ALA Labs
ALA Labs provides resources and articles from the Atlas of Living Australia's Science and Decision Support team. On the website, you can find:
- Posts: Code, articles, analyses and visualisations that will hopefully help you in your own work
- Research: Highlighted summaries of scientific...
Keywords: Ecology, R, Python, Rstats, Biodiversity data, Open science, Reproducibility, Coding, Data cleaning, Data visualisation, Species Distribution Modelling, Beginner R coding
ALA Labs
https://labs.ala.org.au/
https://dresa.org.au/materials/ala-labs
ALA Labs provides resources and articles from the Atlas of Living Australia's Science and Decision Support team. On the website, you can find:
- Posts: Code, articles, analyses and visualisations that will hopefully help you in your own work
- Research: Highlighted summaries of scientific research that has used data from the Atlas of Living Australia
- Software: R & Python packages that the Science & Decision Support team manage
- Books: Long-form resources with best-practice data wrangling and visualisation
- Gallery: Showcasing external work that uses tools from ALA Labs
Atlas of Living Australia support@ala.org.au
Ecology, R, Python, Rstats, Biodiversity data, Open science, Reproducibility, Coding, Data cleaning, Data visualisation, Species Distribution Modelling, Beginner R coding
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://zenodo.org/records/7865494
https://dresa.org.au/materials/webinar-alphafold-what-s-in-it-for-me-4d1ea222-4240-4b68-b9ae-7769ac664ee0
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)
Morton, Craig (orcid: 0000-0001-5452-5193)
Bioinformatics, Machine Learning, Structural Biology, Proteins, Drug discovery, AlphaFold, AI, Artificial Intelligence, Deep learning
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/records/6766951
https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists-81aa00db-63ad-4962-a7ac-b885bf9f676b
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
NCI training strategy and impact story to address pressing needs from user community
This presentation looks at how NCI provides training opportunities, supporting users to develop their digital skills with the aim of underpinning the integrity of research. NCI's new training strategy is outlined along with how training is evaluated and impact is measured. Through extensive...
Keywords: training impact, evaluation, skills training, training strategy, community, survey design, training material
NCI training strategy and impact story to address pressing needs from user community
https://zenodo.org/records/5739725
https://dresa.org.au/materials/nci-training-strategy-and-impact-story-to-address-pressing-needs-from-user-community-70a328d3-a1e1-45ce-bac0-d8b896db4ca0
This presentation looks at how NCI provides training opportunities, supporting users to develop their digital skills with the aim of underpinning the integrity of research. NCI's new training strategy is outlined along with how training is evaluated and impact is measured. Through extensive internal polling the training team have identified a number of gaps. Based on the gaps an end-to-end learning journey has been created. The presentation also provides an overview of immediate, middle term and community impacts of training at NCI.
You can watch the video on YouTube here:https://youtu.be/LVn5TZFufjI
contact@ardc.edu.au
Wang, Jingbo (orcid: 0000-0002-3594-1893)
training impact, evaluation, skills training, training strategy, community, survey design, training material
Evaluating training at Pawsey: Motivated, confident & "changed"
This presentation outlines the digital reserach skills training evaluation methods used at Pawsey. Using the Kirpatrick Training Evaluation model in designing their training evaluation survey, Pawsey measure learning motivation (How did the participant respond to the training?), improved...
Keywords: training impact, evaluation, behavioual change, survey design, skills training, motivation, confidence, training material
Evaluating training at Pawsey: Motivated, confident & "changed"
https://zenodo.org/records/5739608
https://dresa.org.au/materials/evaluating-training-at-pawsey-motivated-confident-changed-a2435a20-bfa5-457d-afa3-08193a199f24
This presentation outlines the digital reserach skills training evaluation methods used at Pawsey. Using the Kirpatrick Training Evaluation model in designing their training evaluation survey, Pawsey measure learning motivation (How did the participant respond to the training?), improved confidence of the learner (Did participants understand the training?) and were there any behavioual changes (How participants applied their new knowledge in practice?).
