Galaxy Australia – a 2020 update

Dr Gareth Price1, Mr Simon Gladman2, Professor Andrew Lonie3

1QCIF Facility for Advanced Bioinformatics, St Lucia, Australia
2University of Melbourne, Carlton, Australia
3Australian BioCommons, Carlton, Australia

Introduction

Galaxy Australia is in its third year of operation as a national platform, backed by years of institutional operation. The platform has shown user number growth in the thousands per year. The platform has matured from year-on-year funding to long term secured support and is now looking to “industrialise” itself to further meet the needs of Australian researchers that are continuing to turn to Galaxy Australia as a reliable, reproducible and transparent platform for data analysis in the life sciences.

Methods

Optimisation of the Galaxy deployment, by the Galaxy Australia team and infrastructure providers have increased service uptime over the last year. Additionally policies and procedures for operation of the broadening tool set, reference data and user request types have strengthened operational efficiency.

Results

Galaxy Australia has seen growth in the last two years of; 4,000+ users and 500+ tools, with 70+ associated peer reviewed publications. The platform has deployed new Pulsar’s at Pawsey and University of Melbourne. The platform is now establishing high-memory nodes, more Pulsars, a new head node configuration, to allow new analysis modalities (long-read sequencing, plant and mammalian genome assemblies, proteomics and metabolomics). Presented here is a schematic review of the roadmap for Galaxy for the next 3 to 5 years.

Conclusion

Galaxy Australia is planning on a tripling of user numbers in 3 years, with eight times more data being analysed. To achieve these goals the platform is building on its robust deployment to strengthen availability, utility and ongoing relevance to Australian researchers.


Biography:

Dr Gareth Price is Head of Computational Biology at QCIF Facility for Advanced Bioinformatics. In this role Gareth manages the diverse spectrum of researcher lead questions involving genomic data, provides training in genomic data analysis, as well as leading Galaxy Australia (https://usegalaxy.org.au) as Platform Manager.

Gareth has 20 years’ experience as a Bioinformatician and Genomics Scientist.

Gareth’s view is that research is at its best when coupled with the most accurate, highest throughput and innovative technology and analysis modalities.

The Australian Characterisation Commons at Scale

Prof. Wojtek James Goscinski1, Jason Andrade2, Jane Frazier1, Dr Paula Martinez3, AProf Brad Moffat4, Dr Ryan Sullivan5, Dr Lance Wilson1, Chris Myers6, Farnoosh Sadeghian1, Dean Taylor7, Edan Scriven8, Dr David Poger9, Jay van Schyndel1, Jafar Lie1, Dr Varvara Efremova10, Dr James Wilmot10, Joshua Silver2, AProf David Abbott11

1Monash University
2University of Wollongong
3National Imaging Facility
4University of Melbourne
5University of Sydney
6AARNET
7University of Western Australia
8University of Queensland
9Microscopy Australia
10University of New South Wales
11The Florey Institute of Neuroscience and Mental Health

The Australian Characterisation Commons at Scale (ACCS) is a project that commenced in 2020 and is funded by the Australian Research Data Commons and 11 project partners and other investors. Together we are developing a coherent and accessible informatics landscape that promotes collaboration, increases return on investment, and delivers value to researchers.

The ACCS is deploying a Characterisation Commons for thousands of researchers who use characterisation techniques, facility scientists who run instruments, and researchers using imaging collections, and will uplift the research capability offered to industry. The outcome will be a rich ecosystem of computing systems, data repositories, workflows, and services all connected with instruments. Through a number of work packages we are developing a suite of resources, with many entry points; all will be accessible from a user portal.

The ACCS underpins a range of characterisation techniques including electron and light microscopy, magnetic resonance imaging (MRI), magnetoencephalography (MEG), electroencephalography (EEG), positron emission tomography (PET), X-ray Computerised Tomography (CT), nuclear and synchrotron techniques, cytometry, secondary-ion mass spectrometry, X-ray diffraction, scattering techniques, and nuclear magnetic resonance.

In this presentation, we will provide an overview of the strategy of the project, present an update on the way we have bootstrapped the project, and provide an overview of the way we are applying technologies such as software-defined models, containerisation, and CI-CD.


Biography:

Prof Wojtek James Goscinski is Associate Director at the Monash University eResearch Centre, the coordinator of MASSIVE, and the project director of the Australian Characterisation Commons at Scale, a $5m+ NCRIS-funded program to deploy national-scale digital infrastructure for computational imaging.

