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.
Dr Paula Andrea Martinez Software Project Coordinator, ARDC,
Dr Paula Andrea Martinez is the Software Project Coordinator at the Australian Research Data Commons (ARDC). She leads projects that improve the recognition of research software and research software authors. She is also an advocate of open science and diversity and active in various community projects such as the Research Software Alliance (ReSA), the Visible Research Software Interest Group (VRS), the Association of Research Software Engineers in Australia and New Zealand (RSE AUNZ).
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.
Andrew White Data Consultant, ARDC,
Andrew (Andy) White works for the Australian Research Data Commons (ARDC) as an Engagements Data Consultant. His role is to provide engagements with ARDC partners on activities related to national data management infrastructure including facilitating the Data Repositories Community of Practice, State based Data Roundtables and FAIR workshops.
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.
Indi Tansey Director, Women in Tech,
I use strategy and design as a force for good, to create tools and systems that help purposeful, values-driven leaders make better decisions.
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.
Dr Melina Vidoni Lecturer at ANU,
Dr Vidoni is a newly joined academic (Lecturer, eq. to Assistant Professor) at the Australian National University in the CECS School of Computing, where she continues her domestic and international collaborations with Canada and Germany. Dr Vidoni’s main research interests are mining software repositories, technical debt, software development, and empirical software engineering when applied to data science and scientific software.
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
Amy Walduck Coordinator, Digital Library Initiatives, State Library of Queensland,
Amy Walduck is a librarian, an extrovert, a creative and has embraced a colourful career across state, academic, special, and public libraries. As a creative problem-solver, she thrives in busy, collaborative environments working with passionate people. At State Library of Queensland, Amy is currently working on digital, open data and collections as data initiatives such as the Digital Collections Catalyst and Making Meaning: Collections as Data Symposium.
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.
Dr Cameron Hyde Software EngineerSoftware Engineer, QCIF,
Cameron graduated with a PhD in genomics at the University of the Sunshine Coast in 2020, where his research in non-model organisms motivated the development of new tools for data mining and sharing of transcriptome data. Today he works as a bioinformatician and software developer for the Queensland Cyber Infrastructure Foundation (QCIF) building tools and resources for biological data analysis.
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!
Dr Adi Gafni Director, Data, Analytics, and Custom Solutions, Children's Health Queensland Hospital and Health Service,
I graduated in 2012 with a B.Sc. in Industrial Engineering and Management, with a major in Information Systems and specialised in Business Intelligence.
In April 2018, I completed a Graduate Diploma of Data Science, and in November 2021 I completed an Executive MBA. My graduation project as an industrial engineer got me my first BI developer job and I have been in different roles in the BI space across fisheries, fitness, finance and now health industries, ever since. I chose this path as it brings together aspects like systems thinking, design thinking, creativity, and science to solve big and meaningful problems across multiple domains and industries, all aspects that I greatly enjoy.
In my current role, I am the Director of Data, Analytics, and Custom Solutions (DACS) at Children's Health Queensland (CHQ).
Evolving from leading self to leading teams and functions has been a fantastic journey and a very rewarding one, as it allows me to contribute through leadership and partnerships to the development of others and to the overall mission of the organisations I am working for, and more importantly to their consumers.
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!
Rhetta Chappell Acting Director, Relational Insights Data Lab (RIDL),
Rhetta has a strong background in data analytics, statistical standards, data collection, reporting and survey design. Originally from Canada, she previously worked for the National Centre for Vocational Education Research as researcher and project officer. Rhetta is a strong proponent of open source technologies and women in STEM and can often be found presenting and enjoying the free pizza at events in the data science and technology scenes in Brisbane. After completing a degree in Anthropology, Rhetta has gone on to complete post graduate study in data science and machine learning.
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!
Dr. Alexander Wailan Bioinformatician, QoVAX SET Program, Queensland Health,
I'm a highly social and energetic personality with a high analytical and strategic mindset. For my personal work I am a mental health advocate while professionally I am a bioinformatician.With the 10 years experience in computational & bioinformatics analysis my international career was recognised by being awarded on a 30 under 30 international outstanding young scientist. I have a strong determination and discipline to strategically complete tasks at a high quality and efficient manner. I also have a strong mentoring skill set with an emphasis on skillset development, complimented with improvisation, creativity and organisation skills and high communication skills. I'm flexible and versatile with the capacity to grasp new concepts efficiently and have a strong interest in mental health to achieve high performance.
