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://zenodo.org/record/7710785
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
Williams, Jason (orcid: 0000-0003-3049-2010)
research, training, skills, superheroes, formal, career, change, workshops, milestones, community, principles, bicycle principles, professionalizing, training material
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://zenodo.org/record/7711377
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
Ghatak, Nisha (orcid: 0000-0002-1213-2196)
Burke, Melissa (orcid: 0000-0002-5571-8664)
Mori, Giorgia (orcid: 0000-0003-3469-5632)
Backhaus, Ann (orcid: 0000-0002-9023-055X)
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
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://zenodo.org/record/7710621
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
Russell, Keith (orcid: 0000-0001-5390-2719)
research, training, skills, training material, ARDC, research data commons, digital research skills agenda
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://griffithunilibrary.github.io/redcap-intro/
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
Yuri Banens
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://griffithunilibrary.github.io/intro-text-mining-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;
Yuri Banens
Sharron Stapleton
Ben McRae
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://griffithunilibrary.github.io/intro-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
Belinda Weaver
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://griffithunilibrary.github.io/advanced-data-wrangle-2/
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
Sharron Stapleton
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://griffithunilibrary.github.io/data-cleaning-intro/
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://zenodo.org/record/7587668
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
ARDC
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://zenodo.org/record/7587657
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
ARDC
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://zenodo.org/record/7587651
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
ARDC
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://zenodo.org/record/7439804
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)
Deshpande, Nandan (orcid: 0000-0002-0324-8728)
Chew, Tracy (orcid: 0000-0001-9529-7705)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
Morgan, Steven (orcid: 0000-0001-6038-6126)
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://intersect.org.au/training/course/spss102
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://zenodo.org/record/7425920
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)
Baker, Naomi
Vissers, Joep (orcid: 0000-0003-0435-6824)
Nisselle, Amy (orcid: 0000-0002-8908-5906)
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://zenodo.org/record/7251310
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)
Price, Gareth (orcid: 0000-0003-2439-8650)
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
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://www.melbournebioinformatics.org.au/tutorials/tutorials/unix/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).
Morgan, Steven (orcid: 0000-0001-6038-6126)
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://zenodo.org/record/7281360
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)
Williams, Jason (orcid: 0000-0003-3049-2010)
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://doi.org/10.5281/zenodo.7259746
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
Sara King
Brian Ballsun-Stanton
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://www.ecocommons.org.au/learn-support/
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
Emilia Decker
Abhimanyu Singh
Robert Clemens
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://github.com/Adrian-W-Chew/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)
Dr Adrian W. Chew
Dr Adele Haythornthwaite
Brock Askey
Dr Jacky Cho
Dr Anesh Nair
Dr Kyle Hemming
Iftikhar Hayat
Joanna Dziedzic
Janice Chan
Kaitlyn Houston
Linlin Zhao
Caitlin Savage
Jessica Suna
Dr Emilia Decker
Sharron Stapleton
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://vosonlab.github.io/
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://zenodo.org/record/7095271
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)
Deshpande, Nandan (orcid: 0000-0002-0324-8728)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
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://zenodo.org/record/7072910
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)
Williams, Sarah
Mehdi, Ahmed (orcid: 0000-0002-9300-2341)
Matigan, Nick
Barugahare, Adele (orcid: 0000-0002-8976-0094)
Harrison, Paul (orcid: 0000-0002-3980-268X)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Whitfield, Holly (orcid: 0000-0002-7282-387X)
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://zenodo.org/record/7024058
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)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Genome mapping, Variant calling, Bioinformatics, Workflows
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://zenodo.org/record/7024050
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)
Ienasescu, Hans
Kalaš, Matúš (orcid: 0000-0002-1509-4981)
Bioinformatics, Research software, EDAM, Workflows, FAIR
Programming and tidy data analysis in R
A workshop to expand the skill-set of someone who has basic familiarity with R. Covers programming constructs such as functions and for-loops, and working with data frames using the dplyr and tidyr packages. Explains the importance of a "tidy" data representation, and goes through common steps...
Keywords: R, Tidyverse, Programming
Resource type: tutorial
Programming and tidy data analysis in R
https://monashdatafluency.github.io/r-progtidy/
https://dresa.org.au/materials/programming-and-tidy-data-analysis-in-r
A workshop to expand the skill-set of someone who has basic familiarity with R. Covers programming constructs such as functions and for-loops, and working with data frames using the dplyr and tidyr packages. Explains the importance of a "tidy" data representation, and goes through common steps needed to load data and convert it into a tidy form.
To be taught as a hands on workshop, typically as two half-days.
Developed by the Monash Bioinformatics Platform and taught as part of the Data Fluency program at Monash University. License is CC-BY-4. You are free to share and adapt the material so long as attribution is given.
Paul Harrison paul.harrison@monash.edu
Paul Harrison
Richard Beare
R, Tidyverse, Programming
phd
ecr
researcher
Linear models in R
A workshop on linear models in R. Learning to use linear models provides a foundation for modelling, estimation, prediction, and statistical testing in R. Many commonly used statistical tests can be performed using linear models. Ideas introduced using linear models are applicable to many of the...
