| Title | Author |
|---|---|
| Value addition to agricultural products in Rural Australia | Thuy Van Dao |
| Live imaging kidney development and regeneration | Raeesah Hayatudin |
| Developing AI approaches to unravel factors that drive disease relapse in low-risk, early-stage colorectal cancer | Charla Lu Chai |
| Open Research Skills Knowledge Framework | Sally Tape |
| Framework for secondary use of clinical trials data in health research | Amany Gouda-Vossos |
| Ten Simple Rules for Researchers: Upskilling for a Rapidly Evolving Workforce | Amany Gouda-Vossos |
| Electron density as an effective input for neural networks to predict atomisation energies | Peter Halat |
| Externally validated machine learning models for predicting caesarean section following induction of labour using real-world, population-based administrative datasets | Yanan Hu |
| Segmentation and shape clustering of algal microscopic images: Initial steps toward automatic identification of microalgae and cyanobacteria species | Negar Taheriashtiani |
| Non-destructive defect detection & analysis of AM metal in CSAM system | Sana Awan |
| Accelerate your Health and Medical Research '24; Introduction to ARDC's People Research Data Commons | Richard Ferrers |
| A Smartphone Sensing-Based Approach to Support Mental Health Treatment | Lin Sze Khoo |
| Discover Clinical Trials Data with Health Data Australia | Richard Ferrers |
David Powell Prof., Monash eResearch
Professor David Powell is the Director of the Monash eResearch, where he leads initiatives to support research through digital expertise and high-end infrastructure across multiple research disciplines. Holding a PhD in Computer Science, he brings deep technical expertise to his role in research infrastructure leadership. In his previous position as Director of the Monash Bioinformatics Platform, he collaborated extensively, applying his analytical expertise to complex biological data. Before returning to Monash University in 2012, Professor Powell gained valuable industry experience leading software development teams and worked in small startup companies, where he contributed to developing innovative technological solutions.
Jacek J. Jasieniak Prof., Monash University
Jacek Jasieniak completed a Bachelor of Science (1st Class Honours) from Flinders University (2003, University Medal) and PhD from the University of Melbourne (2008, Chancellor’s Prize) under the supervision of Prof. Paul Mulvaney. He then undertook postdoctoral work as an OCE fellow at the Commonwealth Scientific and Industrial Research Organisation (CSIRO) with Dr Scott Watkins and Dr Ezio Rizzardo (2008-11) and was a Fulbright Fellow with Nobel Laureate, Prof. Alan Heeger, at the University of California Santa Barbara (2011-12). In 2012 he returned to CSIRO, progressing to a Senior Research Scientist and then Group Leader. In 2015 he moved to Monash University as an Associate Professor, where he was also appointed Director of the cross-disciplinary Monash Energy Institute. In 2020 he was promoted to Full Professor and also became the Associate Dean of Research for the Faculty of Engineering. In December 2021, Jacek was promoted to the role of Pro Vice-Chancellor (Research Infrastructure) at Monash University.
Luke Bampton , Monash University
Luke Bampton is the Application Security Lead at Monash University, with over 12 years in the tech industry. He excels in vulnerability assessment, threat modelling, and secure coding, ensuring robust application security.
Luke’s career began in Application Support, transitioning to cyber security where he bridges the gap between development and security. He holds a Bachelor of Information Technology and Systems, alongside various cybersecurity certifications, reflecting his dedication to continuous learning and professional growth
Join Monash University's Application Security team to deploy and run an intentionally vulnerable web application and implement fixes within your own NECTAR cloud instance. In this workshop, you will get a peek into life as an offensive security expert and learn how easy it can be to resolve some major security flaws
Rashina Hoda Prof., Monash University
Rashina Hoda is a Professor of Software Engineering and Associate Dean of Equity, Diversity, and Inclusion at the Faculty of Information Technology, Monash University. She is an expert in qualitative empirical research and developed Socio-Technical Grounded Theory (STGT), a modern extension of sociological Grounded Theory. With nearly 20 years of experience, she investigates the human and socio-technical aspects of software engineering and artificial intelligence. Rashina has published over 150 research outputs, been awarded over $5M in research funding, received multiple awards, and serves as an Associate Editor of IEEE Transactions on Software Engineering. A champion for women in STEM, she frequently shares insights at conferences, industry events, and public platforms such as TEDx, SXSW, Agile Australia, ABC Radio National, and more, see rashina.com for more.
In this key story Prof. Hoda will share her passion for qualitative research, exploring the growing socio-technical nature of many research fields and its implications for researchers at all levels. She will offer insights into conducting rigorous research and achieving robust outcomes, drawn from her years of practice, reviewing, and editing qualitative and mixed methods research. Attendees can delve deeper into these concepts in her newly released Springer book, Qualitative Research with Socio-Technical Grounded Theory, available on SpringerLink and Amazon. Everyone is warmly invited to join her for the book launch immediately following her talk at ResBaz 2024.
Darren Brain , GALE
Damian Almeida , GALE ANZ
Damian Almeida is the Academic Engagement Manager at Gale ANZ based in Melbourne. He works with the Gale sales team to enhance customer engagement through technical training and promotion of Gale’s products and resources.
In this role, Damian helps customers maximize their usage of Gale resources. He conducts comprehensive product training sessions, both online and in-person, ensuring clients are well-equipped to utilise the offerings effectively. Additionally, he serves as the primary contact for Gale’s Text & Data Mining Platform, the Gale Digital Scholar Lab, with a focus on Digital Humanities.
Text mining historical primary sources is an innovative approach that leverages computational techniques to analyse vast collections of documents, manuscripts, and artifacts from the past. This methodology facilitates the extraction of meaningful patterns, trends, and insights that might be overlooked in traditional qualitative analyses.
By applying natural language processing (NLP) and machine learning algorithms, researchers can uncover hidden relationships within historical texts, enabling a deeper understanding of societal changes, cultural dynamics, and historical narratives. The integration of text mining with digital humanities allows for the exploration of large datasets, transforming how historians and scholars engage with primary sources.
The Gale Digital Scholar Lab offers a straightforward entry point into Digital Humanities for new researchers and for more experienced scholars, the Gale Digital Scholar Lab provides access to large data sets that can be easily mined and exported for use in custom applications and open-source analytical tools. With the Gale Digital Scholar Lab, Gale has created a research platform to help bridge the gap that often exists between primary sources that are available in the library and the research needs and workflows of faculty and students. As an extension of your primary source collections, Gale Digital Scholar Lab will encourage the use of archival holdings to support broader research needs, content can be analysed in the Lab using the visualization tools available. This research can then be constructed into research articles within the Lab and published to Gale Research Showcase.
The Gale Research Showcase is an open-access repository of student-written digital scholarship. Projects in the Gale Research Showcase are write-ups of individual or group research conducted in the Gale Digital Scholar Lab. All projects are submitted via a straightforward submission form accessed via Gale Digital Scholar Lab. Submitted work is reviewed to provide feedback on methodology, providing professional visibility and experience with the peer review process.
This session will explore how the Gale Digital Scholar Lab and Gale Research showcase how students and researchers are engaging with primary sources.
Patrick Splawa-Neyman , Monash University
Patrick Splawa-Neyman has had a decade of experience working in research data management and for the last two years in research data governance. He has worked in research data management support for two Australian universities and an open data vendor. Patrick previously ran the Introduction to Data Organisation session for researchers at Monash University and is now co-developing an online training session on the fundamentals of research data management. Patrick is particularly interested in closely engaging with researchers to provide practical solutions to tricky research data management issues. His primary aim is to support researchers so they can spend more time on research and less time on “administrivia”.
Research data management is vital to good research. It’s a topic that is of interest to researchers but it can be confusing and time-consuming. It can also be overly technical in nature, leaving many researchers feeling that it’s beyond their current abilities. However, while good research data management does have a technical element, it also requires an understanding of how non-technical aspects can make research data management easier and more effective. This session will focus on those non-technical aspects of research data management under your control. Among other topics, we’ll cover research data and lifecycles, data governance, the role of human error with examples, data classification, and considerations in file naming and organisation.
Dianne Cook Prof., Monash University
Dianne Cook is a Professor of Statistics in Econometrics and Business Statistics at Monash University in Melbourne, Australia. She has a PhD in Statistics from Rutgers University. Her research focuses on statistical graphics, which involves interactive visualisation of high-dimensional data, and statistical inference for data visualisation. In her role at Monash University, she regularly teaches courses on machine learning and data analysis, and she has conducted workshops on data visualisation.
This is for scientists and data science practitioners who regularly work with high-dimensional data and models and are interested in learning how to better visualise them. You will learn about recognising structure in high-dimensional data, including clusters, outliers, non-linear relationships, and how this can be used with methods such as supervised classification, cluster analysis and non-linear dimension reduction.
Defining your data plots using a grammar of graphics makes them into statistics. As such, you can use computational tooling to conduct tests for the presence of patterns and determine if a particular plot design is more powerful than another. This talk will explain how to approach this, including for biological data.