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.
Dr. Ali Chauvenet Senior Lecturer, School of Environment and Science, Griffith University,
Dr Ali Chauvenet is a conservation scientist interested in protecting biodiversity from extinction by making the best decisions for the conservation and management of species and ecosystems. Her PhD was conferred by Imperial College London, UK, in 2013. She then worked as an ecological modeller for the British government until 2014, followed by a post-doctoral Research Fellowship at the University of Queensland, Brisbane. In 2018, she became a lecturer in the School of Environment and Science at Griffith University, and a member of the Centre for Planetary Health and Food Security. Her research currently focuses on measuring the benefits of protected areas for biodiversity and human well-being through a combination of spatial ecology, data science, and computer simulations. She teaches environmental data analytics and R programming to undergraduate students. In 2021, she developed an R Shiny app for an industry partner to help them make conservation decisions based on spatial analyses.
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!
Amanda Miotto Senior eResearch Analyst, Griffith University/Queensland Cyber Infrastructure Foundation,
Amanda Miotto is a Senior eResearch Analyst for Griffith University and QCIF. She started off in the field of Bioinformatics and learnt to appreciate the beauty of science before discovering the joys of coding. She is also heavily involved in Software Carpentry, Hacky Hours and ResBaz, and has developed on platforms around HPC and scientific portals.
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.
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.
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.
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
Dr. Sam Hames Research Fellow, School of Languages and Culture, University of Queensland,
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
Clare Van Dorssen Knowledge Translator and Impact Coordinator, School of Health Sciences and Social Work,
Clare is a Knowledge Translator and Impact Coordinator with the Healthy Primary Care team in the School of Health Sciences and Social Work. With a Master’s in Science Communication Outreach, Clare has experience in creating interactive STEM demonstrations to entertain audiences of all ages.
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.
Emilia Decker Business Analyst, EcoCommons Australia,
Emilia is an environmental scientist who wrote her PhD thesis on using ecoacoustics as a monitoring tool for freshwater systems and presented it at TEDx Byron Bay. As the Business & Scientific Analyst for EcoCommons, she reviews requirements and testing plans to ensure the EcoCommons platform is meeting planned milestones.
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
Angela Ellis Queensland Health,
Angela Ellis is a highly motivated Registered Nurse (RN) with 40+ years’ experience spanning medical, two private enterprises, women’s health, sexual health, and health promotion initiatives to socially diverse populations, building networks and mentoring future leaders. In the last 14 years Angela was a Hospital in the Home (HITH) Clinical Nurse. Her doctoral thesis on HITH RN scope in practice has identified challenges currently facing HITH RNs. Remaining passionate about nursing practice, as a HITH Society Australasia board executive representing nursing, she is leading discussions on nursing issues with the board and the project group to critically review HITH nursing skills, roles, and attributes with the aim this body of work will guide and enhance HITH RN capacity in Australian nursing, thus implementing her thesis recommendations in building a HITH nursing career and integrated education pathway.
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
Jessica Stokes-Parish Assistant Professor, Faculty of Health Sciences and Medicine, Bond University,
Jessica is a practicing intensive care nurse and educator, who holds a PhD in Medical Education. In addition to 13+ years of bedside nursing, her areas of work include health professions workforce development, including policy, education, and science communication. She is an experienced science communicator and shares her work at @j_stokesparish on all platforms.
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 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.
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
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.
Sharron Stapleton Library Research Specialist, Griffith University,
Sharron & Ben provide training and advice to Griffith University researchers on open access publishing, finding external data and primary sources for research and preparing data for analysis and visualisation.
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.
Dr. Dan Jess Senior Lecturer, Australian College of Strategic Marketers,
Dr Dan Jess is a strategic marketing and leadership specialist, and practice-based researcher with 16+ years’ experience leading award-winning digital marketing agencies. He is currently completing a second research doctorate at USQ, exploring the strategic ambidexterity construct and how it operates in an Australian Chief Marketing Officer capability context. He holds academic positions at the Australian College of Strategic Marketers and Australian College of Vocal Arts, and is currently CEO at Fragment Digital. Qualifications include: DSM (USA), MBA (Strategic Marketing).
