30 materials found
Difficulty level:
Beginner
EcoCommons written support material, species distribution models explained and platform guides
These written descriptions on how to use the EcoCommons platform, the descriptions of the variety of species distribution models (SDM) available and the how to design and run and SDM have proven very popular with students whose instructors are using EcoCommons to teach basic SDM. They also...
Keywords: Species Distribution Modelling, Ecology, EcoCommons
EcoCommons written support material, species distribution models explained and platform guides
https://support.ecocommons.org.au/support/home
https://dresa.org.au/materials/ecocommons-written-support-material-species-distribution-models-explained-and-platform-guides
These written descriptions on how to use the EcoCommons platform, the descriptions of the variety of species distribution models (SDM) available and the how to design and run and SDM have proven very popular with students whose instructors are using EcoCommons to teach basic SDM. They also provide useful references for anyone using the platform.
https://www.ecocommons.org.au/contact/
Species Distribution Modelling, Ecology, EcoCommons
ugrad
masters
mbr
phd
Get started with R: an introduction for beginners
These two videos walk through the "R for Ecologists" module offered by the Data Carpentries https://datacarpentry.org/R-ecology-lesson/
The first video: Manipulating Data covers:
Opening R, setting your working directory, reading and downloading csv files, selecting and filtering data, using...
Keywords: Beginner R coding, The Carpentries, R studio, Beginer ecological modelling
Resource type: video, lesson
Get started with R: an introduction for beginners
https://www.ecocommons.org.au/educational-material3-get-started-with-r/
https://dresa.org.au/materials/get-started-with-r-an-introduction-for-beginners
These two videos walk through the "R for Ecologists" module offered by the Data Carpentries https://datacarpentry.org/R-ecology-lesson/
The first video: Manipulating Data covers:
Opening R, setting your working directory, reading and downloading csv files, selecting and filtering data, using pipeline operators, creating new columns based on existing ones, and summarising data
The second video: Visualising data with ggplot2 covers:
A recap of module 1 and getting started with ggplot2 to create plots and a variety of data visualisations
Links to the R scripts are provided
https://www.ecocommons.org.au/contact/
Beginner R coding, The Carpentries, R studio, Beginer ecological modelling
ugrad
mbr
phd
Discovering Species Distribution Modelling with BCCVL
A set of 10 videos that provide an excellent introduction to species distribution modelling. These modules include: 1. Introduction to SDM, 2. Ecological theory of SDM, 3. Data for SDMs, 4. Design an SDM, 5. Presence only models, 6. Statistical models, 7. Machine learning models, 8. Model...
Keywords: Species Distribution Modelling, Ecology, EcoCommons, Beginer ecological modelling, Climate projections
Discovering Species Distribution Modelling with BCCVL
https://www.ecocommons.org.au/educational-material2-discovering-species-distribution-with-bccvl/
https://dresa.org.au/materials/discovering-species-distribution-modelling-with-bccvl
A set of 10 videos that provide an excellent introduction to species distribution modelling. These modules include: 1. Introduction to SDM, 2. Ecological theory of SDM, 3. Data for SDMs, 4. Design an SDM, 5. Presence only models, 6. Statistical models, 7. Machine learning models, 8. Model evaluation, 9. SDMs and climate change projections, 10. Case studies in BCCVL
https://www.ecocommons.org.au/contact/
BCCVL
Species Distribution Modelling, Ecology, EcoCommons, Beginer ecological modelling, Climate projections
ugrad
mbr
EcoCommons Modelling Made Easy
These ten videos walk users through some of the point-and-click functionality available on the EcoCommons platform including: 1. Navigating the EcoCommons platform, 2. Exploring environmental and climate grids available on the platform, 3. Importing your own data, 4. How to run a Species...