Nadine Andrew A/Prof., Monash UniversityNational Centre for Healthy Ageing
A/Prof Nadine Andrew is a senior researcher at Monash University and Research Data Lead for the National Centre for Healthy Ageing. She is nationally recognised as a leader in generating and translating knowledge in the application of big data to health services research through data linkage, leading a number of large grant-funded projects in this area. She is chair of the Monash Helix data linkage community of practice (M-Link), running workshops through Data Fluency, hosting bi-annual events with external speakers from government and other external organisations, and providing resources and support for Monash researchers wanting to access linked data.
A wealth of health data is collected and stored electronically, yet much of this data remains siloed and underutilised. Maximising the use of improved electronic data collections, linkage systems that enable data to be linked at the person level and analytic advancements have great potential to maximise data sharing and increase the potential for ‘big data’ research. Opportunities exist to better deliver higher-impact research at scale through capacity building and knowledge sharing in data linkage.
This workshop will introduce how large datasets can be reliably linked and used to provide novel insights, using health research as an example. Attendees will also be introduced to M-Link, a community of practice developed to support and oversee data linkage practice at Monash University. Areas of focus include: knowledge sharing; ethics, governance and data security; technical infrastructure and linkage methods and access to external administrative datasets.
Paul Harrison Dr., Monash Genomics and Bioinformatics Platform
Paul Harrison is a bioinformatician working with the Monash Genomics and Bioinformatics Platform. He received his PhD in Computer Science in 2006 at Monash University and worked for the Victorian Bioinformatics Consortium until 2014. Paul has developed several bioinformatics and data visualization packages in R, Python, and Javascript. He has also been involved in developing and running various R and bioinformatics workshops at Monash.
R is a popular language and environment for data exploration, visualization, and statistical analysis. This workshop will be an introduction to working with data using R, and is aimed at complete beginners to coding. Attendees will learn how to load tabular data, and common data manipulations such as filtering, sorting, and joining tables, and then go on to plotting with ggplot2 and summarizing data. We will cover the R way of thinking about data, including vectors, factors, and data frames, as well as the idea of 'tidy' data. By writing R code, we create a data analysis that is easy to reproduce, modify, and share. The workshop will feature a live demonstration, with frequent opportunities to try what you are learning for yourself. Attendees will be equipped to start exploring the broad range of R packages that are available, both general and specialized.
The material in this workshop will be very similar to Monash Data Fluency's 'Introduction to R' workshops.
Prerequisites
None - This is very much an introductory workshop.
Attendee instructions
Please ensure you have an account on posit.cloud. Monash attendees can use their Monash Google account. You can also use R on your laptop, in which case you will need to install both R and RStudio.
What if there was a way to let the whole world visualize and interact with your data, using code you have written, with video-game-like smoothness, and with software they already have on their laptop or phone? You can with a web page. Also you can do this for free and it will probably keep on working for decades to come.
This workshop will provide a first step writing the elements of a web page that can interactively present your data.
Prerequisites
Some experience with another programming language will be helpful, such as Python or R.
Attendee instructions
Please make sure you have a text editor. Some options are VSCode, VSCodium, Geany, Notepad, or Nano. Also please ensure you have an account on github.com, we will use this to put your web page on the web.
Kiowa Scott-Hurley , Defence Science and Technology
Kiowa Scott-Hurley is a Dja Dja Wurrung woman who spends her 9-5 leading a team of awesome Machine Learning engineers at the Defence Science and Technology Group. She's currently studying a Masters in Cybersecurity, and her unique mix of skills across ML, Cybersec and HPC means you can always catch her grumbling about GPU drivers. In her free time you'll find her drawing and cramming cat comics into slide decks, using LLMs for evil, and committing diversity-tax evasion.
What unique challenges do staff in Research & Digital Platforms face when it comes to diversity and inclusion? In this question-driven panel, we will share our personal experiences and discuss the challenges faced by underrepresented individuals in our field. We’ll explore what diversity and inclusion in eResearch could look like, why it matters, and practical ways to purposefully cultivate a more inclusive and diverse workplace.
Deanna Deveson Lucas Dr., CSL
Deanna obtained a Bachelor of Science with Honours, majoring in Molecular Biology and Microbiology from Monash University. She began her career at Pfizer Animal Health in the Research & Development Bioprocess Improvement Group (2004–2007), where she contributed to vaccine research, development, and optimization. She then pursued an industry-based PhD, based at the Department of Microbiology, Monash University and Pfizer Animal Health, where she focused on investigating the bovine immune response to Leptospira spp. After completing her PhD in 2014, Deanna worked as a postdoctoral researcher in the Bacterial Pathogenesis Laboratory, Dept. Microbiology, Monash University. Her research involved several omics-based projects, including the study of antibiotic resistance mechanisms in Gram-negative pathogens. In 2019, Deanna transitioned to the Monash Bioinformatics Platform as Platform Manager, where she led bioinformatics initiatives across a broad range of research areas and facilitated the delivery of training at a local and national level. From September 2022, she concurrently held the roles of Manager (Bioinformatics) and Acting Director of the Monash Genomics and Bioinformatics Platform, playing a key role in the successful merger of the genomics (MicroMon) and bioinformatics platforms. In July 2024, Deanna joined CSL’s R&D Enabling Technology team, where she now focuses on supporting the implementation of an operational model for the Laboratory Data Repository, furthering her expertise in data management within a global research context.
What unique challenges do staff in Research & Digital Platforms face when it comes to diversity and inclusion? In this question-driven panel, we will share our personal experiences and discuss the challenges faced by underrepresented individuals in our field. We’ll explore what diversity and inclusion in eResearch could look like, why it matters, and practical ways to purposefully cultivate a more inclusive and diverse workplace.
Claudia Del Campo Dr., Monash University
Dr. Claudia Del Campo is the Operations Manager at the Monash Data Futures Institute, Monash University in Australia. She leads strategic initiatives to bring together AI and Data Science expertise across Monash faculties, and engagement with national and international partners.
Dr. Del Campo is passionate about interdisciplinary research and cross-sector collaborations. At the Monash Data Futures Institute, she oversees the delivery of the research agenda with a focus on applying AI for Climate Change, Geopolitical Security and Thriving Communities. Dr Del Campo worked in academic research for more than 15 years in Colombia, Israel, USA and Australia in the areas of biomedicine, ecology and water resources management.
What unique challenges do staff in Research & Digital Platforms face when it comes to diversity and inclusion? In this question-driven panel, we will share our personal experiences and discuss the challenges faced by underrepresented individuals in our field. We’ll explore what diversity and inclusion in eResearch could look like, why it matters, and practical ways to purposefully cultivate a more inclusive and diverse workplace.
James Trauer A/Prof., Monash University
A/Prof James Trauer is an expert in infectious disease modelling, with a particular focus on COVID-19 and tuberculosis. He leads the Epidemiological Modelling Unit at Monash University, where his team uses mechanistic simulation models to guide public health strategies for infectious disease control.
His work has been important in shaping the response to the COVID-19 pandemic and informing TB control programs across the Asia-Pacific, including through extensive collaboration with the World Health Organization's Western Pacific and South-East Asia Regions. The team has recently shifted to a capacity building approach for epidemic modelling to enable locally led responses to infectious diseases. As a practising respiratory physician, James brings a clinical perspective to his research, but also remains closely involved in platform development.
Infectious disease (ID) modelling came to the fore during the pandemic, but there are few or no qualifications to identify competence in the field. ID modellers come from a broad range of backgrounds, with mathematicians, physicists, medical doctors and others often contributing to modelling applications. The interdisciplinary nature of these teams brings the perspectives needed to execute such ID modelling analyses. Despite this, analyses typically rely on the individual modeller to write, execute and describe their model, as well as translate the results for policy.
The Epidemiological Modelling Unit (EMU) at Monash University has strived to take a different approach, including consistently including a role for a Python developer within its team structure. This has provided many benefits, which include: confidence that the code runs as intended, logistical efficiency in reporting and extending the pipeline beyond the modelling process to include the full pathway from inputs through to building the final report. Moreover, our developers have introduced us to benefits that we had not previously anticipated, such as the improved ergonomics of faster execution.
Dianne Brown , Monash University
Dianne Brown (BEc(Hons), GradCert(Epi)) is a data governance consultant at Monash University working with clinical quality registries and other sensitive data research to improve their data governance capabilities.
When it comes to survey data collection for research two platforms seem to be duking it out - Qualtrics and REDCap. One is a sleek, commercial, easy-to-use platform widely used in industry. The other is a university-based, community-enabled workhorse. So which one should you use? What things will you need to trade off when choosing one over the other? How do they compare head-to-head in survey design, usability, analysis, visualisation, and auditing?
Come see our “Great Debate” between experienced researchers, statisticians and technical experts who will help you to make up your mind.