You can watch the video of the presentation on YouTube here: https://youtu.be/IOKVrBumEBQ
contact@ardc.edu.au
Backhaus, Ann (orcid: 0000-0002-9023-055X)
training impact, evaluation, behavioual change, survey design, skills training, motivation, confidence, training material
Accelerating skills development in Data science and AI at scale
At the Monash Data Science and AI platform, we believe that upskilling our research community and building a workforce with data science skills are key to accelerating the application of data science in research. To achieve this, we create and leverage new and existing training capabilities...
Keywords: AI, machine learning, eresearch skills, training, train the trainer, volunteer instructors, training partnerships, training material
Accelerating skills development in Data science and AI at scale
https://zenodo.org/records/4287746
https://dresa.org.au/materials/accelerating-skills-development-in-data-science-and-ai-at-scale-2d8a65fa-f96e-44ad-a026-cfae3f38d128
At the Monash Data Science and AI platform, we believe that upskilling our research community and building a workforce with data science skills are key to accelerating the application of data science in research. To achieve this, we create and leverage new and existing training capabilities within and outside Monash University. In this talk, we will discuss the principles and purpose of establishing collaborative models to accelerate skills development at scale. We will talk about our approach to identifying gaps in the existing skills and training available in data science, key areas of interest as identified by the research community and various sources of training available in the marketplace. We will provide insights into the collaborations we currently have and intend to develop in the future within the university and also nationally.
The talk will also cover our approach as outlined below
• Combined survey of gaps in skills and trainings for Data science and AI
• Provide seats to partners
• Share associate instructors/helpers/volunteers
• Develop combined training materials
• Publish a repository of open source trainings
• Train the trainer activities
• Establish a network of volunteers to deliver trainings at their local regions
Industry plays a significant role in making some invaluable training available to the research community either through self learning platforms like AWS Machine Learning University or Instructor led courses like NVIDIA Deep Learning Institute. We will discuss how we leverage our partnerships with Industry to bring these trainings to our research community.
Finally, we will discuss how we map our training to the ARDC skills roadmap and how the ARDC platforms project “Environments to accelerate Machine Learning based Discovery” has enabled collaboration between Monash University and University of Queensland to develop and deliver training together.
contact@ardc.edu.au
Tang, Titus
AI, machine learning, eresearch skills, training, train the trainer, volunteer instructors, training partnerships, training material
Intersect: Training portfolio
This presentation explores Intersect's training evaluation model. Short term evaluation for immediate satisfaction and value of the training. Long term evaluation methods with a specific survey design to determine behavioural change and impact over time of the training on researchers' workflows,...
Keywords: training impact, evaluation, short-term evaluation, long-term evaluation, behavioural change, survey design, skills training, training material
Intersect: Training portfolio
https://zenodo.org/records/5739603
https://dresa.org.au/materials/intersect-training-portfolio-8c82060d-5eea-4091-af7b-396c9c073dab
This presentation explores Intersect's training evaluation model. Short term evaluation for immediate satisfaction and value of the training. Long term evaluation methods with a specific survey design to determine behavioural change and impact over time of the training on researchers' workflows, use of support services post training and looking for links between digital tools/technologies training and research outputs and grants.
You can watch the full video on YouTube here: https://youtu.be/J3tCC-t_eO4
contact@ardc.edu.au
Papaioannou, Anastasios (orcid: 0000-0002-8959-4559)
training impact, evaluation, short-term evaluation, long-term evaluation, behavioural change, survey design, skills training, training material
MetaSat. An open, collaboratively-developed metadata toolkit to support the future of space exploration.
MetaSat is an open metadata toolkit for describing small satellite (and even large satellite) missions in a uniform and shareable way. Optimised for small satellite missions, MetaSat fills an informatics gap. Although there have been a number of relevant metadata sets, there has been a...