Keywords: Species Distribution Modelling, Climate projections , EcoCommons, Ecology
Resource type: video
EcoCommons Modelling Made Easy
https://www.ecocommons.org.au/educational-material-1-ecocommons-modelling-made-easy/
https://dresa.org.au/materials/ecocommons-modelling-made-easy
These ten videos walk users through some of the point-and-click functionality available on the EcoCommons platform including: 1. Navigating the EcoCommons platform, 2. Exploring environmental and climate grids available on the platform, 3. Importing your own data, 4. How to run a Species Distribution Model (SDM), 5. Predicting how distributions will change under climate change, 6. Running simple (averaged) ensemble models of SDMs, 7. An introduction to toy species trait problems that highlight how variation in species traits can be predicted spatially, 8. An introduction to Biosecurity Risk Mapping, 9. How to run SDMs for multiple species, 10. A multiple species SDM use case
support@ecocommons.org.au
Species Distribution Modelling, Climate projections , EcoCommons, Ecology
ugrad
mbr
phd
Introduction to the Five Safes Framework
Resources include:
* Facilitator notes
*PowerPoint presentation
This is an introduction to the Five Safes framework and has been developed for anyone with no or little knowledge of the framework can develop their own workshop.
Keywords: research data management, sensitive data, Five Safes, training material, workshop materials
Introduction to the Five Safes Framework
https://zenodo.org/records/10414022?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6IjkzN2FjYjAwLTU2MzYtNDZhYy1hOWQxLTk0MjQyZGJiMzdjZiIsImRhdGEiOnt9LCJyYW5kb20iOiIzMjZhOWZmZDQ2MDliOGRjNTI1MjFmYWZkODQ4ODA1ZSJ9.kJshHeKFIa6LE1Pd5Fk8UBpDIJtUBZK3Z-U8FIo9LdFD0E242FoBN7j9_e7p6ZIIN8AbfTLf5WzR08XZTpKYMg
https://dresa.org.au/materials/introduction-to-the-five-safes-framework
Resources include:
* Facilitator notes
*PowerPoint presentation
This is an introduction to the Five Safes framework and has been developed for anyone with no or little knowledge of the framework can develop their own workshop.
Yolante Jones
yolante.jones@anu.edu.au
Yolante Jones
research data management, sensitive data, Five Safes, training material, workshop materials
masters
ecr
phd
support
professional
Fluoroquinolone antibiotics and Aortic Aneurysm or Dissection
The main objective of this project was to provide education on the use of data translated to the OMOP common data model. We aimed to showcase how the Atlas interface tool could be used to generate evidence for a highly relevant and significant research question. The clinical question that was...
Keywords: OMOP, Aortic Aneurysm, Fluoroquinolone antibiotics
Fluoroquinolone antibiotics and Aortic Aneurysm or Dissection
https://ohdsi-australia.org/full_tutorial.pdf
https://dresa.org.au/materials/fluoroquinolone-antibiotics-and-aortic-aneurysm-or-dissection
The main objective of this project was to provide education on the use of data translated to the OMOP common data model. We aimed to showcase how the Atlas interface tool could be used to generate evidence for a highly relevant and significant research question. The clinical question that was used to demonstrate the process revolved around investigating the potential association between the use of fluoroquinolones to treat urinary tract infection and the risk of experiencing aortic aneurysm and dissection within 30 days, 3 months, or 12 months of treatment initiation compared to other commonly used antibiotics. The workshop aimed to describe how data are translated to the OMOP CDM, how cohorts can be derived in these data, how to execute a robust analysis, and lastly, how to interpret the results of the study. Specifically, we described the process of translating Australian medicines dispensing data to the OMOP CDM, including the translation of the Australia Pharmaceutical Benefits Schedule data to the international RxNorm standard vocabulary.
The outcome of the project is an on-line training resource that highlights the process of study execution from start to finish. This training package will serve as an exemplar for researchers in Australia to unlock the value of their data that has been translated into the OMOP CDM. The audience for this project was database programmers, researchers, and decision-makers, and all those interested in using data to inform healthcare.
Roger Ward, Nicole Pratt
Roger Ward
Nicole Pratt
Christine Hallinan
OMOP, Aortic Aneurysm, Fluoroquinolone antibiotics
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
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
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
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
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 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
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
Network Know-how and Data Handling Workshop
This workshop is a ‘train-the-trainer’ session that covers topics such as jargon busting, network literacy and data movement solutions. The workshop will also provide a peek at some collaborative research tools such as Jupyter Notebooks and CloudStor. You will learn about networks, integrated...
