Learn the Art of Visual Storytelling!
Indi is a visual storyteller who brings complex strategies and deep research to life, via delightful and impactful data-driven graphics and illustrations that are meaningful to larger audiences. In this session Indi will share how visual storytelling can be used as a research communication tool and will give all attendees her cheat sheet for transforming research into accessible and visual stories, that stick.
Fundamentals of Reproducible Research
On completion of this workshop, participants should be able to:
- identify ways to make their research better organised, more reproducible and transparent
- identify time-saving processes such as automation of common tasks
- safeguard themselves against fraud
- secure their data against loss or accidental disclosure
- identify best practices in reproducibility for current and future research projects
No prior knowledge or equipment/installs needed
Learn how to share your code and results with end users: Shiny app fundamentals in R
Ever wanted to share your R code with industry partners or end users who weren’t familiar with the language? Or wished that you could build an interactive app that only required non-technical stakeholders to click a few buttons?
Shiny is a popular R package that allows you to build highly interactive web applications—without needing any other programming languages. Using Shiny you can share your analyses as dashboards and visualisations and create interactive platforms for anybody to use the tools you create (see examples here https://shiny.rstudio.com/gallery/).
This is a workshop aimed at anyone with a working knowledge of R who is interested in better communicating their results with non-technical stakeholders. In the first part of this workshop, you will be introduced to the basic syntax and principles of R Shiny. Then we will develop an app that allows users to upload data, run analyses, and display the results in a figure and/or a map.
The Social Dilemma: Leveraging Social Media Strategically
Social media is considered essential for dissemination of research in today’s academic climate. Research has highlighted the impact of using social media to amplify work, but not without strategy.
In this workshop I will introduce the 3 domains of social media use (Consumption, Curation and Creation).
From here, we will explore approaches to achieving your goals for social media practice.
We will cover different platforms, formats, and online safety. This introductory workshop will leave you with awareness of how you can integrate social media in your academic practice.
Please bring a laptop or mobile device
How to Describe your Research Impact in one sentence
Researchers will learn how to succinctly describe their work in one sentence to the right audience. This will then be printed onto a poster that can be used will recruiters, applications and self-promotion.
No Prior knowledge needed - please bring a laptop and something to write with
Collecting Twitter Data for Comparative Text Analytics
This hands-on workshop will show you how to collect and prepare Twitter data for analysis, using the example research question of “Which monotreme is the coolest?”. Starting from scratch, we will show you how to get Twitter developer API access and then use it to collect research data using the twarc toolkit for Python.
This workshop leads into the Comparative Text Analytics with R workshop, but can be taken on its own.
Participants will need a laptop that they can install Python on, and a Twitter account.
Comparative Text Analytics with R
This workshop will introduce participants to text analytics in R. Starting with some comparative text data, participants will conduct introductory analysis of the content of the text, including breaking text down into words, handling emoji, and comparative frequency analysis.
This workshop follows on from the “Collecting Twitter Data for Comparative Text Analytics” workshop, but can be taken on its own.
Familiarity with R needed
Participants will need a laptop with an internet connection. Examples will be demonstrated in an online R notebook environment.
Network Analysis with R
This workshop will cover an introduction to network theory and the fundamental principles of using R for network analysis, including loading networks into R, quantitative properties of networks, and network visualisation.
The data used for the workshop will be an open-source dataset of Twitter data relating to the 2019 Federal Election. Attendees can choose to follow along by running the code in their own RStudio session, or choose to focus on the slides and go through the code in RStudio later.
Before the workshop, attendees who would like to follow along in their own RStudio session should visit https://bit.ly/resbaz-network-analysis and follow the instructions in the pre-workshop-instructions.pdf file.
Topic Modelling with R
Following on from the network analysis workshop, this session will show you how to conduct a topic model analysis of political tweets to understand and interpret the content of a large dataset.
This workshop will use the same dataset as “Network Analysis with R”, but can be taken independently.
Familiarity with R needed
Participants will need a laptop with an internet connection. Examples will be demonstrated in an online R notebook environment.