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.
Dr. Tony Howes Honorary Associate Professor, School of Chemical Engineering, University of Queensland,
Tony Howes is an honorary academic in the School of Chemical Engineering at The University of Queensland. As a Python enthusiast and Orienteering tragic, Folium is a wonderful tool for the two interests together.
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
James Todd Assistant Professor of Data Analytics, Bond Business School, Bond University,
James is an Assistant Professor of Data Analytics at Bond University. His research focuses on how data can be used to improve decision-making in organisations, particularly in the healthcare sector.
Using the LaTeX document processing system as an alternative to Microsoft Word.
Please bring a laptop signed into Overleaf (www.overleaf.com)
Julie Somers Digital Capability Advisor, Academic Engagement Services, Griffith University,
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
Tati Viegas-Gurry Change and Communications Manager, Research, Specialised and Data Foundations, Griffith University,
I am a training and project delivery professional specialising in business best practices by establishing, implementing, and monitoring change, controls and training in projects for clients in private and public sectors across various industries. With 20 years across national and international organisations, where project budgets range from $100K to $100 million, I am qualified in Business Administration, Project Management, Training and Assessment, Change Management (Prosci) and Prince2; knowledge of PMBOK, Agile, SCRUM, Scheduling (EVM), Finance, EDRMS, and ERP Systems. I am passionate about supporting people on journeys of change in fast-paced environments. I am fluent in Brazilian Portuguese and Spanish and a big advocate of diversity. I enjoy helping graduates and professionals achieve their career goals and crafting beadwork in my spare time.
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.
Dr. Nicole Fortuna Postdoctoral Research Fellow, School of Biological Sciences, University of Queensland,
I completed my PhD in 2021 where I modelled the evolution of host-parasite coevolution. Currently I am a postdoc for the CoE for Pant Success where I am developing models of plant hormone interactions.
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.
Katya Henry University Copyright Officer, Queensland University of Technology,
Katya Henry is the University Copyright Officer at Queensland University of Technology (QUT) and the Creative Commons Global Network Representative for the Creative Commons Australia Chapter. She is a passionate advocate for open access and open education and is deeply committed to the role librarians play in enabling access to information.
Introduction to The Living Book of Digital Skills (you never knew you needed until now) and an introduction to GitHub and version control
Dr. Sara King Training and Engagement Lead, Australia's Academic and Research Network,
Dr Sara King is the Training and Engagement Lead for AARNet. She is focused on outreach within the research sector, developing communities of interest around training, outreach and skills development in eResearch. She is currently working on creating reusable guidance information for Jupyter Notebooks and other AARNet services to be adapted for Carpentry training workshops. She is passionate about helping others develop the infrastructure and digital literacies required for working in a data-driven world, translating technology so it is accessible to everyone.
Introduction to The Living Book of Digital Skills (you never knew you needed until now) and an introduction to GitHub and version control
Nica Tsakmakis Senior Library Coordinator, Library Academic and Research Services, Australian Catholic University,
Nica Tsakmakis is a Senior Librarian at Australian Catholic University and Co-Convenor of the CAUL Digital Dexterity Champions Community of Practice. With a heavy humanities background she fell into Digital Dexterity and discovered a real passion for exploring and sharing all things digital from Library Carpentries to VR in the classroom.
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)
Mathew Fletcher Liaison Librarian, Faculty of Business and Law, Queensland University of Technology,
Mathew Fletcher is a Librarian for Economics & Finance at QUT with an interest in scientometrics and knowledge representation.
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)
Dr. Quentin Pope Liaison Librarian, Faculty of Business and Law, Queensland University of Technology,
Dr Quentin Pope, Law Librarian at QUT, has a PhD in Biological Sciences and has published over 40 scientific papers. She has a special interest in history of ideas and representations of knowledge networks.
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.