Amr Hassan Dr.,
Joseph John , National Computational Infrastructure (NCI)
Joseph John is a Staff Scientist at the National Computational Infrastructure (NCI), Australia. His primary research focuses on programming models for high-performance computing. He is also keenly interested in exploring libraries and tools for scaling large-scale multi-GPU HPC applications.
Gadi is Australia’s most powerful CPU-based supercomputer, a highly parallel cluster comprising more than 180,000 processor cores on ten different types of compute nodes. Gadi accommodates various tasks, from running climate models to genome sequencing, designing molecules, and astrophysical modelling.
The session will introduce supercomputers, how to access Gadi, files and directories, and computing resources. Join us if you are a new user or want to refresh your knowledge of the basics of Gadi.
Python is a useful programming tool for prototyping but has scalability limitations. This workshop will familiarise you with tools to scale up your Python code and adapt it for an HPC machine.
This training is for anyone with Python programming experience who needs to scale up their Python code. It will introduce the attendees to tools that can help scale their Python code (e.g., Numba and cuPY).
NCI ,
Yang Liao Dr., Bioinformatician
Yang Liao is a skilled bioinformatician with a strong background in computer science. He earned his Bachelor's degree from Tsinghua University in 2002 and subsequently completed his PhD in information science at the University of Melbourne in 2012.
Yang has been working in the field of bioinformatics for more than a decade, contributing to the development of tools and methods for analysing high-throughput sequencing data. He is a co-author of the widely used Subread and Rsubread packages. He has also collaborated with many researchers on a variety of biology and immunology projects.
Yang has been a postdoctoral researcher in Professor Wei Shi's lab at Monash BDI since 2024, specialising in the development of bioinformatics methods for analysing high-throughput sequencing data, including bulk RNA-seq, single-cell RNA-seq, and long-read sequencing data.
This presentation will delve into the development and optimization of featureCounts, a widely used tool for NGS read quantification. I will explore the technical details that drive featureCounts' efficiency, including strategies for detecting features overlapping with reads, processing large BAM files in parallel, and efficiently matching read pairs in unsorted paired-end SAM or BAM files. Additionally, I will discuss the maintenance practices that contribute to featureCounts' high usability and stability.
Building upon this foundation, I will introduce cellCounts, a novel single-cell expansion tool that outperforms existing solutions like Cell Ranger in terms of speed. The presentation will illuminate the technical innovations that underpin cellCounts' superior performance, offering insights into the future development of single-cell analysis tools.
Jathan Sadowski Dr., Monash University
Jathan Sadowski is a Senior Lecturer and ARC DECRA Fellow in the Emerging Technologies Research Lab, Department of Human-Centred Computing, Faculty of Information Technology at Monash University. His work analyses the political economy and social impacts of technology, with a specific focus on the development of risk governance systems in the insurance industry.
This workshop will expand our understanding of AI/ML by placing the design and application of these technologies in a broader societal context. Through group discussion of the participant’s own projects and interests, we will consider the human values, ethical choices, and social motives that are integral parts of technical systems. This will allow us to critically question how and why we build AI/ML, what its purposes and uses should be, and how to ensure it achieves socially beneficial outcomes. Through collective reflection, participants gain greater skills for thinking more deeply (and differently) about their own projects and responsibilities.
Eva Fisch ,
Mitchell Hargreaves , Monash eResearch
Mitchell Hargreaves is experienced with training and deploying deep learning models as well as building data engineering pipelines. He is passionate about reducing barriers of entry and making these tools more available for all. He is the primary developer and system administrator for Machine Learning eResearch Platform (MLeRP).
The Machine Learning eResearch Platform (MLeRP) was developed to offer a premium Jupyter notebook experience backed by the power of a GPU cluster, persistent storage, and full control over your software environment.
MLeRP was designed to take advantage of the Dask and SubmitIt frameworks, allowing users to decouple a Jupyter notebook from a GPU in the cluster rather than only attaching it as a reservation. This means that we can create more user seats and have the capacity to serve more users than otherwise possible. Such flexibility provides users with the ability to offload to differently sized GPU slices or even CPU clusters from within the same notebook for different stages of their pipeline. The MLeRP service also supports batch job submission via a web portal application when they are ready for training and transitioning their code to a more classical GPU HPC environment.
In this workshop we will discuss how users like you can use MLeRP as a stepping stone, allowing you to take on cluster concepts when you’re ready and preparing you for when they eventually outgrow our platform and scale to HPC.
Christoph Bergmeir Dr., University of Granada, SpainMonash University
Christoph Bergmeir is a María Zambrano (Senior) Fellow in the Department of Computer Science and Artificial Intelligence at the University of Granada, Spain, and an Adjunct Senior Research Fellow in the Department of Data Science and Artificial Intelligence at Monash University. Before this, he was a Visiting Research Data Scientist at Meta Inc. (formerly Facebook Inc.) in California in the US, and a Senior Lecturer at Monash University. He has a track record of working in forecasting for capacity planning, sustainable energy, and supply chain, and has led teams that have delivered systems for short-term power production forecasting of wind and solar farms, and energy price forecasting. Christoph holds a PhD in Computer Science from the University of Granada, and an M.Sc. degree in Computer Science from the University of Ulm, Germany. He has over 5,800 citations and an h-index of 30. He has received more than AUD 2.7 million in external research funding. Four of his publications on time series forecasting over the last years have been Clarivate Web of Science Highly Cited Papers (top 1% of their research field).
In this workshop, we will look into time series forecasting with machine learning techniques. Time series forecasting has traditionally been a field of Econometrics and Statistics, but over the last decade, machine learning methods have become competitive and are now oftentimes the methods of choice for forecasting problems. Generic machine learning models such as neural networks, and CNNs. Transformers usually need to be adapted to work well for forecasting tasks, and also other topics like evaluation and benchmarking are not trivial and require special attention.
In this workshop, we will aim to discuss where the field of forecasting is right now, and how machine and in particular deep learning can work for forecasting. We will also touch on the newest developments around foundational models for forecasting and will discuss several specialised subtopics of forecasting, with a theory and a practice session.
Sara King Dr., AARNet
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 a Carpentries Trainer and 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.
Fed Up with Slow or Disrupted Data Transfers?
Ever lost a file transfer halfway through? Or wondered why, despite your fast internet, large data transfers crawl at a snail’s pace? Good news: there are tools that go beyond basics like FileZilla and rsync. Meet Globus—a powerful, secure, and ultra-reliable data transfer solution. With Globus, interrupted transfers are a thing of the past, and data-sharing becomes seamless no matter the distance.
In this session, experts from AARNet will walk you through setting up and using Globus for fast, dependable data transfers. You’ll get answers to key questions: How do you access Globus? What network tweaks might you need? And who can help if you need support?
Join us to learn how to make data transfers easy and efficient!
Collaborative research brings with it the need for the sharing of information, documents and data. Over time the amount of data grows, and it becomes harder to transfer large datasets both internally and externally.
Australia’s Academic and Research Network (AARNet) helps researchers with digital tools to transfer their data safely and securely to where it’s needed.
In this session, you will learn about two of these solutions: FileSender and Globus.
Matthew Belousoff Dr., Monash Institute of Pharmaceutical Sciences
Dr. Matthew Belousoff is a senior research scientist at the Monash Institute of Pharmaceutical Sciences. His scientific interests are in the field of structural biology, where he has used both X-ray diffractions as well as cryogenic electron microscopy techniques to examine the molecular structures of everything from archeal ribosomes to mammalian G-coupled protein receptors.
Single particle cryo-electron microscopy is fast becoming the premier technique for the structural determination of protein structures. The session run by Dr. Matthew Belousoff will involve a lecture providing the theoretical framework for the technique followed by a practical hands-on session (in the context of the MASSIVE High performance compute cluster) to analyse some electron micrograph images and obtain an intermediate resolution 3D reconstruction of an antibody.
Attendees require a laptop and access to M3
Gin Tan , Monash eResearch
Gin Tan is the Associate Director of Monash eResearch. Starting her career in both enterprise and research computing, she eventually found her true passion in high-performance computing (HPC).
Over her eight years at Monash University, Gin has been instrumental in the development and setup of a new HPC cluster and has since grown into a technical leadership role. She enjoys diving deep into the technical aspects of her work while also excelling at translating complex needs into practical, effective solutions.
What unique challenges do staff in Research & Digital Platforms face when it comes to diversity and inclusion? In this question-driven panel, we will share our personal experiences and discuss the challenges faced by underrepresented individuals in our field. We’ll explore what diversity and inclusion in eResearch could look like, why it matters, and practical ways to purposefully cultivate a more inclusive and diverse workplace.
Tara Stewardson , Defence Science and Technology Group
Tara Stewardson is a DevSecOps cadet working in Research IT with the Defence Science and Technology Group. She is simultaneously completing a Bachelor of Science in Computing and Software Systems at the University of Melbourne. As a young, neurodivergent woman in tech, Tara is passionate about active inclusion and the benefits of diversity within the workplace and beyond.