Intermediate Python Topics: Project Environments and Testing
This workshop will cover two intermediate topics in Python software development for research code:
1. Setting up a project environment for productive collaboration with a team
2. Testing your software
Basic knowledge of Python, Git and using a Command Line. It is expected that participants will have been programming for at least six months, and are starting to run into the limitations of their current workflows.
Laptop with Python and Git installed
Introduction to R with Ecology data
EcoCommons is building the platform of choice to analyse and model ecological and environmental problems while also increasing digital literacy of researchers and students. This workshop will focus on improving your computational skills by showing you how the statistical program R can be used for data analysis and visualisation in Ecology.
The course starts with some basic information about the R syntax, the RStudio interface, and moves through how to import CSV files. We will also show you the structure of data frames, how to deal with factors and how to add/remove rows and columns. By the end of the workshop participants will have an overview of how to run their R code in the EcoCommons cloud environment and how to use the R package {tidyverse} to manipulate and visualise their data. In particular, we will demonstrate how to use the functions ‘select’ and ‘filter’ to manipulate your data and how to use the ‘pipe operator’ for more complex data manipulation in combination with ‘summarise’, ‘group_by’ and ‘count’ for quick summary statistics. At the end, we will show you how to visualise your data using different plots in the R package {ggplot2}.
This workshop is suitable for early career researchers, undergraduates and ecologists who have a keen interest to learn how to code in R while harnessing the power of cloud computing to solve environmental challenges. This course is very suitable for researchers, students and practitioners who have no or little R experience and coding skills and have the desire to learn how to use code within the cloud-computing resources of EcoCommons. It is also well suited for people who would like to refresh their coding skills in R.
This workshop is based on the Carperntries course: https://datacarpentry.org/R-ecology-lesson/
This workshop is brought to you by EcoCommons Australia. EcoCommons is a partnership of nine organisations including the NCRIS-funded Australian Research Data Commons (ARDC), the Atlas of Living Australia (ALA), CEBRA at the University of Melbourne, CSIRO’s Land and Water unit, Griffith University, Macquarie University, QCIF, TERN, and the University of NSW. It also involves investment from the Queensland Government’s Research Infrastructure Co-investment Fund (RICF).
No prior knowledge needed
It is essential that you install and test R and RStudio well before the workshop.
Please carefully follow the instructions on https://datacarpentry.org/R-ecology-lesson/index.html to download, install and configure R and RStudio on your computer. If you already have R installed, please make sure it is version 4.0.0 or higher, or update it otherwise.
Introduction to FIJI (ImageJ)
This workshop provides a basic foundation to the open source image analysis program, FIJJ (FIJI Is Just ImageJ). It is intended for people who have never used the program before, or require a re-fresher on how to open images, merge channels, perform projections etc.
FIJI is an open source image analysis program which builds upon ImageJ as it comes 'batteries included' meaning extra plugins and libraries are included by default for an easy installation. The software works on Windows, Mac & Linux and can be run headless on HPC.
Topics Covered
The intention of this workshop is to introduce new users to the program and covers the basic concepts around opening, saving and ethical manipulations to images.
- Opening/Saving/Closing Images (.tifs and Bio-Formats compatible files)
- Merging channels, and dealing with multiple channel images
- Adjusting Brightness & Contrast and using histograms
- Adjusting bit-depth
- Adding scale to images & adding scale bars
- Image Stacks (Montages, Projections, Re-Slicing, Orthogonal Views)
- Basic Measurements (Area, Intensity, Shape descriptors, Line Scans)
- Creating Selections (Manual, ROI Manager)
- Overlays
No prior knowledge is required, this is considered a beginners or foundation level course.
FIJI Imaging software (Download from: fiji.sc) Workshop files and content: https://osf.io/zq32x/
The Impostor Syndrome...And why you may feel like you are a fake
Do you feel like everyone around you is smarter than you, and you are worried that they may discover you don't belong here? Or that you are faking it? Does it feel like you have gotten to your position due to a lucky break and not skill?