Keywords: Networks, data handling
Resource type: lesson, presentation
Network Know-how and Data Handling Workshop
https://zenodo.org/record/6403757#.Yk-Gl8gza70
https://dresa.org.au/materials/network-know-how-and-data-handling-workshop
This workshop is a ‘train-the-trainer’ session that covers topics such as jargon busting, network literacy and data movement solutions. The workshop will also provide a peek at some collaborative research tools such as Jupyter Notebooks and CloudStor. You will learn about networks, integrated tools, data and storage and where all these things fit in the researcher’s toolkit.
This workshop is targeted at staff who would like to be more confident in giving advice to researchers about the options available to them. It is especially tailored for those with little to no technical knowledge and includes a hands-on component, using basic programming commands, but requires no previous knowledge of programming.
Sara King - sara.king@aarnet.edu.au
King, Sara (orcid: 0000-0003-3199-5592)
Mason, Ingrid (orcid: 0000-0002-0658-6095)
Burke, Melissa (orcid: 0000-0002-5571-8664)
Networks, data handling
The Living Book of Digital Skills
The Living Book of Digital Skills (You never knew you needed until now) is a living, open source online guide to 'modern not-quite-technical computer skills' for researchers and the broader academic community.
A collaboration between Australia's Academic Research Network (AARNet) and the...
Keywords: digital skills, digital dexterity, community, open source
Resource type: guide
The Living Book of Digital Skills
https://aarnet.gitbook.io/digital-skills-gitbook-1/
https://dresa.org.au/materials/the-living-book-of-digital-skills
*The Living Book of Digital Skills (You never knew you needed until now)* is a living, open source online guide to 'modern not-quite-technical computer skills' for researchers and the broader academic community.
A collaboration between Australia's Academic Research Network (AARNet) and the Council of Australian Librarians (CAUL), this book is the creation of the CAUL Digital Dexterity Champions and their communities.
**Contributing to the Digital Skills GitBook**
The Digital Skills GitBook is an open source project and like many projects on GitHub we welcome your contributions.
If you have knowledge or expertise on one of our [requested topics](https://aarnet.gitbook.io/digital-skills-gitbook-1/requested-articles), we would love you to write an article for the book. Please let us know what you'd like to write about via our [contributor form](https://github.com/AARNet/Digital-Skills-GitBook/issues/new?assignees=sarasrking&labels=contributors&template=contributor-form.yml&title=Contributor+form%3A+).
There are other ways to contribute too. For example, you might:
* have a great idea for a new topic to be included in one of our chapters (make a new page)
* notice some information that’s out-of-date or that could be explained better (edit a page)
* come across something in the GitBook that’s not working as it should be (submit an issue)
Sara King - sara.king@aarnet.edu.au
Sara King
Miah de Francesch
Emma Chapman
Katie Mills
Ruth Cameron
digital skills, digital dexterity, community, open source
ugrad
masters
mbr
phd
ecr
researcher
support
Create a website resume
Written for the Qld Research Bazaar conference 2021, this self paced lesson breaks down how to use Github pages to make a resume, with a simple and basic template to start off with. It discusses how to use Markdown and minimum HTML to customize the template, and offers explanations on how the...
Keywords: personal development, website
Resource type: tutorial, guide
Create a website resume
https://amandamiotto.github.io/ResumeLesson/HowIMadeThis
https://dresa.org.au/materials/create-a-website-resume
Written for the Qld Research Bazaar conference 2021, this self paced lesson breaks down how to use Github pages to make a resume, with a simple and basic template to start off with. It discusses how to use Markdown and minimum HTML to customize the template, and offers explanations on how the components work together.
a.miotto@griffith.edu.au
Amanda Miotto
personal development, website
10 Reproducible Research things - Building Business Continuity
The idea that you can duplicate an experiment and get the same conclusion is the basis for all scientific discoveries. Reproducible research is data analysis that starts with the raw data and offers a transparent workflow to arrive at the same results and conclusions. However not all studies are...