What unique challenges do staff in Research & Digital Platforms face when it comes to diversity and inclusion? In this question-driven panel, we will share our personal experiences and discuss the challenges faced by underrepresented individuals in our field. We’ll explore what diversity and inclusion in eResearch could look like, why it matters, and practical ways to purposefully cultivate a more inclusive and diverse workplace.
Andrew Harrison , Monash University
Andrew Harrison is an Open Scholarship and Data Services Liaison Librarian at Monash University. He has been working at Monash University for more than 30 years. He has been responsible for implementing a digital taped lecture service, a digitisation centre for exam and reading list content, and has been working on Institutional Repositories space for twenty years and has implemented and managed repositories using four different software platforms (ePrints, VITAL/Fedora, and Figshare). He has extensive experience in working with relevant standards, protocols, persistent identifiers, harvesting and migration techniques. He has also been involved in several large national and international projects (including ARROW and NEREUS) looking at improving exposure to Australian research outputs, and has in the past run Monash's ERA evidence repository.
This session will delve into the benefits of publishing your research outputs in open journals and repositories, emphasizing the increased visibility, citation rates, and impact such practices can offer. We'll explore funder requirements and preferences for open publishing and open data, shedding light on how to meet these mandates effectively through utilising Read and Publish agreements and rights retention statements. The session will also explore Monash's institutional data repository, Bridges, showcasing its features for storing, managing, and sharing research data and supplementary materials.
By attending this session, participants will gain a comprehensive understanding of how to navigate the landscape of open-access publishing, fulfil funder requirements, and enhance the dissemination and impact of their research outputs.
Susie Philips , Monash University
Susie Phillips is an Open Scholarship and Data Services Liaison Librarian at Monash University. With several years of experience in scholarly and educational open publishing, she specialises in reading and Publishing agreements and open textbooks. Susie is enthusiastic about advocating for open practices in education and research and enjoys collaborating with academics to support them in publishing their work openly.
This session will delve into the benefits of publishing your research outputs in open journals and repositories, emphasizing the increased visibility, citation rates, and impact such practices can offer. We'll explore funder requirements and preferences for open publishing and open data, shedding light on how to meet these mandates effectively through utilising Read and Publish agreements and rights retention statements. The session will also explore Monash's institutional data repository, Bridges, showcasing its features for storing, managing, and sharing research data and supplementary materials.
By attending this session, participants will gain a comprehensive understanding of how to navigate the landscape of open-access publishing, fulfil funder requirements, and enhance the dissemination and impact of their research outputs.
Sophie Wright , Monash University
Sophie Wright has been working in STEM Librarianship since 2017, where she collaborates closely with researchers and faculty across Science, Engineering, and Information Technology at Monash University. She provides specialised research support and consultation services, helping researchers navigate complex information ecosystems and enhance their capabilities. With expertise in advanced literature searching for reviews, Sophie is focused on leveraging emerging AI tools for research discovery to optimise workflows and maximise research quality. She is committed to making scholarly research discovery and synthesis both accessible and efficient for the Monash community.
Explore cutting-edge AI-powered research tools in this interactive session. We'll dive into how AI can revolutionise your research process, from scoping literature and visualising information landscapes, to summarising key findings. Through hands-on activities and discussions, you'll explore how tools like Elicit, Consensus and Research Rabbit can be integrated into a connected workflow, each adding unique value to your research process. We'll also address important considerations such as transparency and data sources. Whether you're new to AI tools or looking to expand your toolkit, this session will offer valuable insights for researchers at all levels. Join us to share experiences, try out new tools, and explore how AI is transforming the discovery of academic literature.
Please bring your laptop to this session. All necessary tools will be accessible via a web browser, so no software installation is required. We also encourage you to come prepared with your current research topic, as you'll have the opportunity to work on it during the session.
Ines Sincock , Monash University
Ines Sincock is a Liaison Librarian working with the faculties of Engineering, Information Technology, and Science at Monash University. She provides expert guidance on resource discovery, complex search strategies, and scholarly communication. Ines is passionate about empowering researchers through innovative technologies, including integrating AI-powered tools into the research workflow, from literature scoping to knowledge synthesis. Ines is dedicated to helping researchers with their academic discovery process and enhancing the impact of their work.
Explore cutting-edge AI-powered research tools in this interactive session. We'll dive into how AI can revolutionise your research process, from scoping literature and visualising information landscapes, to summarising key findings. Through hands-on activities and discussions, you'll explore how tools like Elicit, Consensus and Research Rabbit can be integrated into a connected workflow, each adding unique value to your research process. We'll also address important considerations such as transparency and data sources. Whether you're new to AI tools or looking to expand your toolkit, this session will offer valuable insights for researchers at all levels. Join us to share experiences, try out new tools, and explore how AI is transforming the discovery of academic literature.
Please bring your laptop to this session. All necessary tools will be accessible via a web browser, so no software installation is required. We also encourage you to come prepared with your current research topic, as you'll have the opportunity to work on it during the session.
Peter Reynolds , Monash University
Peter Reynolds is an experienced librarian in the Engineering, IT and Science team at Monash University Library. With a strong background in supporting innovative technologies, he employs a practical and collaborative approach to support educators, researchers, and students with information discovery, effective use of metrics, reference management, and various aspects of the publishing process. He has contributed to the development of innovative online resources and training sessions. Currently, he is focused on supporting researchers in utilising emerging tools such as ResearchRabbit, Scopus AI, and Elicit for scoping and information discovery.
Explore cutting-edge AI-powered research tools in this interactive session. We'll dive into how AI can revolutionise your research process, from scoping literature and visualising information landscapes, to summarising key findings. Through hands-on activities and discussions, you'll explore how tools like Elicit, Consensus and Research Rabbit can be integrated into a connected workflow, each adding unique value to your research process. We'll also address important considerations such as transparency and data sources. Whether you're new to AI tools or looking to expand your toolkit, this session will offer valuable insights for researchers at all levels. Join us to share experiences, try out new tools, and explore how AI is transforming the discovery of academic literature.
Please bring your laptop to this session. All necessary tools will be accessible via a web browser, so no software installation is required. We also encourage you to come prepared with your current research topic, as you'll have the opportunity to work on it during the session.
Andrew Perry Dr., Monash Genomics and Bioinformatics Platform
Andrew Perry is a software developer and bioinformatician working within the Monash Genomics and Bioinformatics Platform. He completed his PhD in 2007 studying protein structure by Nuclear Magnetic Resonance at the University of Melbourne, followed by several years as a Postdoctoral Fellow in structural biology and structural bioinformatics at Monash University. Today he works on web application and pipeline development, and various genomics analysis and biology-centric data science projects, mostly using Python, R, TypeScript, Unix shell scripting, containerization technologies and HPC.
R is a popular language and environment for data exploration, visualization, and statistical analysis. This workshop will be an introduction to working with data using R, and is aimed at complete beginners to coding. Attendees will learn how to load tabular data, and common data manipulations such as filtering, sorting, and joining tables, and then go on to plotting with ggplot2 and summarizing data. We will cover the R way of thinking about data, including vectors, factors, and data frames, as well as the idea of 'tidy' data. By writing R code, we create a data analysis that is easy to reproduce, modify, and share. The workshop will feature a live demonstration, with frequent opportunities to try what you are learning for yourself. Attendees will be equipped to start exploring the broad range of R packages that are available, both general and specialized.
The material in this workshop will be very similar to Monash Data Fluency's 'Introduction to R' workshops.
Prerequisites
None - This is very much an introductory workshop.
Attendee instructions
Please ensure you have an account on posit.cloud. Monash attendees can use their Monash Google account. You can also use R on your laptop, in which case you will need to install both R and RStudio.
Victoria Mar Prof., Monash University
Prof. Victoria Mar is a Fellow of the Australasian College of Dermatologists, Director of the Victorian Melanoma Service at the Alfred Hospital and Professor of Dermatology at Monash University School of Public Health and Preventive Medicine.
Prof Mar holds an NHMRC Investigator Grant focusing on early diagnosis of melanoma and skin cancer and surveillance of high-risk individuals, including the use of artificial intelligence. She is the Victorian Lead for the Australian Centre of Excellence for Melanoma Imaging and Diagnosis and a Board member of the Melanoma and Skin Cancer Trials Group. She has been a member of the Melanoma Guidelines Working Group since 2015 and the TGA Advisory Committee on Medicines since 2023.
Abishek Sriramulu Dr., Tymestack
Abishek Sriramulu is the Founder of Tymestack, a forward-thinking startup focused on advancing AI-driven forecasting and optimization solutions. With both a PhD and a Master's in Data Science from Monash University, Dr. Sriramulu has dedicated his career to harnessing artificial intelligence for improved decision-making and enhanced outcomes.
Specialising in forecasting, Dr. Sriramulu brings extensive experience in developing and deploying production-grade machine learning systems across a variety of industries. His research interests span graph neural networks, multi-modal analytics, and constrained machine learning, with a clear focus on addressing complex, real-world challenges. Passionate about making cutting-edge AI technologies more accessible, Dr. Sriramulu is committed to driving meaningful impact across diverse applications.
In this workshop, we will look into time series forecasting with machine learning techniques. Time series forecasting has traditionally been a field of Econometrics and Statistics, but over the last decade, machine learning methods have become competitive and are now oftentimes the methods of choice for forecasting problems. Generic machine learning models such as neural networks, and CNNs. Transformers usually need to be adapted to work well for forecasting tasks, and also other topics like evaluation and benchmarking are not trivial and require special attention.
In this workshop, we will aim to discuss where the field of forecasting is right now, and how machine and in particular deep learning can work for forecasting. We will also touch on the newest developments around foundational models for forecasting and will discuss several specialised subtopics of forecasting, with a theory and a practice session.
Amanda Walmsley Dr., Monash University
Amanda has a PhD specialising in molecular biology and a Masters of Law specialising in Intellectual Property Law. Through her own research and in managing research at the department, faculty and university level, she has experience across many fields of science, medicine, engineering, commercialisation, law and technology implementation at a national and international level.
Throughout her career, she has developed and reviewed a large number of successful funding proposals. While with the World Mosquito Program at Monash University, she developed and submitted 13 proposals in 3 years, 10 of which were successful, resulting in over AU$142 million in funding for the Program. She has substantial experience writing, editing and reviewing a broad range of complex documents aiming to teach grantpersonship and value-add. Amanda has been with Monash for 15 years and with the MRO for 18 months.
"Major Initiatives" can mean different things to different people. Most of the time Major Initiatives are those worth over $3M, however, from a university perspective, it can mean any initiative of significance to the university. Significance could be due to the large number of applicants (ARC Discovery Projects, DECRAs, Future Fellowships ) or the prestige/funding involved (ARC Centres of Excellence, Australian Laureates, and Industrial Transformation Program). Using tips and case studies, this presentation takes a look at the schemes that should be on the horizon of a mid-career researcher and the strategies to be taken to develop a strong proposal.
Currently securing grant funding is a real challenge due to the high level of competition across the Australian research funding landscape. This presentation will explore the current funding trends and provide practical tips on preparing a competitive grant application. It will cover the importance of presenting a clear value proposition, targeting the needs of the funding body, and what items you can prepare now to set yourself up for future successes such as building consumer engagement and partnerships.
Neil Owens , Monash University
Dr Neil Owens is an experienced research development manager with experience in both university and medical research institute settings. He completed a PhD in cardiovascular neuroscience (UniMelb), furthering his research training with postdoctoral positions at The Florey and RMIT where he attracted Heart Foundation grants and an NHMRC Early Career Fellowship.
A change in career direction led him to the Faculty of Medicine Nursing and Health Sciences at Monash, where he developed numerous large projects. He then moved to Prince Henry’s Institute where he established and managed the grants office. Since then, he has developed funding applications in university, medical research institute, and commercial consulting settings.
In Dec 2022, he commenced his current role as Senior Manager MRFF initiatives, where he leads Monash’s development efforts aimed at increasing the amount MRFF funds secured.
Neil has extensive experience in developing applications for NHMRC, MRFF, ARC and philanthropy, having worked with researchers across STEM and HASS disciplines. He is passionate about positioning research that has meaning and impact for the community. Further details on Neil's experience can be found on LinkedIn.
"Major Initiatives" can mean different things to different people. Most of the time Major Initiatives are those worth over $3M, however, from a university perspective, it can mean any initiative of significance to the university. Significance could be due to the large number of applicants (ARC Discovery Projects, DECRAs, Future Fellowships ) or the prestige/funding involved (ARC Centres of Excellence, Australian Laureates, and Industrial Transformation Program). Using tips and case studies, this presentation takes a look at the schemes that should be on the horizon of a mid-career researcher and the strategies to be taken to develop a strong proposal.
Currently securing grant funding is a real challenge due to the high level of competition across the Australian research funding landscape. This presentation will explore the current funding trends and provide practical tips on preparing a competitive grant application. It will cover the importance of presenting a clear value proposition, targeting the needs of the funding body, and what items you can prepare now to set yourself up for future successes such as building consumer engagement and partnerships.
Zhuang Li Dr., Monash University
Zhuang Li is a Research Fellow and an incoming Lecturer at RMIT University. His research centres on low-resource and multicultural natural language processing, generative AI, and cross-cultural dialogue systems. With professional experience at Microsoft and Monash University, Zhuang brings expertise in data optimisation and multilingual AI research.
This workshop will provide a brief understanding of textual data processing and analysis using Natural Language Processing (NLP) techniques. Participants will engage with foundational methods for text processing and analysis, followed by advanced applications in generative AI for text analysis. Through hands-on sessions and interactive discussions, participants will learn how to process, analyze, and apply AI models to textual data, enabling a better understanding of how AI systems interpret language. The workshop will cover practical skills in handling textual data and applying generative models for more sophisticated analyses, providing attendees with both theoretical knowledge and practical expertise.
Simon Michnowicz , Monash eResearch
Simon Michnowicz works at Monash e-Research in the High Performance Computing Team. He is passionate about using the best in IT technologies to assist researchers in doing their work more effectively.
Simon works closely with the Monash University Engineering Team - DeepNeuron, and has supervised several student projects and teams that have won awards in international Student Cluster Competitions.
This tutorial will be an introduction to regular expressions for those who have never used them before. Regular expressions are a pattern-matching technology, found in most search engines and commonly used in Life Sciences. This tutorial will explain what they are, how they work, and where to get more information.
Attendee instructions
Attendees need to bring a laptop with an internet connection so that they can access a Web Page.
Debjit Bhowmick Dr., Monash University
Dr. Debjit Bhowmick is a Postdoctoral Research Fellow at Monash University with a strong background in Transportation Engineering and Geospatial Information Science. He specialises in the analysis of spatial datasets and their application in urban mobility. His research focuses on bike riding behaviour that supports planners and policymakers in developing data-driven infrastructure and policy solutions to promote sustainable and active transportation.
Want to learn how to create your own maps? This 2-hour workshop introduces you to QGIS, a powerful and free tool for working with maps and spatial data. No experience with GIS? No problem! We’ll start from scratch, showing you how to load data, explore it on a map, and style it to make it visually appealing. By the end of the session, you’ll have built your own map and exported it, ready to share. Come ready to learn, and let’s have some fun with maps!
Attendee instructions
Please install QGIS on your laptops prior to attending the workshop so we can maximise the use of time. QGIS is open-source and completely free to download and use. Check out the following link. QGIS
Riccardo Bonacci , Monash University
Riccardo Bonacci is a PhD candidate at Monash university in the school of Physics and Astronomy. He is a part of the LHCb collaboration, a particle physics experiment situated at the Large Hadron Collider at CERN (Geneva, Switzerland). His research focuses on analysing data taken from the LHCb, and using this to study particles containing the beauty and charm quarks.
Neural networks (or perceptrons) have become increasingly popular over the last 30 years, and have been shown to be multidisciplinary. The original idea for the neural network stems from a simplistic interpretation of how our brain works, with neurons (or nodes) sending signals to other neurons, which in turn ’activate’ (or ’fire’) to send an output signal. This is truly an over-simplified model of how our brain works, though the mathematical description of this network has shown itself to be extremely flexible in learning structures and patterns from large data sets. This is to an extent that they are known as universal interpolaters.
In this workshop, we will build step-by-step our own neural networks to test on mock data. We will also compare the performance of the networks we created to ones created by PyTorch, which is a common machine learning library used on Python. This workshop will be performed using Python on a jupyter notebook.
Attendee instructions
Working knowledge of common Python and its common modules, e.g. Numpy is recommended.
Please have Python 3.8> and the Numpy, Matplotlib and PyTorch modules installed. Make sure you also can run Jupyter notebook.
Rob J Hyndman Prof., Monash University
Rob J Hyndman FAA FASSA is a Professor of Statistics in the Department of Econometrics and Business Statistics at Monash University, and an elected Fellow of both the Australian Academy of Science and the Academy of Social Sciences in Australia. He is the author of over 200 research papers and 5 books in statistical science. In 2007, he received the Moran medal from the Australian Academy of Science for his contributions to statistical research, especially in the area of statistical forecasting. In 2021, he received the Pitman medal from the Statistical Society of Australia. For over 30 years, Rob has maintained an active consulting practice, assisting hundreds of companies and organizations around the world. He has won awards for his research, teaching, consulting and graduate supervision.
I will demonstrate the digital tools that underpin the efficiency and reproducibility of my research workflow. Utilizing GitHub as the platform for version control and collaboration, and R as a foundational tool, I leverage the renv package for managing project-specific R dependencies, and the targets package to avoid unnecessary computation. I employ Quarto for generating multiple versions of my research papers for online repositories and journal submissions, ensuring seamless integration of code and text, without duplication. I'll illustrate the workflow using a recent paper I coauthored on Forecasting Interrupted Time Series.