Dr. Min Zhao Senior Research Fellow, Bioinformatics and Genomics,
Dr. Min Zhao has about 20 years of experience in the field of bioinformatics and genomics. His research focuses on the investigation of regulatory machines in aquatic genomes and disease genomes. In addition to 4 review manuscripts, he has published 90 research papers in peer-reviewed international journals including 50 first and corresponding author papers in total. In total, his papers have been cited over 4000+ times (H-index 31). About 50% of his publications are presented in the top 10% most cited papers worldwide in Scopus database. Additionally, ten of his manuscripts have been published in very high profile journals (top 5%; including Nature, Nature communication, cell research, American Journal of Respiratory and Critical Care Medicine, Nucleic Acids Research, Molecular ecology resource). The research articles include author contributions from a diversity of institutions/universities external from USC and International (primarily USA, Japan, China, and Thailand). He currently leads as Chief Investigator 1 ARC Discovery Projects (with USC as administering organisation), and is co-contributor for Reef2050 grant.
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.
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).
Dr. Mark Crowe Skills Development Manager, QCIF,
Mark Crowe is the Skills Development Manager with QCIF, and is an Instructor and an Instructor-Trainer with The Carpentries, an international digital skills training organisation. Since the start of the pandemic, Mark has held a ridiculous number of Zoom meetings, including having organised and hosted over 180 online training workshops for nearly 5000 participants.
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/
Dr. Ido Bar Research Fellow, Centre for Planetary Health and Food Security, Griffith University,
I am a lecturer (Biosciences) and a research fellow at the Centre for Planetary Health and Food Security (formerly EFRI), with strong knowledge, skills and expertise in molecular biology, genomics and bioinformatics. My research foci are crop genomics, crop-pathogen molecular interactions and development of novel pathogen diagnostics methods. I aspire to develop applied research solutions in tight collaboration with the agriculture and aquaculture industries to overcome diseases and other production bottlenecks to help future food security. My group has several ongoing projects suitable for Capstone and WIL projects, as well as Honours and PhD programs, please contact me if interested in any of the research areas above. As a lecturer, I am responsible to develop, deliver and convene under/postgraduate level academic courses, including Introduction to Bioinformatics (3030NSC), Molecular Biology (2012NSC) and Scientific Data Analysis (6003ESC). I have initiated and I am coordinating the “Bioinformatics@Griffith” group, providing essential support, training resources and networking opportunities to HDR students and researchers using bioinformatics from multiple disciplines across the University.
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/
Dr. Nicholas Condon Senior Microscopist, Institute for Molecular Bioscience, University of Queensland,
Nicholas Condon is a cell biologist, microscopist and imaging scientist. He has expertise in using advanced light microscopy and novel image analysis techniques to make discoveries. He is developing custom image analysis pipelines, and high-performance computing pipelines for the processing and analysis of complex big datasets from modern microscopes. He is an expert in many light microscopy technologies as well as the associated image analysis methods for both 2D and 3D data. Nicholas is currently supported by a 5-year Chan Zuckerberg Initiative Imaging Scientist fellowship to support the teaching and training of users around microscopy and data analysis. Deborah is a biomedical engineer, immunologist and imaging scientist. She has experience with intravital multiphoton microscopy, preclinical imaging using MRI, PET and CT, as well as microscopy and flow cytometry based immune assays. Deborah has developed image analysis pipelines for dynamic imaging, immune microenvironments, and most currently a fluorescence lifetime imaging analysis program. Deborah is interested in developing machine learning programs for image analysis.
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
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
Belinda Weaver Head of Library Academic Engagement Services, Academic Engagement Services, Griffith University,
Belinda Weaver is a certified Software Carpentry instructor who has taught more than 40 workshops.
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.
Alice Miller Senior Data Scientist/Developer, Digital Observatory, Queensland University of Technology,
Alice is a data scientist with a background in social science research.
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.
Rani McLennan Copyright Information Officer, Queensland University of Technology,
Rani McLennan is the Copyright Information Officer at Queensland University of Technology (QUT) and the Open Educational Resource (OER) Collective Project Officer at the Council of Australian University Librarians (CAUL). She has over a decade of experience in public, school, and academic libraries. Her interests include the communication of complex information through text and visuals and openly licensed image collections.
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.
Dr. Catherine Kim Postdoctoral researcher, School of Earth and Atmospheric Sciences, Queensland University of Technology,
Catherine is a postdoctoral researcher in the School of Earth and Atmospheric Sciences at the Queensland University of Technology. Currently, she is modelling generation of coral rubble across the Great Barrier Reef for the Reef Restoration and Adaptation Program.