Welcome to the Impostor Syndrome. This is a strange psychological phenomenon that makes ordinary people – even brilliant ones – feel like they're frauds, fakes, inadequate, and undeserving. Even incredibly successful people like Neil Armstrong and Emma Watson feel like this sometimes.
Anyone can feel like this, especially if you are in a career in tech or research. Its particularly prevalent if you are from a diverse background (Women in STEM, international, etc). It can affect you at any stage of your career.
Come learn more about it from a fellow Impostor and hear about coping mechanisms to help you sidestep this feeling!
Data Cleaning with OpenRefine
Learn how to prepare messy, structured or semi-structured data and transform it into a structured and organised format to enable computational processing and analysis. On completion of this workshop, participants should be able to:
•clean, organise, and prepare data for analysis
•explore data through facets and filters
•implement tidy data principles
•use basic features of OpenRefine
•extract and reuse a reproducible script to repeat processing on similar data
Please bring a Laptop (not tablet) and install OpenRefine software. Instructions to be sent prior to workshop.
Note taking Apps and OneNote as a Laboratory Notebook
1. Giving introduction to today's common digital tools for note taking
2. How to use OneNote as a Laboratory Notebook
Please bring: Laptop, OneNote, Notepad++
Come and Try the Nectar Cloud’s Virtual Desktop
Wondering whether the Cloud is for you? Come to this session to learn more about why its useful for research, and then learn basic skills to get started on our Virtual Desktop Service!
Prerequisites: Internet access, laptop and please log into the Virtual Desktop for the first time: https://desktop.rc.nectar.org.au
How to bring Change with your Research (Change management skills)
We live and breathe change everyday – join us to learn more about how to encourage your audiences to embrace changes you propose – along with some tips!
Please bring laptop, paper and pen
Academic & Professional Capability: Strategies to Effectively Transition Your Skills, Knowledge and Competences
The ‘capable practitioner’ (O’Reilly et al., 1999) can be characterised as one who demonstrates: self-efficacy, intelligent judgement, ethical practice, and is functionally competent across a range of competences that are wisely (selectively and constructively) applied in ways that reflect excellence, not just mere proficiency (Lester, 2014; Stephenson, 1998). This highly accessible presentation explores and reflects on the literature that defines academic and professional capability, and provides strategies to help practice-based researchers effectively transition their skills, knowledge and competences between these two capacities.
Machine Learning Crash Course - Principles and Tools in R
This workshop will cover:
- What we mean by 'machine learning' in the context of 'supervised learning'
- Using the caret package in R for implementing machine learning models
- How to align the purpose of a model and the choice of a model
Prerequisites: Basic knowledge of R and Rstudio, particularly data frames. Please come with R and Rstudio installed
Introduction to Python for Data Scientists
This workshop is recommended for researchers looking for scripting capabilities to run batch analyses and link processes to create a basic pipeline, or to automated repeated tasks for efficiency and reproducibility. While it is designed to be suitable for people with no previous experience with Python or other programming languages, participants do need to be confident and experienced with using computers, and a familiarity with command-line interfaces will be helpful.
Learning Objectives
Use Python to read and write data from and to files
Perform simple scripting operations using loops and conditionals to carry out batch analyses
Generate data plots with Python
Syllabus
The workshop will use the training material at swcarpentry.github.io/python-novice-gapminder/. Topics covered will include:
- Fundamental programming concepts and how to apply them in Python
- Python data types and data structures
- Importing functions into Python using modules
- Programming structures: loops, conditionals, and functions
- Using scripting language to automate data analysis pipelines
No prior knowledge needed – this workshop will assume you have no prior knowledge of programming and will take you through beginner steps
Please bring to class Laptop, internet connection, with installs completed as per http://swcarpentry.github.io/python-novice-gapminder/setup.html
Please note – if you are from Griffith University and using a GU computer, install Spyder from their website directly: https://www.spyder-ide.org/#section-download . Feel free to get in touch with Amanda Miotto at Griffith for assistance with this install
Document Processing with LaTeX
Using the LaTeX document processing system as an alternative to Microsoft Word.