Linda Kalejs A/Prof., La Trobe University
Nick May , La Trobe University
Sam Ryan Dr., La Trobe University
Eva Fisch , Monash University
Maria del Mar Quiroga Dr., Melbourne Data Analytics Platform
Dr. Maria del Mar Quiroga is a Senior Research Data Specialist at the Melbourne Data Analytics Platform, where she works with researchers across all faculties and domains to bring the benefits of data-led methods to their fields. She is currently leading the HASS Taskforce, an exciting initiative that aims to empower and inspire researchers in the Humanities, Arts, and Social Sciences to embrace the potential of digital methodologies and create communities of practice and peer support.
In 2022, at the University of Melbourne, we established the HASS Taskforce: an initiative to help researchers in the Humanities, Arts, and Social Sciences strengthen their digital research literacy through targeted, hands-on digital training and support. In this session, we will discuss the challenges and opportunities in working towards a more digitally engaged, capable, and empowered humanities, arts, and social science academy.
Stephen Firth , Monash University
Stephen Firth holds a Bachelor of Applied Science in Biotechnology, followed by a Master’s Degree in Research. Stephen spent two years in Virology, before transitioning to a decade-long role in human molecular genetics. In 2002, he established the confocal microscopy facility at the Centre for Cellular and Molecular Biology at Deakin University. In 2005, Stephen joined Monash University as an Optical Microscopist at the Monash Micro Imaging Optical Microscopy Core Facility, becoming the Manager of the Clayton facility in 2012, and later, the Manager of all three MMI facilities in 2020.
For the past two decades, Stephen has been deeply committed to teaching microscopy to biologists, with a strong emphasis on practical, hands-on learning.
What unique challenges do staff in Research & Digital Platforms face when it comes to diversity and inclusion? In this question-driven panel, we will share our personal experiences and discuss the challenges faced by underrepresented individuals in our field. We’ll explore what diversity and inclusion in eResearch could look like, why it matters, and practical ways to purposefully cultivate a more inclusive and diverse workplace.
Tim Powers Dr., Monash eResearch
Dr. Tim Powers leads Monash Statistical Consulting Services, where he mentors over 200 PhD students and research staff annually in statistical analysis, leveraging both academic and industry expertise. His recent work spans interdisciplinary university research projects, providing guidance on large-scale survey design, statistical analysis, and comprehensive project coordination. With a solid background in business operations and management development, Tim has consulted for federal and state governments, associations, and industry groups, utilising surveys, focus groups, and interviews to gain insights into membership and client needs. Known for engaging deeply with stakeholders, he delivers data-driven solutions to complex challenges, bridging academic rigour with practical, impactful outcomes across both academic and industry settings.
When it comes to survey data collection for research two platforms seem to be duking it out - Qualtrics and REDCap. One is a sleek, commercial, easy-to-use platform widely used in industry. The other is a university-based, community-enabled workhorse. So which one should you use? What things will you need to trade off when choosing one over the other? How do they compare head-to-head in survey design, usability, analysis, visualisation, and auditing?
Come see our “Great Debate” between experienced researchers, statisticians and technical experts who will help you to make up your mind.
David Shipman , Monash EMU (Epidemiological Modelling Unit)
David Shipman is the lead software engineer at Monash EMU (Epidemiological Modelling Unit). He has worked in the (rather niche!) field of modelling platform development for several decades, across multiple domains including finance, hydrology, and epidemiology. He specialises in Python, numerical computing and expressive domain-specific APIs, with an interest in signal processing and compiler development. He eventually realised that code is a means to an end - the real work is understanding users and what they want to express - then building tools to empower them.
Our team focuses on the development of epidemiological time-series models using Python, often in time-critical contexts, so our work requires a combination of fast execution and rapid, expressive model development. This talk is about the journey our primary modelling toolkit, Summer2 has taken, particularly with regards to performance, and how we arrived at Jax - a fast, auto-differentiating compiler from Google, which now forms the basis for much of our new model development.
There will be a technical introduction to Jax and its surrounding ecosystem, a discussion of our experiences in converting existing modelling code, and finally, how it influences our design choices and modelling work (plus some important lessons learned along the way!)
While the technical content of this talk relates to numerical computing in Python, it aims to be broadly accessible to anyone with an interest in modelling or the software development process in general.
Kit Greenhill , Australian Research Data Commons (ARDC)
Kit Greenhill is ARDC’s Skills Development Lead (HASS & Indigenous). She helps researchers build better skills to create, analyse and retain HASS and Indigenous data. She applies expertise developed as a university lecturer and a professional librarian to support HASS and Indigenous researchers and data custodians to build communities identifying and addressing skills gaps.
Get hands-on with 2 tools from the ARDC HASS and Indigenous Research Data Commons, the Crate-O metadata editor and the Trove Data guide. After 2 forty minute deep dives, learn how other parts of the Research Data Commons help researchers solve another 8 research challenges, in a series of 5-minute lighting tours.
By the end of the session, you will know how to use a tool to package your research data and its metadata together in an RO-Crate and be better equipped to locate and manipulate data from the National Library's Trove research portal. You will also have new leads for research with Indigenous data; social media data; data about creative arts; and social sciences data.
Attendee instructions
Please bring your own laptop. Tablets and hand held devices are not suitable for this workshop.
No software installation or pre-reading is required.
You will need a sample data set to package into an RO-Crate. This should consist of a specific folder (directory) with at least one data file in it - the format and content of the data file(s) is not important for this exercise. [We will provide a sample set of data for those who do not bring their own].
Optionally, participants can look at these resources before the session:
Crate-O and Trove Data Guide
Simon Musgrave , Language Data Commons of Australia
Simon Musgrave is the Training and Communication Lead for the Language Data Commons of Australia and an Adjunct Research Fellow in the School of Languages, Literatures, Cultures and Linguistics, Monash University. Starting as a syntactician specialising in Austronesian languages, his research interests extended to cover areas including language endangerment, communication in medical settings and the use of technology for linguistic research. This last interest, through work on the Australian National Corpus project, led to work in the digital humanities and to his current work in research infrastructure for the humanities.
Concordances are a very useful tool for anyone who works with textual data. Concordancing tools (also referred to as Keyword in Context or KWIC tools) provide us with a listing of all occurrences of a word in a text along with some surrounding context. A concordance is therefore an excellent starting point to explore how a word is used in a text. Most KWIC tools also have the capability to sort results according to the context of the instances, by preceding words or following words or a combination of the two and these capabilities allow us to extract more specific information from concordances.
In this workshop, you will:
Attendee instructions
Attendees must bring their own computer and are encouraged to bring text which they are interested in exploring (but sample text will be provided for those who cannot do this).
Installing Antconc is also recommended.
Get hands-on with 2 tools from the ARDC HASS and Indigenous Research Data Commons, the Crate-O metadata editor and the Trove Data guide. After 2 forty minute deep dives, learn how other parts of the Research Data Commons help researchers solve another 8 research challenges, in a series of 5-minute lighting tours.
By the end of the session, you will know how to use a tool to package your research data and its metadata together in an RO-Crate and be better equipped to locate and manipulate data from the National Library's Trove research portal. You will also have new leads for research with Indigenous data; social media data; data about creative arts; and social sciences data.
Attendee instructions
Please bring your own laptop. Tablets and hand held devices are not suitable for this workshop.
No software installation or pre-reading is required.
You will need a sample data set to package into an RO-Crate. This should consist of a specific folder (directory) with at least one data file in it - the format and content of the data file(s) is not important for this exercise. [We will provide a sample set of data for those who do not bring their own].
Optionally, participants can look at these resources before the session:
Crate-O and Trove Data Guide
Meirian Lovelace-Tozer , Australian Research Data Commons (ARDC)
Meirian Lovelace-Tozer is a Skills Development Lead (Services) at the Australian Research Data Commons (ARDC). With over 10 years of experience in education, Meirian is committed to making an impact through empowering Australian research communities with a competitive advantage. Meirian delivers training and resources that support researchers to effectively leverage ARDC services. For more information and to contact Meirian, please visit https://meirian.gitbook.io/home
Does your computer struggle with your research workload? Would you like to access extra resources and share a computer with collaborators?
Whether it's data analysis, simulation, or other computing work, the ARDC Nectar Research Cloud provides researchers with more computational power. This service gives you access to fast, secure, and powerful cloud computers, helping you to accelerate your research!
Cooper Smout Dr.,
Dr Cooper Smout is a designer, researcher and lifelong student of human behaviour. Inspired by a Vipassana meditation retreat, he left a promising career in architecture to study Psychology and Neuroscience at the University of Queensland, winning prizes for both his Honours and PhD theses in the neural mechanisms of visual awareness.
Cooper's passion for good design found a counterpart in the scholarly publishing industry, igniting a new interest in Open Science and the problem of cultural change in academia. He founded the world's first collective action platform for researchers (Free Our Knowledge) and spent several years campaigning for open and reproducible research practices, later drawing on these experiences to design a decentralised peer-review model with disruptive potential. Realising he could make faster progress outside of academia, he founded a citizen-science project (Open Heart + Mind) and prototyped by peer-reviewing contributions to community gatherings, before validating the model for use in academia by peer-reviewing contributions to Open Science conferences.
Alongside his interests in Open Science and decentralised technologies, Cooper enjoys playing games, snowboarding, rock climbing, meditating, dancing, and spending time in nature.
In this talk, I'll introduce WISDOM, an open-value accounting framework that empowers communities to recognise diverse contributions and directly reward contributors for their efforts.
I'll begin with an overview of the framework, showing how it began life as an open peer-review model and evolved through active experimentation to become a generalisable framework for diverse communities. I'll highlight the key innovation: the use of pairwise comparisons as both an inclusive review protocol and a 'standard unit of contribution', which serve to peg the value(s) of all other contributions in a decentralised and autonomous manner.
I'll demonstrate the framework's adaptability by sharing data from diverse communities in the arts, science and technology sectors, before focussing on an academic use case where we used WISDOM to quantify the value of contributions to the two most recent AIMOS metaresearch and open science conferences.
I'll show how WISDOM
(a) revealed community values and several contributions that might otherwise have gone unnoticed,
(b) incentivised open peer review, and
(c) estimated contribution value on multiple dimensions of interest.
I'll highlight how WISDOM facilitates metaresearch by sharing the results of several analyses we've conducted, then invite questions and suggestions from the audience.
I'll close with a vision for how WISDOM can help connect diverse communities in the research space and beyond, along with an invitation to use WISDOM to review, recognise and reward contributions to ResBaz itself.
Kevon Graham , Monash University
Kevon Graham is a dynamic Information Security Specialist with a strong passion for aligning application security architecture plans and processes with industry standards and business objectives. He has extensive experience in developing and testing security frameworks for cloud-based and on-premise applications, and wireless infrastructure while working within agile development environments.
Recognized for excellence in conducting comprehensive information security assessments and architecture reviews, Kevon is skilled in directing cybersecurity auditing programs along with developing network defence strategies and data protection policies. He is also adept at conducting cyber security awareness training sessions, sharing best practices for managing security testing cycles, and leading cross-functional teams to deliver secure, high-availability solutions. A proactive professional, Kevon excels at analysing security policies, identifying vulnerabilities, and implementing strategic improvements to enhance organizational security.
Join Monash University's Application Security team to deploy and run an intentionally vulnerable web application and implement fixes within your own NECTAR cloud instance. In this workshop, you will get a peek into life as an offensive security expert and learn how easy it can be to resolve some major security flaws
Tomasz Skora , GitLab
Tomasz Skora is a Staff Solution Architect at GitLab, based in Melbourne. He helps organisations achieve strategic objectives, focusing on DevSecOps excellence and digital transformation. He has extensive experience in implementing and driving impactful DevSecOps initiatives, resulting in improved software delivery, compliance, and security.
Discover how GitLab supports collaborative research by enabling teams to share code, data, and documentation effectively. Learn how InnerSourcing principles can promote knowledge sharing and streamline efforts across different projects.
Nitika Kandhari , Monash Genomics and Bioinformatics Platform
Nitika Kandhari is a bioinformatician with extensive experience in genomics and computational biology, currently working with the Monash Genomics and Bioinformatics Platform. She earned her Master’s degree in Bioinformatics and is pursuing her PhD at Monash University's RNA Systems Biology Lab, analyzing high-throughput transcriptomic data. Additionally, Nitika has been actively involved in promoting data fluency within the scientific community at Monash, delivering workshops on programming in R, Python, Unix/CLI, and other essential data analysis and bioinformatics tools.
R is a popular language and environment for data exploration, visualization, and statistical analysis. This workshop will be an introduction to working with data using R, and is aimed at complete beginners to coding. Attendees will learn how to load tabular data, and common data manipulations such as filtering, sorting, and joining tables, and then go on to plotting with ggplot2 and summarizing data. We will cover the R way of thinking about data, including vectors, factors, and data frames, as well as the idea of 'tidy' data. By writing R code, we create a data analysis that is easy to reproduce, modify, and share. The workshop will feature a live demonstration, with frequent opportunities to try what you are learning for yourself. Attendees will be equipped to start exploring the broad range of R packages that are available, both general and specialized.
The material in this workshop will be very similar to Monash Data Fluency's 'Introduction to R' workshops.
Prerequisites
None - This is very much an introductory workshop.
Attendee instructions
Please ensure you have an account on posit.cloud. Monash attendees can use their Monash Google account. You can also use R on your laptop, in which case you will need to install both R and RStudio.
Adele Barugahare , Monash Genomics and Bioinformatics Platform
Adele Barugahare is a bioinformatician working with the Monash Genomics and Bioinformatics Platform and Stephen Turner’s research lab. She has extensive experience with epigenetics and transcriptomics and is an experienced R programmer. Adele has helped develop, administrate and teach multiple workshops at Monash.
R is a popular language and environment for data exploration, visualization, and statistical analysis. This workshop will be an introduction to working with data using R, and is aimed at complete beginners to coding. Attendees will learn how to load tabular data, and common data manipulations such as filtering, sorting, and joining tables, and then go on to plotting with ggplot2 and summarizing data. We will cover the R way of thinking about data, including vectors, factors, and data frames, as well as the idea of 'tidy' data. By writing R code, we create a data analysis that is easy to reproduce, modify, and share. The workshop will feature a live demonstration, with frequent opportunities to try what you are learning for yourself. Attendees will be equipped to start exploring the broad range of R packages that are available, both general and specialized.
The material in this workshop will be very similar to Monash Data Fluency's 'Introduction to R' workshops.
Prerequisites
None - This is very much an introductory workshop.
Attendee instructions
Please ensure you have an account on posit.cloud. Monash attendees can use their Monash Google account. You can also use R on your laptop, in which case you will need to install both R and RStudio.
Shani Amarasinghe Dr., Monash University
Shani Amarasinghe is currently working as a bioinformatics research officer with over a decade of experience, producing impactful research across various biological disciplines while raising a young family. With a career spanning >1000 citations since 2018, Shani has developed multiple bioinformatics tools used widely by the research community. After completing a PhD in bioinformatics focused on bulk transcriptomics from the University of Adelaide, she has worked extensively with cutting-edge technologies like long-read sequencing (ONT, PacBio) and single-cell techniques (scRNA-Seq, scATAC-Seq). Currently, she’s working on intestinal regeneration-focused single-cell, spatial and bulk transcriptomics data analyses at the Abud and Jarde laboratories at the BDI.
Shani and Andrew will be discussing their experience analysing gut regeneration and colorectal cancer (CRC) using the Nanotring GeoMx and CosMx platforms respectively. They will discuss the advantages and disadvantages of each and the types of research questions spatial transcriptomics can be used to answer. They will also share the results of some of the analyses that they have performed, with some practical suggestions for analysing your own spatial transcriptomics data.
Andrew Pattison Dr., Monash University
Andrew Pattison is currently working as a father to a 21 month old toddler and 4 month old baby with a secondary role as a computational biologist studying colorectal cancer in the Abud lab at Monash University. He obtained his PhD in biochemistry/computational biology from Monash University in 2018. His background is in sleeping at night, RNA biology, cancer genomics and scRNA-Seq analyses with a focus on immunotherapy. While he hasn’t recently spent too much time working in his old field, he is very passionate about one day returning to it. Currently he is analysing single cell/spatial transcriptomic data and supporting the Abud lab members with their computational analyses.
Shani and Andrew will be discussing their experience analysing gut regeneration and colorectal cancer (CRC) using the Nanotring GeoMx and CosMx platforms respectively. They will discuss the advantages and disadvantages of each and the types of research questions spatial transcriptomics can be used to answer. They will also share the results of some of the analyses that they have performed, with some practical suggestions for analysing your own spatial transcriptomics data.
Richard Beare A/Prof., Monash University
Richard Beare is a research engineer with over 20 years experience in development and translation of computational methods to medical research and clinical practice. He is currently the technical lead for the National Centre for Healthy Ageing data platform, with a focus on applications of natural language processing to improve coding of electronic health record data for research purposes, and a Principal Research Fellow with the Murdoch Children's Research Institute Developmental Imaging group. Previous research areas include geospatial modelling to optimise service delivery for acute stroke, advanced tractography for paediatric neurosurgery and the use of ultra low field MRI to support randomised control trials in low and middle income countries.
A wealth of health data is collected and stored electronically, yet much of this data remains siloed and underutilised. Maximising the use of improved electronic data collections, linkage systems that enable data to be linked at the person level and analytic advancements have great potential to maximise data sharing and increase the potential for ‘big data’ research. Opportunities exist to better deliver higher-impact research at scale through capacity building and knowledge sharing in data linkage.