Keywords: Small satellites, metadata, vocabularies, training material
MetaSat. An open, collaboratively-developed metadata toolkit to support the future of space exploration.
https://zenodo.org/records/5832057
https://dresa.org.au/materials/metasat-an-open-collaboratively-developed-metadata-toolkit-to-support-the-future-of-space-exploration-49af7d4d-f0d1-4f95-9fbe-afbd45170a6a
MetaSat is an open metadata toolkit for describing small satellite (and even large satellite) missions in a uniform and shareable way. Optimised for small satellite missions, MetaSat fills an informatics gap. Although there have been a number of relevant metadata sets, there has been a longstanding need for a vocabulary to span these community standards. A vocabulary to annotate the data and information outputs of these satellite missions, to enable search across disparate data repositories, and provide support for application of analytical services to retrieved datasets.
A common problem among small satellite teams is finding information about how other small satellites were put together, what parts worked well, what weren't compatible, what were the mission goals and outcomes. A lot of this information can be found, but it's not usually described in a consistent and searchable way across projects. MetaSat helps by building a uniform language of description which can be embedded into small satellite databases and tools to connect information across projects.
Although a relatively new vocabulary initiative, MetaSat has secured early adoption by SatNOGS, a global network of ground stations that collects, manages & enables access to satellite observations. Also partnering with NASA's Small Satellite Reliability Initiative, and in discussion with NASA concerning implementation of the vocabulary in other areas of its information infrastructure.
You can watch the full presentation on YouTube here: https://www.youtube.com/watch?v=uaCOzNL1eh4
contact@ardc.edu.au
Bouquin, Daina (orcid: 0000-0003-2626-3688)
Chivvis, Daniel (orcid: 0000-0001-6656-160X)
Small satellites, metadata, vocabularies, training material
ARDC Training Materials Metadata Checklist v1.1
The ARDC Training Materials Metadata Checklist aims to support learning designers, training materials creators, trainers and national training infrastructure providers to capture key information and apply appropriate mechanisms to enable sharing and reuse of their training materials
Keywords: checklist, Training material, FAIR, standard, requirements, metadata
ARDC Training Materials Metadata Checklist v1.1
https://zenodo.org/records/5276003
https://dresa.org.au/materials/ardc-training-materials-metadata-checklist-v1-1
The ARDC Training Materials Metadata Checklist aims to support learning designers, training materials creators, trainers and national training infrastructure providers to capture key information and apply appropriate mechanisms to enable sharing and reuse of their training materials
contact@ardc.edu.au
Martinez, Paula Andrea (orcid: 0000-0002-8990-1985)
Unsworth, Kathryn (orcid: 0000-0002-5407-9987)
checklist, Training material, FAIR, standard, requirements, metadata
Show & Tell - Tackling 'no shows'
In this session, questions were asked on how to tackle 'no shows' for training events:
What are the motivations behind ‘no shows’?
What % of ‘no shows’ is acceptable? Any data on that?
Do we need to lay some gentle guilt trips?
Community Slides
Tackling ‘no shows’. What is your...
Keywords: training attendance, no shows, skills training, training material
Show & Tell - Tackling 'no shows'
https://zenodo.org/records/4289344
https://dresa.org.au/materials/show-tell-tackling-no-shows-9f0d32c0-b2af-4624-9df1-d4e087da81b6
In this session, questions were asked on how to tackle 'no shows' for training events:
- What are the motivations behind ‘no shows’?
- What % of ‘no shows’ is acceptable? Any data on that?
- Do we need to lay some gentle guilt trips?
- Community Slides
- Tackling ‘no shows’. What is your approach? What would you be willing to try?
contact@ardc.edu.au
Unsworth, Kathryn (orcid: 0000-0002-5407-9987)
training attendance, no shows, skills training, training material
Monash University - University of Queensland training partnership in Data science and AI
We describe the peer network exchange for training that has been recently created via an ARDC funded partnership between Monash University and Universities of Queensland under the umbrella of the Queensland Cyber Infrastructure Foundation (QCIF). As part of a training program in machine learning,...