Please bring a laptop signed into Overleaf (www.overleaf.com)
Tidy Data and Good Spreadsheet Design
Lots of research relies on data entered and stored in spreadsheets. Yet poor data organisation within a spreadsheet can make any subsequent data analysis very difficult. This workshop outlines the principles for designing good spreadsheets from the outset.
Some knowledge of spreadsheet programs such as excel is needed.
Follow the instructions here: https://librarycarpentry.org/lc-spreadsheets/setup.html
Data Orientated Career Pathways - How did I get here, and how can you?
Come hear from a panel of data focused professionals, how they came to be in their careers and what career pathways are available in their spaces.Meet our great panel!
Zooming to the Next Level: Tips and Tricks using Zoom
Zoom is a fact of life for most researchers now, yet many of its useful features often get overlooked. In this workshop we’ll introduce you to some Zoom techniques that QCIF uses in our training courses, and which we hope you can use to improve your online meetings and workshops. We’ll also encourage you to share your own hints and tips for Zoom meetings.
Prerequisites/prior knowledge needed: Attendees should have experience with setting up simple (one-on-one) meetings using Zoom. More experienced users are welcome.
Laptops/software installation needed: Please bring a laptop with Zoom installed and updated to the most recent version possible, configured for Eduroam wifi (and tested before the workshop).
Copyright considerations for Researchers
This interactive session will demystify some of the questions you might have about copyright and your research. We will explore how to use other’s copyright material legally, and how to protect your own copyright. We’ll take a look at publishing agreements, Creative Commons licensing, provide some strategies on retaining your rights, and more.
Building R packages and publishing them on GitHub
In this workshop, you will learn how to properly document and organise your functions to create an R package. Creating an R package is beneficial both when it comes to sharing code with other people, but also for home use. It makes it easier to call up your repertoire of functions and provides you with help files so that it is easy for you to remember how to use your functions long after you have built them. While the main purpose of this workshop is to construct an R package, I will also demonstrate how to use git to 'save' different versions of your package, as well as how to push your package onto GitHub so that it can be accessible to other people.
Prerequisites/prior knowledge needed: Enough knowledge of the R programming language to build a function. Students do not need to be proficient.
Laptops/software installation needed: Participants should bring a laptop, with R and RStudio installed. Having git installed and a GitHub account is beneficial, but not necessary. Having some existing R functions ready that the participant would like to turn into a function is encouraged, however I will provide some dummy functions for participants to work on if they do not bring their own.
Introduction to Git
Workshop Description
You’ll learn about the concepts behind version control software and how to use Git to track the changes in local and remote repositories. We’ll discuss and demystify the terminology: commits, merges, forks, etc. and the basics of how to collaborate using Git and GitHub.
No prior Git experience is necessary.
You will need to bring your own laptop, and please follow these instructions https://carpentries.github.io/workshop-template/#git to get Git (and Git Bash if you’re on Windows) installed.
Hands-On Knowledge Mapping in R (library Bibliometrix )
This workshop provides a practical introduction to the R Package, Bibliometrix (Aria & Cuccurullo, 2017). This workshop will focus upon data preparation, document clustering & visualising citation networks.
Basic R knowledge is needed. BYO your your own laptop and install R Studio & Bibliometrix (see - bit.ly/3y3hCkA)
Running bioinformatics pipeline using Nextflow
Nextflow is a scripting language for computational pipelines that enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. (https://www.nextflow.io/). This workshop will introduce Nextflow and its basic principles and features and will teach users how to set it up on their HPC account and launch commonly practiced bioinformatics pipelines in a scalable and easy-to-monitor fashion. Laptops, HPC account (Griffith or QRIS), basic Linux skills needed. Lessons available here: https://carpentries-incubator.github.io/workflows-nextflow/
Interactive maps using Python and Folium
The workshop will be a practical demonstration of Folium (a wrapper for Python of the JavaScript Leaflet library) to generate interactive maps and display data on Open Street Maps. Data for the workshop will be generated by any ResBaz attendees who are able to take a guided stroll through the campus before the workshop.