This workshop will introduce how large datasets can be reliably linked and used to provide novel insights, using health research as an example. Attendees will also be introduced to M-Link, a community of practice developed to support and oversee data linkage practice at Monash University. Areas of focus include: knowledge sharing; ethics, governance and data security; technical infrastructure and linkage methods and access to external administrative datasets.
Milinda Abayawardana , Monash University
Milinda Abaywardana has a diverse background in aviation, mechanical engineering, and epidemiological modelling. His expertise encompasses database design, Python, Power BI, and data analysis. At Monash University, he has been involved in several projects. These include integrating outputs from SEIR compartmental models at the Epidemiological Modelling Unit within the School of Public Health and Preventive Medicine. During the peak of the COVID-19 pandemic, he designed, developed, and delivered Power BI dashboards that provided critical insights to policymakers in the Philippines, Malaysia, Sri Lanka, Vietnam, Nepal, and Australia. Driven by a passion for all things data, he is currently collaborating with the office of the Pro-Vice Chancellor of Research Infrastructure to create a research insights value pipeline that connects awarded funding to utilisation spending and publication outcomes. He holds a B.Eng from Nanyang Technological University and a Masters in Data Science from Monash University.
Research infrastructure is a crucial element of any university. However, in many cases, data on infrastructure utilisation—when it exists—is often siloed, and key performance indicators (KPIs) are limited to isolated contexts. To address this, a more integrated reporting framework is needed, enabling universities to assess the value of their research equipment and services objectively. In this session, we will explore Monash University's efforts to overcome these challenges, focusing on integrating four previously siloed datasets: Research Awards, Research Income, Research Utilization, and Research Outputs. If time allows, we will also delve into the challenges and successes encountered throughout this process.
Chris Hines Dr., Monash eResearch
Chris Hines has been part of the Australian eResearch sector for longer than he'd like to admit (even to himself). With a background in physics, he brings the classic physicist's confidence that every problem could be solved if we'd just approximate our cows as spheres. An adaptable systems administrator, programmer, and HPC consultant, Chris applies his expertise wherever Monash University and partners' research needs him most.
HPC (High-performance Computing) can seem very intimidating, with arcane rules about what you are and are not allowed to do. It's off-putting and a barrier to entry. But at the end of the day, HPC systems are run by friendly people who want to help you do research.
To break down that barrier I'll try to explain the who what where why and how of HPC:
Chelsea Cobb (Moderator) Dr., Monash University
Chelsea Cobb is the Director of Research Infrastructure at Monash University, overseeing the operational sustainability and strategic growth of the university's research infrastructure portfolio. She also works to elevate the visibility of Monash’s Research Platforms within the research community.
Previously, Chelsea served as Associate Director of Research Translation and Innovation at the University of Melbourne, where she developed research translation strategies and managed key industry partnerships. She holds a PhD in genomics from Monash University and has extensive experience in corporate consulting, having worked at PwC on R&D tax incentives, sustainability, and social impact initiatives aimed at improving STEM education in Australia.
Outside of work, Chelsea is a mum of two kids and two dogs who enjoys exercising and spending time outdoors!
What unique challenges do staff in Research & Digital Platforms face when it comes to diversity and inclusion? In this question-driven panel, we will share our personal experiences and discuss the challenges faced by underrepresented individuals in our field. We’ll explore what diversity and inclusion in eResearch could look like, why it matters, and practical ways to purposefully cultivate a more inclusive and diverse workplace.
Greg D'Arcy , AARNet
Greg D'Arcy is an experienced Research Analyst and Program Manager working across several product development projects and research collaborations at AARNet. Greg has over twenty years’ experience in the research and education sectors working across several large-scale digital transformation and infrastructure initiatives.
Fed Up with Slow or Disrupted Data Transfers?
Ever lost a file transfer halfway through? Or wondered why, despite your fast internet, large data transfers crawl at a snail’s pace? Good news: there are tools that go beyond basics like FileZilla and rsync. Meet Globus—a powerful, secure, and ultra-reliable data transfer solution. With Globus, interrupted transfers are a thing of the past, and data-sharing becomes seamless no matter the distance.
In this session, experts from AARNet will walk you through setting up and using Globus for fast, dependable data transfers. You’ll get answers to key questions: How do you access Globus? What network tweaks might you need? And who can help if you need support?
Join us to learn how to make data transfers easy and efficient!
Chris Myers , AARNet
Chris Myers has 30 years of experience working in the telecommunications and higher education sector, especially in large data projects. Chris supports a wide array of data movement projects in training, consultation, and design in the areas of astro/high energy physics, HPC, scientific instruments, archives and film, cloud solutions, data centre fabrics and cybersecurity.
Fed Up with Slow or Disrupted Data Transfers?
Ever lost a file transfer halfway through? Or wondered why, despite your fast internet, large data transfers crawl at a snail’s pace? Good news: there are tools that go beyond basics like FileZilla and rsync. Meet Globus—a powerful, secure, and ultra-reliable data transfer solution. With Globus, interrupted transfers are a thing of the past, and data-sharing becomes seamless no matter the distance.
In this session, experts from AARNet will walk you through setting up and using Globus for fast, dependable data transfers. You’ll get answers to key questions: How do you access Globus? What network tweaks might you need? And who can help if you need support?
Join us to learn how to make data transfers easy and efficient!
John Liman , Monash University
John Liman is the Senior Data Manager at Monash University’s School of Public Health and Preventive Medicine. He oversees the data management of five major Clinical Quality Registries, of which four out of five are using REDCap. John has been using REDCap for more than 7 years.
When it comes to survey data collection for research two platforms seem to be duking it out - Qualtrics and REDCap. One is a sleek, commercial, easy-to-use platform widely used in industry. The other is a university-based, community-enabled workhorse. So which one should you use? What things will you need to trade off when choosing one over the other? How do they compare head-to-head in survey design, usability, analysis, visualisation, and auditing?
Come see our “Great Debate” between experienced researchers, statisticians and technical experts who will help you to make up your mind.
Sze-Ee Soh A/Prof., Monash University
Sze-Ee is an Associate Professor in the School of Primary and Allied Health Care at Monash University. She is a physiotherapist by background and is currently the Course Director of the Doctor of Physiotherapy program. Her research has spanned the areas of chronic disease, health services, patient-reported outcomes and the psychometric properties of measurement tools. She has a broad range of experience in developing and using surveys as part of her teaching, clinical and research work. Sze-Ee also delivers a survey design short course alongside her colleagues at the School of Public Health and Preventive Medicine.
When it comes to survey data collection for research two platforms seem to be duking it out - Qualtrics and REDCap. One is a sleek, commercial, easy-to-use platform widely used in industry. The other is a university-based, community-enabled workhorse. So which one should you use? What things will you need to trade off when choosing one over the other? How do they compare head-to-head in survey design, usability, analysis, visualisation, and auditing?
Come see our “Great Debate” between experienced researchers, statisticians and technical experts who will help you to make up your mind.
Carina Kemp Dr., Amazon Web Services (AWS)
Dr. Carina Kemp is the Global Lead for Academic Research at AWS. Carina is passionate about enabling researchers to leverage the power of the cloud to accelerate their research. Previously Dr. Kemp was the Director of eResearch at AARNet where she led Research Cloud Services enabling researchers with tools and advice for all their data and digital infrastructure needs. Dr. Kemp joined AARNet from Geoscience Australia, where she provided scientific and digital leadership as the CIO. At GA, Dr. Kemp also led the development of virtual laboratories and high-performance computing to enable geophysical applications for pre-competitive dataset delivery. In her career, Dr. Kemp has always strived to enable research and innovation working for higher ed, industry, government and NGOS. Her interests include open data, data science, machine learning, high-performance computing, communication of science, improving collaboration across science and information technology disciplines, and encouraging leadership and women in science.
Dr. Carina Kemp is the Global Lead for Academic Research at AWS. Carina is passionate about enabling researchers to leverage the power of the cloud to accelerate their research. In her career, Dr. Kemp has always strived to enable research and innovation working for higher ed, industry, government and NGOS.
In today’s world of complex global challenges, interdisciplinary research is vital for driving innovation and finding comprehensive solutions. This presentation explores how Amazon Web Services (AWS) is revolutionizing interdisciplinary research efforts across regional and global scales.
We’ll examine how AWS’s cloud computing infrastructure breaks down barriers between academic disciplines, enabling seamless collaboration. Case studies will demonstrate AWS tools being used to address pressing issues in climate science,healthcare, and social sciences.
The presentation will highlight international collaborations powered by AWS, showcasing how the platform’s scalability and accessibility democratize research capabilities globally. Key topics include:
1. AWS services tailored for interdisciplinary research
2. Data sharing and integration across disciplines
3. Machine learning and AI applications in cross-disciplinary studies
4. Challenges and opportunities in global research collaborations
5. The future of interdisciplinary research in the cloud
Attendees will gain insights into how AWS is reshaping interdisciplinary research, fostering innovation, and contributing to the resolution of complex global issues through enhanced collaboration and data-driven approaches.
Richard Ferrers Dr., Australian Research Data Commons (ARDC)