Keywords: data skills, training partnerships, data science, AI, training material
Monash University - University of Queensland training partnership in Data science and AI
https://zenodo.org/records/4287864
https://dresa.org.au/materials/monash-university-university-of-queensland-training-partnership-in-data-science-and-ai-8082bf73-d20f-4214-ad8c-95123e25a36c
We describe the peer network exchange for training that has been recently created via an ARDC funded partnership between Monash University and Universities of Queensland under the umbrella of the Queensland Cyber Infrastructure Foundation (QCIF). As part of a training program in machine learning, visualisation, and computing tools, we have established a series of over 20 workshops over the year where either Monash or QCIF hosts the event for some 20-40 of their researchers and students, while some 5 places are offered to participants from the other institution. In the longer term we aim to share material developed at one institution and have trainers present it at the other. In this talk we will describe the many benefits we have found to this approach including access to a wider range of expertise in several rapidly developing fields, upskilling of trainers, faster identification of emerging training needs, and peer learning for trainers.
contact@ardc.edu.au
Tang, Titus
data skills, training partnerships, data science, AI, training material
ARDC Skills Impact and Strategy Community Discussion
The focus of this community event arose from the ARDC SKills Summit 2021, hosted in collaboration with eResearch Australasia Conference. Two key themes identified at the Summit formed the focus of this event: 1) How to convince senior management the value of digital skills training so that they...
Keywords: training impact, evaluation, skills training, resourcing, value proposition, training material
ARDC Skills Impact and Strategy Community Discussion
https://zenodo.org/records/5739422
https://dresa.org.au/materials/ardc-skills-impact-and-strategy-community-discussion-e9d63cee-0d9c-4f8d-9c0f-58afe99b649b
The focus of this community event arose from the ARDC SKills Summit 2021, hosted in collaboration with eResearch Australasia Conference. Two key themes identified at the Summit formed the focus of this event: 1) How to convince senior management the value of digital skills training so that they don't question resourcing 2) Evaluating the long-term impact of digital skills training on researchers’ workflows and outputs.
You can watch the full video presentation on YouTube here: https://youtu.be/iSnE7OBILqs
contact@ardc.edu.au
Unsworth, Kathryn (orcid: 0000-0002-5407-9987)
training impact, evaluation, skills training, resourcing, value proposition, training material
Coding and Software Club at the Burnet Institute: a Sisyphean story of normalising peer-to-peer learning
This presentation outlines the Burnet Institute and its Coding and Software Club. What motivated the establishment of the Club and what keeps it going, the tools used to engage, teach and learn and finally, how the Club has impacted people at various levels of the organisation. Also explored are...
Keywords: coding, software, training impact, culture change, community, skills training, training material
Coding and Software Club at the Burnet Institute: a Sisyphean story of normalising peer-to-peer learning
https://zenodo.org/records/5739771
https://dresa.org.au/materials/coding-and-software-club-at-the-burnet-institute-a-sisyphean-story-of-normalising-peer-to-peer-learning-665e90f8-6fd5-49e7-9476-e16b6ffe17c6
This presentation outlines the Burnet Institute and its Coding and Software Club. What motivated the establishment of the Club and what keeps it going, the tools used to engage, teach and learn and finally, how the Club has impacted people at various levels of the organisation. Also explored are the challenges, opportunities and lessons learnt - valuable insights into what it tkaes to keep a community focused and enduring.
You can watch the video on YouTube here: https://youtu.be/c2syM1Dfqbo
contact@ardc.edu.au
Wilkinson, Anna (orcid: 0000-0002-4475-5224)
coding, software, training impact, culture change, community, skills training, training material
Why am I being asked for metadata about my research data?
Find out why metadata are important for your research data collection. This brochure shares the reasons why researchers should use metadata for their data collections.
This brochure was prepared for the ARDC Data Retention Project...