Making Data (more) FAIR with KBase (Virtual)
Data and the FAIR principles are a hot topic which only continue to grow in importance as the production of data accelerates. Despite this fact, it isn't always easy to understand how or why to make data FAIR. In this talk, I discuss what the FAIR data are (and, just as importantly, are not), and how easy or difficult it is to comply with FAIR Principles, as well as the benefits for doing so.
Launch of the Australian Text Analytics Platform
The Australian Text Analytics Platform (ATAP) is an open source environment that provides researchers with tools and training for analysing, processing, and exploring text. Development of the platform has now been underway for more than a year, our work has already been visible online and in various activities, but now it is time to properly launch the platform. Join us to hear more about our work - and to celebrate the event by eating pizza with us!
This event will also include the announcement of the ATAP-linked Graduate Digital Research Fellowship to run in the first part of 2023. This program provides an exciting opportunity for junior scholars who want to improve their knowledge of digital research methods and incorporate them into their research.
Getting to know GitBook
Introduction to The Living Book of Digital Skills (you never knew you needed until now) and an introduction to GitHub and version control
Advanced Data Wrangling with OpenRefine
Building on the introductory session, learn advanced data wrangling skills including combining tabular data, extracting values from messy data, geolocating data, using OpenRefine and geojson.io.
On completion of this workshop, participants should be able to:
- extend data with additional variables from other data,
- visualise geographic locations using Geo.json resulting in an interactive map
- create a webpage to display the geographically visualise data using Github.
The ARDC National ML Service Pilot: How it works, and what you would like it to evolve into
The ARDC recently funded the acquisition of a small amount of high performance GPU hardware to advance the state of ML research in Australia. The (since completed) Environments to Accelerate Machine Learning Based Discovery identified that this hardware would be best used to support researchers beginning to play with ML models, and in particular researchers who had outgrown the capabilities of their desktops but weren't yet familiar with HPC offerings. The MLeRP service attempts to bridge that gap, offering an experience similar to google colab, but with persistent file storage and an HPC batch system behind the scenes to enable our users to grow and develop as needed.
Come along to this workshop and get signed up for a trial account on MLeRP, try the system out and give us your feedback on how we can better serve the Australian research community in their ML journey.
Phylogenomics analysis using large-scale public genome data
A 90 minutes workshop will be held for the phylogenomics analysis on large-scale whole genome data. We will lead participants through a series of computational exercises having the following goals:
- NCBI genome database download (SRA toolkit) and basic Linux command line (wget download).
- Construct orthologous gene assignments using OrthoFinder.
- Display, annotate and visualize phylogenetics trees by using iTOL (Interactive Tree Of Life)
Participants are encouraged to work with their own NGS-based genome/transcriptome datasets, but sample datasets will also be provided and analyzed.
Introduction to the Five Safes for Sensitive Data
Come along to hear how CADRE (Coordinated Access for Data, Research and Environments) and QCIF are working towards making access to sensitive data safe. You will learn how they are using the Five Safes as a framework to guide decision-making as well as educate those stakeholders who have an invested interest in sensitive data.
Building a blog with git, R and quarto
Grassroots communities of practice are a great way to build communities and skill share – creating an online presence and repository for knowledge, tutorials, and code can be a useful tool. We will introduce a workflow using Git, R, and quarto to run a community of practice blog by forking a GitHub repository, creating a blogpost in RStudio, and pushing the post back to GitHub. This workshop will feature the UQ Geospatial Analysis Community Group and use their R blog as an example. Basic understanding of Git + GitHub and R + RStudio is helpful but the workshop will be aimed at beginners with no prior knowledge.
Social catchup and Networking at the Uni Bar
Come join us at the Nathan Campus Uni Bar to meet speakers, teachers, helpers and other attendees. We'll supply the snacks! We'll also host 'Tell us your research in 90 seconds' where you can learn about the amazing research happening across Qld!