An update on the AEDAPT project and NeuroDesk – A cross-platform data analysis environment for reproducible neuroimaging
Dr Steffen Bollmann1,2, Mr Aswin Narayanan1,2, Ms Paris Lyons3, Dr David White3, Dr Ryan Sullivan4, Dr Oren Civier2,3, Dr Will Woods2,3, Professor Tom Johnstone2,3
1The University of Queensland, Brisbane, Australia
2Australian National Imaging Facility, Brisbane, Australia
3Swinburne Neuroimaging (Swinburne University of Technology), Hawthorn, Australia
4University of Sydney, Sydney, Australia
Neuroimaging researchers require a diverse collection of bespoke command-line and graphical tools to analyse data and answer research questions. Installing and maintaining a neuroimaging software setup is challenging and often results in un-reproducible environments. In our ARDC platform project AEDAPT we develop NeuroDesk, a platform built on container technology for processing and analysing neuroimaging data with the aim to lower the barrier of using various neuroimaging software in a reproducible environment.
We developed a modular and open analysis environment consisting of a continuous integration system to automatically build neuroimaging software containers. By providing a separate container for each neuroimaging software package, we allow a fully reproducible environment, while also avoiding dependency conflicts between tools. To keep the system lightweight, we mount the containers on the fly from a world-wide network of distributed and scalable software distribution service nodes running CernVMFS. We encapsulated NeuroDesk within a lightweight Linux desktop container accessible via a browser interface that runs on any operating system, to lower the barrier for entry.
Our open source project (https://github.com/NeuroDesk/) enables researchers to use various neuroimaging software on any operating system, including high performance computing systems.
We develop a scalable, interoperable way of running scientific tools on any compute platform accessible to researchers. The benefits of this setup are an easy-to-use and reproducible environment for neuroimaging data analysis. NeuroDesk enables researchers to run a fully reproducible environment on cloud, on windows/mac or on a classical high-performance computing system and seamlessly transition between different hardware setups.
After obtaining a Master degree in Biomedical Engineering at the Ilmenau University of Technology, Dr Bollmann completed a PhD on multimodal imaging at the University Children’s Hospital and ETH Zurich, Switzerland. Dr Bollmann then joined the Centre for Advanced Imaging at the University of Queensland as a National Imaging Facility Fellow. In 2020 Dr Bollmann joined the School of Information Technology and Electrical Engineering at the University of Queensland developing computational methods to extract clinical and biological insights from magnetic resonance imaging data.