Keywords: metadata, research data, data collections, data citation, data retention project, training material
Why am I being asked for metadata about my research data?
https://zenodo.org/records/5778322
https://dresa.org.au/materials/why-am-i-being-asked-for-metadata-about-my-research-data-03b1895a-44bf-4961-a0a3-bd4770297236
Find out why metadata are important for your research data collection. This brochure shares the reasons why researchers should use metadata for their data collections.
This brochure was prepared for the ARDC Data Retention Project https://ardc.edu.au/collaborations/strategic-activities/data-retention-project/.
It is for researchers at any institution in Australia.
contact@ardc.edu.au
Australian Research Data Commons
metadata, research data, data collections, data citation, data retention project, training material
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://zenodo.org/record/7865494
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)
Morton, Craig (orcid: 0000-0001-5452-5193)
Bioinformatics, Machine Learning, Structural Biology, Proteins, Drug discovery, AlphaFold, AI, Artificial Intelligence, Deep learning
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
Heurist Tutorials
A set of video tutorials with accompanying walkthroughs for building your first Heurist database and website. The first three tutorials show you how to get started in Heurist. The five subsequent tutorials introduce you to the five main menus in the Heurist interface.
Keywords: Heurist, Data management, Data visualisation, Digital Humanities, Databasing, website
Resource type: tutorial
Heurist Tutorials
https://heuristnetwork.org/tutorials
https://dresa.org.au/materials/heurist-tutorials
A set of video tutorials with accompanying walkthroughs for building your first Heurist database and website. The first three tutorials show you how to get started in Heurist. The five subsequent tutorials introduce you to the five main menus in the Heurist interface.
michael.falk@sydney.edu.au
Falk, Michael
Johnson, Ian
Osmakov, Artem
Heurist, Data management, Data visualisation, Digital Humanities, Databasing, website
mbr
phd
ecr
researcher
support
NCI training strategy and impact story to address pressing needs from user community
This presentation looks at how NCI provides training opportunities, supporting users to develop their digital skills with the aim of underpinning the integrity of research. NCI's new training strategy is outlined along with how training is evaluated and impact is measured. Through extensive...
Keywords: training impact, evaluation, skills training, training strategy, community, survey design, training material
NCI training strategy and impact story to address pressing needs from user community
https://zenodo.org/record/5739725
https://dresa.org.au/materials/nci-training-strategy-and-impact-story-to-address-pressing-needs-from-user-community
This presentation looks at how NCI provides training opportunities, supporting users to develop their digital skills with the aim of underpinning the integrity of research. NCI's new training strategy is outlined along with how training is evaluated and impact is measured. Through extensive internal polling the training team have identified a number of gaps. Based on the gaps an end-to-end learning journey has been created. The presentation also provides an overview of immediate, middle term and community impacts of training at NCI.
You can watch the video on YouTube here:https://youtu.be/LVn5TZFufjI
contact@ardc.edu.au
Wang, Jingbo (orcid: 0000-0002-3594-1893)
training impact, evaluation, skills training, training strategy, community, survey design, training material
Evaluating training at Pawsey: Motivated, confident & "changed"
This presentation outlines the digital reserach skills training evaluation methods used at Pawsey. Using the Kirpatrick Training Evaluation model in designing their training evaluation survey, Pawsey measure learning motivation (How did the participant respond to the training?), improved...
Keywords: training impact, evaluation, behavioual change, survey design, skills training, motivation, confidence, training material
Evaluating training at Pawsey: Motivated, confident & "changed"
https://zenodo.org/record/5739608
https://dresa.org.au/materials/evaluating-training-at-pawsey-motivated-confident-changed
This presentation outlines the digital reserach skills training evaluation methods used at Pawsey. Using the Kirpatrick Training Evaluation model in designing their training evaluation survey, Pawsey measure learning motivation (How did the participant respond to the training?), improved confidence of the learner (Did participants understand the training?) and were there any behavioual changes (How participants applied their new knowledge in practice?).
You can watch the video of the presentation on YouTube here: https://youtu.be/IOKVrBumEBQ
contact@ardc.edu.au
Backhaus, Ann (orcid: 0000-0002-9023-055X)
training impact, evaluation, behavioual change, survey design, skills training, motivation, confidence, training material
Intersect: Training portfolio
This presentation explores Intersect's training evaluation model. Short term evaluation for immediate satisfaction and value of the training. Long term evaluation methods with a specific survey design to determine behavioural change and impact over time of the training on researchers' workflows,...
Keywords: training impact, evaluation, short-term evaluation, long-term evaluation, behavioural change, survey design, skills training, training material
Intersect: Training portfolio
https://zenodo.org/record/5739603
https://dresa.org.au/materials/intersect-training-portfolio
This presentation explores Intersect's training evaluation model. Short term evaluation for immediate satisfaction and value of the training. Long term evaluation methods with a specific survey design to determine behavioural change and impact over time of the training on researchers' workflows, use of support services post training and looking for links between digital tools/technologies training and research outputs and grants.
You can watch the full video on YouTube here: https://youtu.be/J3tCC-t_eO4
contact@ardc.edu.au
Papaioannou, Anastasios (orcid: 0000-0002-8959-4559)
training impact, evaluation, short-term evaluation, long-term evaluation, behavioural change, survey design, skills training, training material
Coding and Software Club at the Burnet Institute: a Sisyphean story of normalising peer-to-peer learning
This presentation outlines the Burnet Institute and its Coding and Software Club. What motivated the establishment of the Club and what keeps it going, the tools used to engage, teach and learn and finally, how the Club has impacted people at various levels of the organisation. Also explored are...
Keywords: coding, software, training impact, culture change, community, skills training, training material
Coding and Software Club at the Burnet Institute: a Sisyphean story of normalising peer-to-peer learning
https://zenodo.org/record/5739771
https://dresa.org.au/materials/coding-and-software-club-at-the-burnet-institute-a-sisyphean-story-of-normalising-peer-to-peer-learning
This presentation outlines the Burnet Institute and its Coding and Software Club. What motivated the establishment of the Club and what keeps it going, the tools used to engage, teach and learn and finally, how the Club has impacted people at various levels of the organisation. Also explored are the challenges, opportunities and lessons learnt - valuable insights into what it tkaes to keep a community focused and enduring.
You can watch the video on YouTube here: https://youtu.be/c2syM1Dfqbo
contact@ardc.edu.au
Wilkinson, Anna (orcid: 0000-0002-4475-5224)
coding, software, training impact, culture change, community, skills training, training material
ARDC Skills Impact and Strategy Community Discussion
The focus of this community event arose from the ARDC SKills Summit 2021, hosted in collaboration with eResearch Australasia Conference. Two key themes identified at the Summit formed the focus of this event: 1) How to convince senior management the value of digital skills training so that they...
Keywords: training impact, evaluation, skills training, resourcing, value proposition, training material
ARDC Skills Impact and Strategy Community Discussion
https://zenodo.org/record/5739422
https://dresa.org.au/materials/ardc-skills-impact-and-strategy-community-discussion
The focus of this community event arose from the ARDC SKills Summit 2021, hosted in collaboration with eResearch Australasia Conference. Two key themes identified at the Summit formed the focus of this event: 1) How to convince senior management the value of digital skills training so that they don't question resourcing 2) Evaluating the long-term impact of digital skills training on researchers’ workflows and outputs.
You can watch the full video presentation on YouTube here: https://youtu.be/iSnE7OBILqs
contact@ardc.edu.au
Unsworth, Kathryn (orcid: 0000-0002-5407-9987)
training impact, evaluation, skills training, resourcing, value proposition, training material
MetaSat. An open, collaboratively-developed metadata toolkit to support the future of space exploration.
MetaSat is an open metadata toolkit for describing small satellite (and even large satellite) missions in a uniform and shareable way. Optimised for small satellite missions, MetaSat fills an informatics gap. Although there have been a number of relevant metadata sets, there has been a...