Keywords: R statistics
Resource type: tutorial
Linear models in R
https://monashdatafluency.github.io/r-linear/
https://dresa.org.au/materials/linear-models-in-r
A workshop on linear models in R. Learning to use linear models provides a foundation for modelling, estimation, prediction, and statistical testing in R. Many commonly used statistical tests can be performed using linear models. Ideas introduced using linear models are applicable to many of the more complicated statistical and machine learning models available in R.
To be taught as a hands on workshop, typically as two half-days.
Developed by the Monash Bioinformatics Platform and taught as part of the Data Fluency program at Monash University. License is CC-BY-4. You are free to share and adapt the material so long as attribution is given.
Paul Harrison paul.harrison@monash.edu
Paul Harrison
R statistics
phd
ecr
researcher
Introduction to R
An introduction to R, for people with zero coding experience.
To be taught as a hands on workshop, typically as two half-days.
Developed by the Monash Bioinformatics Platform and taught as part of the Data Fluency program at Monash University. License is CC-BY-4. You are free to share and...
Keywords: R
Resource type: tutorial
Introduction to R
https://monashdatafluency.github.io/r-intro-2/
https://dresa.org.au/materials/introduction-to-r
An introduction to R, for people with zero coding experience.
To be taught as a hands on workshop, typically as two half-days.
Developed by the Monash Bioinformatics Platform and taught as part of the Data Fluency program at Monash University. License is CC-BY-4. You are free to share and adapt the material so long as attribution is given.
Paul Harrison paul.harrison@monash.edu
Paul Harrison
R
phd
ecr
researcher
Introduction to Jupyter Notebooks
This workshop will introduce you to Jupyter Notebooks, a digital tool that has exploded in popularity in recent years for those working with data.
You will learn what they are, what they do and why you might like to use them. It is an introductory set of lessons for those who are brand new,...
Keywords: jupyter, Introductory, training material, CloudStor, markdown, Python, R
Resource type: tutorial
Introduction to Jupyter Notebooks
https://zenodo.org/record/6859121
https://dresa.org.au/materials/introduction-to-jupyter-notebooks
This workshop will introduce you to Jupyter Notebooks, a digital tool that has exploded in popularity in recent years for those working with data.
You will learn what they are, what they do and why you might like to use them. It is an introductory set of lessons for those who are brand new, have little or no knowledge of coding and computational methods in research.
This workshop is targeted at those who are absolute beginners or ‘tech-curious’. It includes a hands-on component, using basic programming commands, but requires no previous knowledge of programming.
sara.king@aarnet.edu.au
Sara King
Mason, Ingrid
jupyter, Introductory, training material, CloudStor, markdown, Python, R
WORKSHOP: R: fundamental skills for biologists
This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.
Event description
Biologists need data analysis skills to be able to...
Keywords: Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
WORKSHOP: R: fundamental skills for biologists
https://zenodo.org/record/6766951
https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists
This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.
**Event description**
Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets.
R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes.
Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R.
Topics covered in this workshop include:
- Spreadsheets, organising data and first steps with R
- Manipulating and analysing data with dplyr
- Data visualisation
- Summarized experiments and getting started with Bioconductor
This workshop is presented by the Australian BioCommons and Saskia Freytag from WEHI with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
**Files and materials included in this record:**
- Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
- Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
- Schedule (PDF): A breakdown of the topics and timings for the workshop
- Recommended resources (PDF): A list of resources recommended by trainers and participants
- Q_and_A(PDF): Archive of questions and their answers from the workshop Slack Channel.
**Materials shared elsewhere:**
This workshop follows the tutorial ‘Introduction to data analysis with R and Bioconductor’ which is publicly available.
https://saskiafreytag.github.io/biocommons-r-intro/
This is derived from material produced as part of The Carpentries Incubator project
https://carpentries-incubator.github.io/bioc-intro/
Melissa Burke (melissa@biocommons.org.au)
Freytag, Saskia (orcid: 0000-0002-2185-7068)
Barugahare, Adele (orcid: 0000-0002-8976-0094)
Doyle, Maria
Ansell, Brendan (orcid: 0000-0003-0297-897X)
Varshney, Akriti
Bourke, Caitlin (orcid: 0000-0002-4466-6563)
Conradsen, Cara (orcid: 0000-0001-9797-3412)
Jung, Chol-Hee (orcid: 0000-0002-2992-3162)
Sandoval, Claudia
Chandrananda, Dineika (orcid: 0000-0002-8834-9500)
Zhang, Eden (orcid: 0000-0003-0294-3734)
Rosello, Fernando (orcid: 0000-0003-3885-8777)
Iacono, Giulia (orcid: 0000-0002-1527-0754)
Tarasova, Ilariya (orcid: 0000-0002-0895-9385)
Chung, Jessica (orcid: 0000-0002-0627-0955)
Moffet, Joel
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Ding, Ke
Feher, Kristen
Perlaza-Jimenez, Laura (orcid: 0000-0002-8511-1134)
Crowe, Mark (orcid: 0000-0002-9514-2487)
Ma, Mengyao
Kandhari, Nitika (orcid: 0000-0002-0261-727X)
Williams, Sarah
Nelson, Tiffanie (orcid: 0000-0002-5341-312X)
Schreiber, Veronika (orcid: 0000-0001-6088-7828)
Pinzon Perez, William
Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation