Event schedule

Key Story - Nature conservation

Moving around from a global, environmental NGO (the Nature Conservancy), to government (Queensland's Chief Scientist) to academia and all the science involved.

Key Story - Exploring Australian GLAM data

More and more institutions in the GLAM sector (Galleries, Libraries, Archives, and Museums) are sharing their collection data online, but what is it, and how do you use it? In this talk, I'll survey the types of data available – including metadata, images, OCRd text, and transcriptions – and explore possible research topics. Using tools and examples from the GLAM Workbench, I’ll show how GLAM data can be harvested, aggregated, analysed, and visualised. What can GLAM data tell us about Australian history, society, and culture?

Key Story - Survey Design

In this talk, Professor Low-Choy will cover the dos and don'ts of survey design and how to avoid the pitfalls of poorly designed surveys.

Key Story - Soils 4 Science

Soils 4 Science is a citizen science project based at UQ's IMB that is dedicated to finding new antibiotics needed in the fight against the scourge of drug-resistant infections, better known as superbugs. More than half of all antibiotics available worldwide have been developed from microbes found in soil and nature, and Queensland is one of the most biodiverse environments in the world, spanning beaches, rainforests, wetlands and deserts. This vast, untapped landscape is ripe for the discovery of microbes that could be developed into new antibiotics, anti-fungals and other medicines.

Registration (in the foyer)

Welcome by Professor Joe Shapter (Auditorium)

Evening Reception

Morning tea (in the foyer)

The best time to talk with speakers and attendees

Lunch (in the foyer)

The best time to talk with speakers and attendees

Knowledge Bazaar (in the foyer)

The Knowledge Bazaar is an open networking session where attendees can find like-minded people.

Software Containers for Reproducible (Neuro) Science

This course will introduce software containers for reproducible data analysis. We will first introduce what containers are (you might have heard of Docker or Singularity already?). Then we will show examples from the neuroimaging domain how such containers can be built and used on different operating systems and high-performance computing environments. We will close with showing our open-source project `neurodesk` which combines all these technologies in a user-friendly way and makes reproducible neuroimaging accessible for a wide audience. Some command line and linux experience is of advantage, but we will cover everything that's needed.Bring a laptop with Docker installed.

Software Carpentry with Python

The workshop will cover task automation in the Unix shell, version control with Git and introduce programming in Python.

Introduction to Jupyter Notebooks

This workshop will introduce you to Jupyter Notebooks, a digital tool that has exploded in popularity in recent years for those working with data. You will learn what they are, what they do and why you might like to use them. It is an introductory set of lessons for those who are brand new, have little or no knowledge of coding and computational methods in research. By the end of the workshop you will have a good understanding of what Notebooks can do, how to open one up, perform some basic tasks and save it for later. If you are really into it, you will also be able to continue to experiment after the workshop by using other people’s notebooks as springboards for your own adventures! This workshop is targeted at those who are absolute beginners or ‘tech-curious’. It includes a hands-on component, using basic programming commands, but requires no previous knowledge of programming.

Gale Digital Scholar Lab - Humanities

How to use the Scholar Lab workbench for digital humanities research.

Create an Open CV

How to use GitHub Pages to create a version controlled, open CV

Gale Digital Scholar Lab - Social Sciences

How to use the Scholar Lab workbench for digital humanities research.

Introduction to Machine Learning for Imaging

A short hands on training workshop introducing machine learning for imaging. In the first part of the workshop a brief introduction to the ideas of machine learning as they apply to image classification and segmentation is given. In the second part, the Trainable WEKA framework available in ImageJ/Fiji is introduced, and the participants are led through a series of hands on exercises on creating and applying classifiers for segmentation.

Collecting Data from the Web

A short hands on training workshop by Sam Hames.

Graduate Digital Research Fellows

Participants in this UQ-run program will talk about how the program has enhanced their research skills.

Galaxy workshop

Galaxy Australia is the Bring Your Own Data analytical service for Australian life science researchers. It is a web portal to nationally distributed computer resources for the running of over 1,000 of the latest and best practice tools. It comes loaded with the most commonly accessed reference data to speed up your analyses. This workshop will introduce Galaxy and through two hands-on tutorials showcase how to use the service to rapidly and reproducibly analyse your data. BYO lLaptop, Chrome browser and web access.

Top tips

A range of talks from participants.

The Ecocommons: its history, and what is coming

Introduction to the ecocommons platform and its uses in eco research.

Free

Free time to network

Research Profiles: working hard or hard work?

This is a 'Bring your own device' session. What will people find when they Google you? Learn about different research profiles available and start creating your professional online identity. Use researcher IDs (e.g. ORCiD) to claim and link your publications.

Network Know-how & Data Handling

This workshop will cover topics such as jargon busting, network literacy and data movement solutions. The workshop will also provide a peek at some collaborative research tools such as Jupyter Notebooks and CloudStor. You will learn about networks, integrated tools, data and storage and where all these things fit in the researcher’s toolkit.

Getting started with HPC

This session will introduce attendees to the uses of HPC and answer entry level questions.

Topic Modelling for Qualitative Content Analysis

Talk by Dr Aneesha Bakharia.

Advanced image processing and analysis with FIJI

Presented by Nick Condon and Deborah Barkauskas

Copyright considerations for researchers

Katya Henry explains.

Open Mic

Free space for attendees to speak or teach

Welcome to Country (Auditorium)

First Peoples' welcome

SAGE Research Methods

Introduction to this useful database.

Introduction to Species Distributions Modelling

Introduction to the EcCommons for SDM.

Hacky Hour

BYO problem or question and be helped by peers.

Stalls in the foyer

A mixture of sponsor and other stalls.

Key Story - Dr Peter Binks: Engagement

What is the CVL? An introduction to the Characterisation Virtual Laboratory (CVL) for processing large imaging and characterisation data sets using GPU processing on HPC

The rate, quantity and quality of imaging science data acquisition is increasing exponentially. Researchers need defined, reliable and rapid pathways that they can use to process these data. The ACCS (Australian Characterisation Commons at Scale) Project offers solutions to this critical need. The flagship capability of the ACCS Project is the CVL (Characterisation Virtual Laboratory) (www.cvl.org.au). The CVL offers a unique virtual space where researchers can access HPC capabilities and analyse their datasets using graphical interfaces for dozens of specialist LINUX packages. CVL is available to all Australian researchers working in imaging and characterisation sciences using their AAF login. Via the Strudel2 deployment over a web interface, researchers can access multiple deployments of CVL across Australia, depending on their specific tool needs and/or institutional affiliation. The CVL enables researchers to easily access HPC setups from their own PCs over the internet for processing large volumes of imaging data on remote systems. With 3 preset virtual desktop configurations, researchers can opt for basic, intermediate or heavy compute setups, enabling rapid analysis of terabyte-sized datasets. CVL comes preinstalled with dozens of imaging tools, and through the ACCS, has a team ready to install new packages in response to the changing needs of the community. The ACCS project aims to show researchers how they acquire data, move it into the CVL, and then export it back to their collections, completing a fully integrated workflow. In this way, CVL and ACCS bring data full circle from acquisition to final FAIR deposition.

Setting up an account to access CVL

In this presentation, I will provide explicit instructions on how to decide which node of CVL is right for you, and then how to access the CVL and set up your account. This will be a hands-on session and I will be stepping you through the pathway to establish your account and integrate your data collection. Accounts to CVL are provisioned manually, so there will be some lag-time between applying for an account and being able to use the CVL. I will run a follow-up session to show you how to work within the CVL environment.

Data transfer methods for CVL

In this follow-up session, CVL account holders can work through the steps to move data in and out of the analysis environment. I will show you how images acquired from instruments can be ingested directly into collections with newly emerging workflows (like Pitschi). Your data collections will then available within the CVL, ready for analysis. For those not yet connected with Pitschi, tools like FileZilla for sFTP or Globus can be used to transfer data collections. We will work through how analysed and annotated data can be exported back to collections, ready for repository storage.

Research software visible, citable and sustained - ARDC Software Program

Across science disciplines, software code is being written by scientists and deemed critical to research conclusions. This is evidenced by an increasing number of papers reporting the use of customised software code to process and analyse data. Although data and code sharing policy exists, publishing the details of bespoke software is not yet a general practice. Accessibility mechanisms for provision of the source code as part of a publication or pre-print are technically a solved problem. For example, we have free access to version control systems, persistent identifiers, archiving tools, licenses and dedicated software repositories. Policy at various levels either recommend or mandate software availability statements. These policies exist in support of validating techniques and results, computational replicability and reproducibility, and the increased likelihood for research peers to use and build on methods. The ARDC is proposing a strategy for culture change, with the greater aim of improving recognition of research software as a first-class research output. To attain this goal we need to coordinate activities with research software authors to See, Shape and Sustain research software. Our target audience are PhDs and EMCRs investing the most of their time writing, testing and maintaining research software. We aim to increase the visibility of research software projects for broadest use and reuse. Boost incentives such as crediting authors for their research efforts and for supporting computational reproducibility. We envision the impact of these activities will encourage more researchers to improve the quality of their code and promote research excellence.

Gold Coast registration - G11 3.56

For Gold Coast one-day event attendees only.

Gold Coast Welcome and icebreaker session - G11 3.56

For Gold Coast one-day event attendees only.

Gold Coast only: Text Mining and Analysis - G11 3.56

Workshop

Gold Coast only: An introduction to digital texts and tools for HASS research - G11 4.29

Workshop

Gold Coast Key Story - Dr Stephanie Chaousis

Dr Chaousis is the Partnerships Manager of Datarwe - G11 3.56

Gold Coast only: Introduction to data wrangling with OpenRefine - G11 3.56

Hands-on workshop on data cleanup.

Gold Coast only: Data visualisation basics - G11 4.29

Hands-on workshop on data visualisation tools and techniques