Keywords: Small satellites, metadata, vocabularies, training material
MetaSat. An open, collaboratively-developed metadata toolkit to support the future of space exploration.
https://zenodo.org/record/5832057
https://dresa.org.au/materials/metasat-an-open-collaboratively-developed-metadata-toolkit-to-support-the-future-of-space-exploration
MetaSat is an open metadata toolkit for describing small satellite (and even large satellite) missions in a uniform and shareable way. Optimised for small satellite missions, MetaSat fills an informatics gap. Although there have been a number of relevant metadata sets, there has been a longstanding need for a vocabulary to span these community standards. A vocabulary to annotate the data and information outputs of these satellite missions, to enable search across disparate data repositories, and provide support for application of analytical services to retrieved datasets.
A common problem among small satellite teams is finding information about how other small satellites were put together, what parts worked well, what weren't compatible, what were the mission goals and outcomes. A lot of this information can be found, but it's not usually described in a consistent and searchable way across projects. MetaSat helps by building a uniform language of description which can be embedded into small satellite databases and tools to connect information across projects.
Although a relatively new vocabulary initiative, MetaSat has secured early adoption by SatNOGS, a global network of ground stations that collects, manages & enables access to satellite observations. Also partnering with NASA's Small Satellite Reliability Initiative, and in discussion with NASA concerning implementation of the vocabulary in other areas of its information infrastructure.
You can watch the full presentation on YouTube here: https://www.youtube.com/watch?v=uaCOzNL1eh4
contact@ardc.edu.au
Bouquin, Daina (orcid: 0000-0003-2626-3688)
Chivvis, Daniel (orcid: 0000-0001-6656-160X)
Small satellites, metadata, vocabularies, training material
Why am I being asked for metadata about my research data?
Find out why metadata are important for your research data collection. This brochure shares the reasons why researchers should use metadata for their data collections.
This brochure was prepared for the ARDC Data Retention Project...
Keywords: metadata, research data, data collections, data citation, data retention project, training material
Why am I being asked for metadata about my research data?
https://zenodo.org/record/5778322
https://dresa.org.au/materials/why-am-i-being-asked-for-metadata-about-my-research-data
Find out why metadata are important for your research data collection. This brochure shares the reasons why researchers should use metadata for their data collections.
This brochure was prepared for the ARDC Data Retention Project https://ardc.edu.au/collaborations/strategic-activities/data-retention-project/.
It is for researchers at any institution in Australia.
contact@ardc.edu.au
Australian Research Data Commons
metadata, research data, data collections, data citation, data retention project, training material
Show & Tell - Tackling 'no shows'
In this session, questions were asked on how to tackle 'no shows' for training events:
What are the motivations behind ‘no shows’?
What % of ‘no shows’ is acceptable? Any data on that?
Do we need to lay some gentle guilt trips?
Community Slides
Tackling ‘no shows’. What is your...
Keywords: training attendance, no shows, skills training, training material
Show & Tell - Tackling 'no shows'
https://zenodo.org/record/4289344
https://dresa.org.au/materials/show-tell-tackling-no-shows
In this session, questions were asked on how to tackle 'no shows' for training events:
- What are the motivations behind ‘no shows’?
- What % of ‘no shows’ is acceptable? Any data on that?
- Do we need to lay some gentle guilt trips?
- Community Slides
- Tackling ‘no shows’. What is your approach? What would you be willing to try?
contact@ardc.edu.au
Unsworth, Kathryn (orcid: 0000-0002-5407-9987)
training attendance, no shows, skills training, training material
ARDC Datacite API Jupyter notebook
This Jupyter notebook presents a low-barrier entry to using the DataCite REST API to mint, update, publish, and deleted DOIs and their associated metadata.
It was designed specifically to not use any third-party libraries so that it can be reused in almost any Jupyter notebook environment
Code...