Keywords: reproducibility, data management
Resource type: tutorial, video
10 Reproducible Research things - Building Business Continuity
https://guereslib.github.io/ten-reproducible-research-things/
https://dresa.org.au/materials/9-reproducible-research-things-building-business-continuity
The idea that you can duplicate an experiment and get the same conclusion is the basis for all scientific discoveries. Reproducible research is data analysis that starts with the raw data and offers a transparent workflow to arrive at the same results and conclusions. However not all studies are replicable due to lack of information on the process. Therefore, reproducibility in research is extremely important.
Researchers genuinely want to make their research more reproducible, but sometimes don’t know where to start and often don’t have the available time to investigate or establish methods on how reproducible research can speed up every day work. We aim for the philosophy “Be better than you were yesterday”. Reproducibility is a process, and we highlight there is no expectation to go from beginner to expert in a single workshop. Instead, we offer some steps you can take towards the reproducibility path following our Steps to Reproducible Research self paced program.
Video:
https://www.youtube.com/watch?v=bANTr9RvnGg
Tutorial:
https://guereslib.github.io/ten-reproducible-research-things/
a.miotto@griffith.edu.au; s.stapleton@griffith.edu.au; i.jennings@griffith.edu.au;
Amanda Miotto
Julie Toohey
Sharron Stapleton
Isaac Jennings
reproducibility, data management
masters
phd
ecr
researcher
support
Data Storytelling
Nowadays, more information created than our audience could possibly analyse on their own! A study by Stanford professor Chip Heath found that during the recall of speeches, 63% of people remember stories and how they made them feel, but only 5% remember a single statistic. So, you should convert...
Keywords: data storytelling, data visualisation
Data Storytelling
https://griffithunilibrary.github.io/data-storytelling/
https://dresa.org.au/materials/data-storytelling
Nowadays, more information created than our audience could possibly analyse on their own! A study by Stanford professor Chip Heath found that during the recall of speeches, 63% of people remember stories and how they made them feel, but only 5% remember a single statistic. So, you should convert your insights and discovery from data into stories to share with non-experts with a language they understand. But how?
This tutorial helps you construct stories that incite an emotional response and create meaning and understanding for the audience by applying data storytelling techniques.
m.yamaguchi@griffith.edu.au
a.miotto@griffith.edu.au
Masami Yamaguchi
Amanda Miotto
Brett Parker
data storytelling, data visualisation
support
masters
phd
researcher
Basic Linux/Unix commands
A series of eight videos (each between 5 and 10 minutes long) following the content of the Software Carpentry workshop "The Unix Shell".
Sessions 1, 2 and 3 provide instructions on the minimal level of Linux/Unix commands recommended for new...
Keywords: HPC, high performance computer, Unix, Linux, Software Carpentry
Resource type: video, guide
Basic Linux/Unix commands
https://www.youtube.com/playlist?list=PLjlLx279X4yP5GodfbqQTJuJ1S9EJU3GM
https://dresa.org.au/materials/basic-linux-unix-commands
A series of eight videos (each between 5 and 10 minutes long) following the content of the Software Carpentry workshop ["The Unix Shell"](https://swcarpentry.github.io/shell-novice/).
Sessions 1, 2 and 3 provide instructions on the minimal level of Linux/Unix commands recommended for new users of HPC.
1 – An overview of how to find out where a user is in the filesystem, list the files there, and how to get help on Unix commands
2 – How to move around the file system and change into other directories
3 – Explains the difference between an absolute and relative path
4 – Overview of how to create new directories, and to create and edit new files with nano
5 – How to use the vi editor to edit files
6 – Overview of file viewers available
7 – How to copy and move files and directories
8 – How to remove files and directories
Further details and exercises with solutions can be found on the Software Carpentry "The Unix Shell" page (https://swcarpentry.github.io/shell-novice/)
QCIF Training (training@qcif.edu.au)
Marlies Hankel
HPC, high performance computer, Unix, Linux, Software Carpentry
Transferring files and data
A short video outlining the basics on how to use FileZilla to establish a secure file transfer protocol (sftp) connection to HPC to use a drag and drop interface to transfer files between the HPC and a desktop computer.