NeuroDesk – A cross-platform, flexible, lightweight, scalable, out-of-the-box data analysis environment

Dr Steffen Bollmann1,2, Dr Oren  Civier2,3, Aswin  Narayanan1,2, Prof Markus Barth1,2, Prof Tom Johnstone2,3

1The University Of Queensland
2Australian National Imaging Facility
3Swinburne Neuroimaging, Swinburne University of Technology

Introduction

Researchers require a diverse collection of tools to analyse data and answer their research questions. Scientific software relies on specific libraries leading to dependency conflicts between different tools and difficulties in installing these. Researchers struggle tremendously to run their analyses on adequate hardware and it is very challenging to move analyses between computing platforms due to the setup work required – ultimately limiting interoperability and reproducibility.

Methods

We developed a modular analysis ecosystem, and applied it first in the field of neuroimaging. The first module consists of a continuous integration system using github actions to automatically build various software containers. Our second module provides wrapper scripts that transparently integrate these containers into any existing workflow. The third layer downloads the containers on demand and manages them to keep the system lightweight, and the final layer provides a lightweight Linux desktop accessible via a browser that runs on any operating system.

Results

Our solution (https://github.com/NeuroDesk/) enables researchers to use any software with any dependency on any operating system. Moreover, as it does not require any installation or specific hardware, it lowers the barriers for entry for less-technical users, while still permitting to scale the analysis at later stages.

Conclusion

We developed a scalable and interoperable way of running various scientific tools on any compute platform accessible to researchers, such as Nectar, the Characterisation Virtual Laboratory (CVL) or the Australian Imaging Service (AIS) XNAT. We are planning to extend our framework to other domains, such as electrophysiology.


Biography:

Dr Steffen Bollmann is a national imaging facility fellow for 7T human MRI at the Centre for Advanced Imaging at the University of Queensland. Utilizing high performance computing and deep learning, he develops new methods for quantitative susceptibility mapping and population anatomy modeling with the goal to understand iron and myelin contributions of the MRI signal. He obtained a bachelor’s degree in biomedical engineering at the Ilmenau University of Technology, followed by a Masters degree in biomedical engineering & bioelectromagnetism. Following this, he completed a PhD utilizing fMRI and spectroscopy in ADHD at the Neuroscience Centre Zurich and ETH.

The Australian BioCommons Bring-Your-Own-Data Platform: Integrating instruments, analysis tools and compute platforms for leadership bioinformatics

Dr Nigel Ward1

1Australian BioCommons,

The Australian BioCommons Bring-Your-Own-Data Platform (BYOD platform) project is a multi-million dollar collaboration between the ARDC, Australian BioCommons, Bioplatforms Australia (BPA) and seven research infrastructure partners: AAF, AARNet, NCI, Pawsey, QCIF, University of Melbourne and University of Sydney. It aims to provide enduring access to digital techniques, reference data, and tools that will enhance Australian environmental, agricultural and biomedical researcher’s ability to understand the molecular basis of life.

From July 2020 – June 2023, the project will deliver via three interrelated work packages:

(1) Improvement of highly accessible Graphical User Interface (GUI) platforms that provide easy access to well-structured, world’s best-practice bioinformatics workbenches for research and training. This will add new tools and workflows to the existing Galaxy Australia service, and establish new GUI platforms such as the Apollo genome annotation curation platform, and Jupyter Notebooks and R Studio “integrative environments”.

(2) Development of a complementary Command Line Interface (CLI)-focussed platform, providing open programmatic resources to create, access and exchange workflows and tools across national and institutional compute infrastructures. The CLI platform will initially be established on co-investing partner sites, but will be designed to allow easy deployment on other infrastructures.

(3) Development of a data infrastructure connecting BPA -omics instruments, BPA Framework datasets, and international reference datasets to the analysis infrastructure, underpinned by national and international data transport.

This presentation will provide background on the challenges that motivated the project and detail on the work plan that aims to address those challenges.


Biography:

Nigel Ward is Associate Director of Platforms within the Australian BioCommons. He works with BioCommons partners to define the shape of and direct the establishment and operation of key national bioinformatics analysis and data platforms. Prior to joining BioCommons, Nigel was eResearch Manager at QCIF where he coordinated application of cloud-based Software Services to support Queensland researchers through projects like EcoCloud, Biodiversity and Climate Change Virtual Laboratory, Characterisation Virtual Laboratory, Humanities & Social Science Virtual Laboratory and Galaxy Australia. Nigel has a background in applied IT research, software engineering, interoperability of distributed systems, web technologies, service and data standardisation.

Recent Comments

    Categories

    About the conference

    eResearch Australasia provides opportunities for delegates to engage, connect, and share their ideas and exemplars concerning new information centric research capabilities, and how information and communication technologies help researchers to collaborate, collect, manage, share, process, analyse, store, find, understand and re-use information.

    Conference Managers

    Please contact the team at Conference Design with any questions regarding the conference.

    © 2018 - 2020 Conference Design Pty Ltd