dresa.org.au/materials/principles-aligned-institutionally-contextualised-pai-c-rdm-training This GitHub repository contains resources for an institution to contextualise a principles-based RDM training with its institution's research data management policies, processes and systems. The adoption of PAI-C across institutions will contribute to a common baseline understanding of RDM across institutions, which in turn will facilitate cross institutional management of data (e.g. when researchers move between institutions, and collaborate across institutions). Dr Adrian W. Chew (w.l.chew@unsw.edu.au) PAI-C, Training, Data Management
VOSON Lab Code Blog

The VOSON Lab Code Blog is a space to share methods, tips, examples and code. Blog posts provide techniques to construct and analyse networks from various API and other online data sources, using the VOSON open-source software and other R based packages.

Keywords: visualisation, Data analysis, data collections, R software, Social network analysis, social media data, Computational Social Science, quantitative, Text Analytics

Resource type: tutorial, other

VOSON Lab Code Blog https://dresa.org.au/materials/voson-lab-code-blog The VOSON Lab Code Blog is a space to share methods, tips, examples and code. Blog posts provide techniques to construct and analyse networks from various API and other online data sources, using the VOSON open-source software and other R based packages. robert.ackland@anu.edu.au visualisation, Data analysis, data collections, R software, Social network analysis, social media data, Computational Social Science, quantitative, Text Analytics researcher support phd masters
WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud

This record includes training materials associated with the Australian BioCommons webinar ‘Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud’. This webinar took place on 20 September 2022.

Event description 

Bioinformatics workflows can...

Keywords: Bioinformatics, Workflows, Nextflow, Containerisation

WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud https://dresa.org.au/materials/webinar-portable-reproducible-and-scalable-bioinformatics-workflows-using-nextflow-and-pawsey-nimbus-cloud This record includes training materials associated with the Australian BioCommons webinar ‘Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud’. This webinar took place on 20 September 2022. **Event description**  Bioinformatics workflows can support portable, reproducible and scalable analysis of omics datasets but using workflows can be challenging for both beginners and experienced bioinformaticians. Beginners face a steep learning curve to be able to build and deploy their own bioinformatics workflows while those with more experience face challenges productionising and scaling code for custom workflows and big data.  Bioinformaticians across the world are using Nextflow to build and manage workflows. Many of these workflows are shared for others to use and supported by the community via nf-co.re. So far, 39 workflows for omics data are available with another 23 under development. These workflows cover common analyses such as RNAseq, mapping, variant calling, single cell transcriptomics and more and can be easily deployed by anyone, regardless of skill level. In this webinar, Nandan Deshpande from the Sydney Informatics Hub, University of Sydney, will discuss how you can deploy freely available Nextflow (nf.co-re) bioinformatics workflows with a single command. We describe how you can quickly get started deploying these workflows using Pawsey Nimbus Cloud. For advanced users, we introduce you to Nextflow concepts to get you started with building your own workflows that will save you time and support reproducible, portable and scalable analysis. In the latter half of the webinar, Sarah Beecroft from the Pawsey Supercomputing Research Centre will talk about their Nimbus Cloud systems. While Nextflow supports portability and can run on many computing infrastructures, we describe why we specifically love using Nimbus with Nextflow for many bioinformatics projects. We will describe some of the nf.co-re workflows that we have used on Nimbus and the research outcomes. We will also cover when not to use Nimbus and the alternatives we recommend.   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. * Nextflow_Nimbus_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/VnLX63yXbJU Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, Nextflow, Containerisation
WORKSHOP: Single cell RNAseq analysis in R

This record includes training materials associated with the Australian BioCommons workshop Single cell RNAseq analysis in R. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022.

Event description

Analysis and interpretation of single cell RNAseq (scRNAseq) data...

Keywords: Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq

WORKSHOP: Single cell RNAseq analysis in R https://dresa.org.au/materials/workshop-single-cell-rnaseq-analysis-in-r This record includes training materials associated with the Australian BioCommons workshop Single cell RNAseq analysis in R. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022. **Event description** Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using Seurat - an R package for QC, analysis, and exploration of single-cell RNAseq data.  We will discuss the ‘why’ behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data. This workshop is presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) 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. * scRNAseq_Slides (PDF): Slides used to introduce topics * scRNAseq_Schedule (PDF): A breakdown of the topics and timings for the workshop * scRNAseq_Resources (PDF): A list of resources recommended by trainers and participants * scRNAseq_QandA(PDF): Archive of questions and their answers from the workshop Slack Channel. Materials shared elsewhere: This workshop follows the tutorial ‘scRNAseq Analysis in R with Seurat’ https://swbioinf.github.io/scRNAseqInR_Doco/index.html This material is based on the introductory Guided Clustering Tutorial tutorial from Seurat. It is also drawing from a similar workshop held by Monash Bioinformatics Platform Single-Cell-Workshop, with material here. Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq
WEBINAR: Getting started with whole genome mapping and variant calling on the command line

This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with whole genome mapping and variant calling on the command line’. This webinar took place on 24 August 2022.

Event description 

Life scientists are increasingly using whole...

Keywords: Genome mapping, Variant calling, Bioinformatics, Workflows

WEBINAR: Getting started with whole genome mapping and variant calling on the command line https://dresa.org.au/materials/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with whole genome mapping and variant calling on the command line’. This webinar took place on 24 August 2022. **Event description**  Life scientists are increasingly using whole genome sequencing (WGS) to ask and answer research questions across the tree of life. Before any of this work can be done, there is the essential but challenging task of processing raw sequencing data. Processing WGS data is a computationally challenging, multi-step process used to create a map of an individual’s genome and identify genetic variant sites. The tools you use in this process and overall workflow design can look very different for different researchers, it all depends on your dataset and the research questions you’re asking. Luckily, there are lots of existing WGS processing tools and pipelines out there, but knowing where to start and what your specific needs are is hard work, no matter how experienced you are.  In this webinar we will walk through the essential steps and considerations for researchers who are running and building reproducible WGS mapping and variant calling pipelines at the command line interface. We will discuss how to choose and evaluate a pipeline that is right for your dataset and research questions, and how to get access to the compute resources you need 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. * WGS mapping and variant calling _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/Q2EceFyizio Melissa Burke (melissa@biocommons.org.au) Genome mapping, Variant calling, Bioinformatics, Workflows