Keywords: sftp, file transfer, HPC, high performance computer
Resource type: video, guide
Transferring files and data
https://www.youtube.com/watch?v=9ABMxcKqfkQ&list=PLjlLx279X4yP3eTLu0S6nOt0HQ7XRf6WF
https://dresa.org.au/materials/transferring-files-and-data
A short video outlining the basics on how to use FileZilla to establish a secure file transfer protocol (sftp) connection to HPC to use a drag and drop interface to transfer files between the HPC and a desktop computer.
QCIF Training (training@qcif.edu.au)
Marlies Hankel
sftp, file transfer, HPC, high performance computer
Connecting to HPC
A series of three short videos introducing how to use PuTTY to connect from a Windows PC to a secure HPC (high performance computing) cluster.
1 - The very basics on how to establish a connection to HPC.
2 - How to add more specific options for the connection to HPC.
3 - How to save the...
Keywords: HPC, high performance computer, ssh
Resource type: video, guide
Connecting to HPC
https://www.youtube.com/playlist?list=PLjlLx279X4yPJBVQuIRhz1CVMfQpTuvZW
https://dresa.org.au/materials/connecting-to-hpc
A series of three short videos introducing how to use PuTTY to connect from a Windows PC to a secure HPC (high performance computing) cluster.
1 - The very basics on how to establish a connection to HPC.
2 - How to add more specific options for the connection to HPC.
3 - How to save the details and options for a connection for future use.
QCIF Training (training@qcif.edu.au)
Marlies Hankel
HPC, high performance computer, ssh
Use the Trove Newspaper & Gazette Harvester (web app version)
This video shows how you can use the web app version of the Trove Newspaper & Gazette Harvester to download large quantities of digitised newspaper articles from Trove. Just give it a search from the Trove web interface, and the harvester will...
Keywords: Trove, newspapers, GLAM Workbench, HASS, Trove Newspaper and Gazette Harvester
Resource type: video
Use the Trove Newspaper & Gazette Harvester (web app version)
https://youtu.be/WKFuJR6lLF4
https://dresa.org.au/materials/use-the-trove-newspaper-gazette-harvester-web-app-version-to-download-large-quantities-of-digitised-articles
This video shows how you can use the web app version of the [Trove Newspaper & Gazette Harvester](https://glam-workbench.net/trove-harvester/) to download large quantities of digitised newspaper articles from Trove. Just give it a search from the Trove web interface, and the harvester will save the metadata of all the articles from the search results in a CSV (spreadsheet) file for further analysis. You can also save the full text of every article, as well as copies of the articles as JPG images, and even PDFs.
The GLAM Workbench is a collection of tools, examples, tutorials, and apps that help you make use of collection data from GLAM organisations (Galleries, Libraries, Archives, and Museums). See: [https://glam-workbench.net/](https://glam-workbench.net/)
Tim Sherratt (tim@timsherratt.org and @wragge on Twitter)
Trove, newspapers, GLAM Workbench, HASS, Trove Newspaper and Gazette Harvester
ugrad
masters
phd
ecr
researcher
support
Research Data Management (RDM) Online Orientation Module (Macquarie University)
This is a self-paced, guided orientation to the essential elements of Research Data Management. It is available for others to use and modify.
The course introduces the following topics: data policies, data sensitivity, data management planning, storage and security, organisation and metadata,...
Keywords: research data, data management, FAIR data, training
Resource type: quiz, activity, other
Research Data Management (RDM) Online Orientation Module (Macquarie University)
https://rise.articulate.com/share/-AWqSPaEI_jTbHwzQHdmQ43R50edrCl0
https://dresa.org.au/materials/macquarie-university-research-data-management-rdm-online
This is a self-paced, guided orientation to the essential elements of Research Data Management. It is available for others to use and modify.
The course introduces the following topics: data policies, data sensitivity, data management planning, storage and security, organisation and metadata, benefits of data sharing, licensing, repositories, and best practice including the FAIR principles.
Embedded activities and examples help extend learner experience and awareness.
The course was designed to assist research students and early career researchers in complying with policies and legislative requirements, understand safe data practices, raise awareness of the benefits of data curation and data sharing (efficiency and impact) and equip them with the required knowledge to plan their data management early in their projects.
