Getting here

How can Collaborative-Coding help your research? by Dr Paula Martinez

Let's face it, as researchers, we know that the best outcomes are produced when we collaborate with others. We can gain and share expertise, learn more, and challenge ourselves to improve. Then, why don't we apply the same guidelines of efficient collaboration to writing analysis code? Collaboration is a strategy in which multiple people work together to accomplish a particular goal; the best is that it can be applied to everything we do. Has the thought of 'cross fertilisation between industry and academia' crossed your mind? One of the ground rules of industry development teams is to 'not work alone'. In academia, we tend to work in silos or be solo drivers. In this talk, I will go through the benefits of collaborative coding and show examples of how it would help your research and give you a competitive advantage in the future.

ARDC: Tools to accelerate your research by Andy White

This session will provide you with an overview of the Australian Research Data Commons, the tools and services on offer and provide a practical overview of FAIR.

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.

Technical Debt and Software Engineering for R Programming: Improving the Development of your Datascience Code by Dr Melina Vidoni (virtually hosted)

Although R programming has been a part of research since its origins in the 1990s, few research studies have addressed scientific software development from a Software Engineering (SE) perspective. The past few years have seen unparalleled growth in the R community, and it is time to push the boundaries of SE research and R programming forwards.

This talk will summarise the findings of SE research at the intersection with technical debt, when applied to R programming. We will discuss testing debt, documentation debt, self-admitted technical debt, and avoidance of CRAN checks. Additionally, it will propose a set of good practices derived from those findings aiming to act as a call-to-arms for both the R and RSE (Research SE) community to explore specific, interdisciplinary paths of research.

The Topography of Searching by Amy Walduck

What we search for reveals something about ourselves: about what we don’t know, what we have forgotten, or what we want to know more about. In a similar vein, what a group of people search for reveals something about the group.

The Digital Collections Catalyst 2021 transformed more than ten years of State Library of Queensland catalogue search terms and created an interactive landscape based on the language, themes, subjects, and terms involved.

The result is a dynamic tool that helps us to understand what, when and how our users are searching the catalogue, and showcases the benefits of supporting developers and creatives to use our digital collections and collections data in highly creative and experimental ways.

https://www.slq.qld.gov.au/digitalcatalyst

A journey in genomics software: from consumer to developer by Dr Cam Hyde

My research Career started in the wet lab seven years ago, doing my Honors project. I was studying the TSH receptor gene in Atlantic salmon – PCRs, genetic cloning, sanger sequencing. With the time between runs I’d dash back to the laptop to complement my experimental work with some bioinformatics. In those days my attempt at sequence analysis was ham-fisted, awkward and tedious, with a lot of manual work that was entirely unnecessary. I was learning the hard way, like many students do. During my PhD I resolved to streamlining these tasks and began learning how to automate analyses with Python. This incredible programming language gradually exposed me to the world of software development. With the publication of my thesis I released a web database which serves as an interface for my research data, and others data like it. During my PhD, the time spend developing this software became a guilty pleasure, a clear indication that this was the path I should follow. Today I work on developing national platforms for bioinformatics, with most of my time spent on Galaxy Australia.

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!

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!

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!

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 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!

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.

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

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

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.

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

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

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

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.

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

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.

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.

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.

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

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)

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

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.

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.

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

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

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)

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)

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.

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.

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).

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/

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/

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

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

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.

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 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.