Keywords: jupyter, notebook, DataCite, api, python, metadata, DOI, training material
ARDC Datacite API Jupyter notebook
https://zenodo.org/record/5574653
https://dresa.org.au/materials/ardc-datacite-api-jupyter-notebook
This Jupyter notebook presents a low-barrier entry to using the DataCite REST API to mint, update, publish, and deleted DOIs and their associated metadata.
It was designed specifically to not use any third-party libraries so that it can be reused in almost any Jupyter notebook environment
Code is presented alongside human readable comments that explain the use of each component of the notebook.
contact@ardc.edu.au
Liffers, Matthias (orcid: 0000-0002-3639-2080)
jupyter, notebook, DataCite, api, python, metadata, DOI, training material
Accelerating skills development in Data science and AI at scale
At the Monash Data Science and AI platform, we believe that upskilling our research community and building a workforce with data science skills are key to accelerating the application of data science in research. To achieve this, we create and leverage new and existing training capabilities...
Keywords: AI, machine learning, eresearch skills, training, train the trainer, volunteer instructors, training partnerships, training material
Accelerating skills development in Data science and AI at scale
https://zenodo.org/record/4287746
https://dresa.org.au/materials/accelerating-skills-development-in-data-science-and-ai-at-scale
At the Monash Data Science and AI platform, we believe that upskilling our research community and building a workforce with data science skills are key to accelerating the application of data science in research. To achieve this, we create and leverage new and existing training capabilities within and outside Monash University. In this talk, we will discuss the principles and purpose of establishing collaborative models to accelerate skills development at scale. We will talk about our approach to identifying gaps in the existing skills and training available in data science, key areas of interest as identified by the research community and various sources of training available in the marketplace. We will provide insights into the collaborations we currently have and intend to develop in the future within the university and also nationally.
The talk will also cover our approach as outlined below
• Combined survey of gaps in skills and trainings for Data science and AI
• Provide seats to partners
• Share associate instructors/helpers/volunteers
• Develop combined training materials
• Publish a repository of open source trainings
• Train the trainer activities
• Establish a network of volunteers to deliver trainings at their local regions
Industry plays a significant role in making some invaluable training available to the research community either through self learning platforms like AWS Machine Learning University or Instructor led courses like NVIDIA Deep Learning Institute. We will discuss how we leverage our partnerships with Industry to bring these trainings to our research community.
Finally, we will discuss how we map our training to the ARDC skills roadmap and how the ARDC platforms project “Environments to accelerate Machine Learning based Discovery” has enabled collaboration between Monash University and University of Queensland to develop and deliver training together.
contact@ardc.edu.au
Tang, Titus
AI, machine learning, eresearch skills, training, train the trainer, volunteer instructors, training partnerships, training material
Monash University - University of Queensland training partnership in Data science and AI
We describe the peer network exchange for training that has been recently created via an ARDC funded partnership between Monash University and Universities of Queensland under the umbrella of the Queensland Cyber Infrastructure Foundation (QCIF). As part of a training program in machine learning,...
Keywords: data skills, training partnerships, data science, AI, training material
Monash University - University of Queensland training partnership in Data science and AI
https://zenodo.org/record/4287864
https://dresa.org.au/materials/monash-university-university-of-queensland-training-partnership-in-data-science-and-ai
We describe the peer network exchange for training that has been recently created via an ARDC funded partnership between Monash University and Universities of Queensland under the umbrella of the Queensland Cyber Infrastructure Foundation (QCIF). As part of a training program in machine learning, visualisation, and computing tools, we have established a series of over 20 workshops over the year where either Monash or QCIF hosts the event for some 20-40 of their researchers and students, while some 5 places are offered to participants from the other institution. In the longer term we aim to share material developed at one institution and have trainers present it at the other. In this talk we will describe the many benefits we have found to this approach including access to a wider range of expertise in several rapidly developing fields, upskilling of trainers, faster identification of emerging training needs, and peer learning for trainers.
contact@ardc.edu.au
Tang, Titus
data skills, training partnerships, data science, AI, training material