This course is divided into four sections
1. Crawl - What is Research Data and why care for it? Policy and legislative requirements. The Research Data Life-cycle. Data Management Planning (~30 mins)
2. Walk - Data sensitivity, identifiability, storage, and security (~60 mins)
3. Run - Record keeping, data retention, file naming, folder structures, version control, metadata, data sharing, open data, licences, data repositories, data citation, and ethics (~75 mins)
4. Jump - Best practice FAIR data principles (~45 mins)
5. Fight - Review - a quiz designed to review and reinforce knowledge (~15 mins)
https://rise.articulate.com/share/-AWqSPaEI_jTbHwzQHdmQ43R50edrCl0 *
*Password: "FAIR"
*Password: "FAIR"
Any queries or suggestions for course improvement can be directed to the Macquarie University Research Integrity Team: Dr Paul Sou (paul.sou@mq.edu.au) or Dr Shannon Smith (shannon.smith@mq.edu.au). Scorm files can be made available upon request.
Macquarie University
Queensland University of Technology
Shannon Smith
Jennifer Rowland
Mark Hooper
Paul Sou
Vladimir Bubalo
Brian Ballsun-Stanton
research data, data management, FAIR data, training
Deep Learning for Natural Language Processing
This workshop is designed to be instructor led and consists of two parts.
Part 1 consists of a lecture-demo about text processing and a hands-on session for attendees to learn how to clean a dataset.
Part 2 consists of a lecture introducing Recurrent Neural Networks and a hands-on session for...
Keywords: Deep learning, NLP, Machine learning
Resource type: presentation, tutorial
Deep Learning for Natural Language Processing
https://doi.org/10.26180/13100513
https://dresa.org.au/materials/deep-learning-for-natural-language-processing
This workshop is designed to be instructor led and consists of two parts.
Part 1 consists of a lecture-demo about text processing and a hands-on session for attendees to learn how to clean a dataset.
Part 2 consists of a lecture introducing Recurrent Neural Networks and a hands-on session for attendees to train their own RNN.
The Powerpoints contain the lecture slides, while the Jupyter notebooks (.ipynb) contain the hands-on coding exercises.
This workshop introduces natural language as data for deep learning. We discuss various techniques and software packages (e.g. python strings, RegEx, NLTK, Word2Vec) that help us convert, clean, and formalise text data “in the wild” for use in a deep learning model. We then explore the training and testing of a Recurrent Neural Network on the data to complete a real world task. We will be using TensorFlow v2 for this purpose.
datascienceplatform@monash.edu
Titus Tang
Deep learning, NLP, Machine learning
Visualisation and Storytelling
This workshop explores how data visualisation techniques could be utilised to better understand data and to communicate research efforts and outcomes. The workshop covers a broad range of techniques from simple and static 2D graphics to advanced 3D visualisations in order to provide a broad...
Keywords: data visualisation, storytelling
Resource type: presentation, tutorial
Visualisation and Storytelling
https://doi.org/10.26180/13100510
https://dresa.org.au/materials/visualisation-and-storytelling
This workshop explores how data visualisation techniques could be utilised to better understand data and to communicate research efforts and outcomes. The workshop covers a broad range of techniques from simple and static 2D graphics to advanced 3D visualisations in order to provide a broad overview of the tools available for data analysis, presentation and storytelling. We explore, among others, animated charts and graphs, web visualisation tools such as scrollytellers, and the possibilities of 3D, interactive, and even immersive visualisations. We use real world, concrete examples along the way in order to tangibly illustrate how these visualisations can be created and how viewers perceive and interact with them. We also introduce the various tools and skill sets you would need to be proficient at presenting your data to the world.
By the conclusion of this workshop, you would gain familiarity with the various possibilities for presenting your own research data and outcomes. You would have a more intuitive understanding of the strengths and weaknesses of various modes of data visualisation and storytelling, and would have a starting point to obtain the right skill sets relevant to developing your visualisations of choice.
datascienceplatform@monash.edu
Daniel Waghorn
Nora Hamacher
Owen Kaluza
data visualisation, storytelling
Introduction to Deep Learning and TensorFlow
This workshop is intended to run as an instructor guided live event and consists of two parts. Each part consists of a lecture and a hands-on coding exercise.
Part 1 - Introduction to Deep Learning and TensorFlow
Part 2 - Introduction to Convolutional Neural Networks
The Powerpoints contain...
Keywords: Deep learning, convolutional neural network, tensorflow, Machine learning
Resource type: presentation, tutorial
Introduction to Deep Learning and TensorFlow
https://doi.org/10.26180/13100519
https://dresa.org.au/materials/introduction-to-deep-learning-and-tensorflow
This workshop is intended to run as an instructor guided live event and consists of two parts. Each part consists of a lecture and a hands-on coding exercise.
Part 1 - Introduction to Deep Learning and TensorFlow
Part 2 - Introduction to Convolutional Neural Networks
The Powerpoints contain the lecture slides, while the Jupyter notebooks (.ipynb) contain the hands-on coding exercises.
This workshop is an introduction to how deep learning works and how you could create a neural network using TensorFlow v2. We start by learning the basics of deep learning including what a neural network is, how information passes through the network, and how the network learns from data through the automated process of gradient descent. Workshop attendees would build, train and evaluate a neural network using a cloud GPU (Google Colab).
In part 2, we look at image data and how we could train a convolution neural network to classify images. Workshop attendees will extend their knowledge from the first part to design, train and evaluate this convolutional neural network.
datascienceplatform@monash.edu
Titus Tang
Deep learning, convolutional neural network, tensorflow, Machine learning
Use QueryPic to visualise searches in Trove's digitised newspapers (part 2)
This video shows how you can construct and visualise more complex searches for digitised newspaper articles in Trove using QueryPic (see part 1 for the basics). This includes limiting the date range of your query, and changing the time...
Keywords: Trove, GLAM Workbench, visualisation, newspapers, HASS
Resource type: video
Use QueryPic to visualise searches in Trove's digitised newspapers (part 2)
https://youtu.be/J_LgNL2EM4M
https://dresa.org.au/materials/use-querypic-to-visualise-searches-in-trove-s-digitised-newspapers-part-2
This video shows how you can construct and visualise more complex searches for digitised newspaper articles in Trove using [QueryPic](https://glam-workbench.net/trove-newspapers/#querypic) (see part 1 for the basics). This includes limiting the date range of your query, and changing the time scale to zoom in and out of your search results.
The GLAM Workbench is a collection of tools, examples, tutorials, and apps that help you make use of collection data from GLAM organisations (Galleries, Libraries, Archives, and Museums). See: https://glam-workbench.net/
Tim Sherratt (tim@timsherratt.org and @wragge on Twitter)
Trove, GLAM Workbench, visualisation, newspapers, HASS
ugrad
masters
phd
ecr
researcher
Use QueryPic to visualise searches in Trove's digitised newspapers (part 1)
This video demonstrates how to use the GLAM Workbench to visualise searches for digitised newspaper articles in Trove. Using the latest version of QueryPic, we can explore the complete result set, showing how the number of matching articles...
Keywords: Trove, GLAM Workbench, visualisation, newspapers, HASS
Resource type: video
Use QueryPic to visualise searches in Trove's digitised newspapers (part 1)
https://youtu.be/vdyKNowv9gw
https://dresa.org.au/materials/use-querypic-to-visualise-searches-in-trove-s-digitised-newspapers-part-1
This video demonstrates how to use the GLAM Workbench to visualise searches for digitised newspaper articles in Trove. Using the latest version of [QueryPic](https://glam-workbench.net/trove-newspapers/#querypic), we can explore the complete result set, showing how the number of matching articles changes over time. We can even compare queries to visualise changes in language or technology. It's a great way to start exploring the possibilities of GLAM data.
The GLAM Workbench is a collection of tools, examples, tutorials, and apps that help you make use of collection data from GLAM organisations (Galleries, Libraries, Archives, and Museums). See: https://glam-workbench.net/
Tim Sherratt (tim@timsherratt.org & @wragge on Twitter)
Trove, GLAM Workbench, visualisation, newspapers, HASS
ugrad
masters
ecr
researcher