Talk 26 - 24 April, 2.00pm AEST - Techniques and Software Framework for Extracting Metadata from Diverse Data Sources

Like many other kinds of government and research institutions, Australia's geological institutions house datasets for which there is a broad variation in the quality of metadata. This creates challenges for data providers and aggregators trying to maintain a certain standard of FAIR compliance across all their offerings.

For example, when the offering is very poor, more research and manual data entry may be required. For aggregators there is the problem of extracting metadata of a consistent standard from a wide variety of catalogue systems.

This talk will outline a software architecture and techniques that attempt to alleviate the burden of metadata collation and curation. The software is designed to homogenize metadata harvested from a variety of common metadata catalogue applications. For metadata-poor sources, extraction of metadata from associated technical reports using textual analysis and machine learning models is utilised. The limitations and viability of such techniques are discussed. At the end of the transformation process, ISO-compliant metadata records are created which are suitable for importing into a geo-network geospatial catalogue.  (Slides, Video)

Speaker

Vincent Fazio is a software developer employed by CSIRO Mineral Resources to implement AuScope's future vision for Australian geoscience research. He has worked in a broad range of industries and research areas over the past 20 years including defence, telecommunications, hand-held devices and protein crystallography.  His current interests include: implementing metadata standards, geospatial information systems, displaying 3D geospatial datasets, website development and open source software. 

 Talk 24 - 30 November, 2.00pm AEDT - Cross-platform GPU programming without the heartburn

Graphics processing units (GPUs) are an important component of high-performance computing and AI infrastructure, as they offer substantially higher performance and efficiency than general CPUs for many scientific workflows. However, programming for GPUs requires close attention to low-level hardware details in order to achieve good performance, while the emergence of HPC-focused GPUs from multiple hardware vendors, each with their own programming languages and APIs, has complicated the programming landscape. This means that porting to a new platform or GPU vendor can require substantial code rewrites, dramatically increasing the costs of software maintenance.

In this talk, I will provide an overview of some recent attempts to overcome this issue in the C++ programming space. I will discuss the current state of vendor-specific programming models, followed by an overview of some promising frameworks for vendor-agnostic development of GPU-accelerated scientific codes in high performance C++. I will compare the ease of use, support for tooling and performance of the Kokkos, SYCL and OpenMP programming models and discuss lessons learned from my time developing high-performance, GPU-accelerated molecular dynamics applications. Finally, I will discuss the implications of the changing GPU landscape for the long-term sustainability of scientific software. (Slides, Video)

Speaker

Dr Emily Kahl is a research software engineer at the Australian Institute for Bioengineering and Nanotechnology (AIBN) at the University of Queensland. Emily develops and maintains software for molecular simulation, with a specific focus on GPU-accelerated computing and machine learning methods in quantum chemistry. She is also an advocate for open-source software in computational science, and code she has developed for atomic and molecular physics has seen widespread use by Australian and international researchers.

 Talk 22 - 24 August, 2.00pm AEST - Knowledge Graphs and Property Graphs

In this Tech Talk, Dr Car will provide a summary of NoSQL and explain the concepts of Graphs, Property Graphs and Labelled Property Graphs. He will then explain and relate the concept of Knowledge Graphs. Example technologies that implement these concepts will be covered, including Neo4J, ArcGIS Pro Knowledge, and Apache Jena Fuseki. He will conclude with some lessons learned from working in this space, and provide some key advice for those looking to explore Property Graphs and Knowledge Graphs. (Slides, Video)

Speaker

• Dr Nicholas Car - Data standards and Semantic Web specialist, KurrawongAI and Adjunct at the ANU.

Dr Nicholas Car is a data standards and Semantic Web specialist working in a small Australia tech company and also as an Adjunct at the ANU. He worked as a researcher at CSIRO for almost 15 years as well as a Data Architect at Geoscience Australia, managing some of their data holdings and aiming at multi-system interoperability. He contributes to W3C and OGC  standards and currently co-chairs the Australian Government Linked Data Working Group. 

Talk 20 - 26 April 23, 2.00pm AEST - Zero to Dev: How LAMMPS Gets Academics Coding in C++

LAMMPS is a molecular dynamics software package which, uniquely, has large chunks of contributed code written (often obviously) by academics who aren't necessarily top-notch coders (like myself!), and that's what I would explore in the talk. LAMMPS has set up a strong internal framework of classes that help academics start writing or modifying code with relatively little C++ knowledge. I can also talk about a package I recently developed with international collaborators which has been accepted into the source code and discuss some of the challenges and lessons from collaborating long-distance over coding and getting recognition for scientific coding (and the consequences when scientists aren't recognised). (Slides 1)

Speaker

• Shern Tee, Postdoc, The Australian Institute of Bioengineering and Nanotechnology, University of Queensland

Contact: s.tee -at- uq.edu.au - Shern Tee is a postdoc at the Australian Institute of Bioengineering and Nanotechnology, University of Queensland, where he works on constant potential methods for molecular dynamics simulations of electrode-electrolyte nano-interfaces. Shern is also an excited advocate for research software engineering as a vital role in modern science -- whenever he's not busy with church, funky jazz, or two young and sleepless children.  

Talk 18 - 22 Nov 22, 1.00pm AEDT - Containers for Scientific Software Distribution Service including security scanning and CVMFS

Installing scientific software on HPC often requires substantial amounts of work. In this Tech Talk we would like to get input from the community on our idea for a community-led system that makes building and distributing scientific software more sustainable. Our goal is to collect container recipes in a GitHub repository, containers are then automatically built and tested and pushed to a container registry. The containers are security rated and HPC admins can select which container subset they would like to offer to their users. The software containers will be available via a national CVMFS server infrastructure. (Slides 1, Slides 2  | Video 1, Video 2)

Speaker

• Steffen Bollman, Research Fellow, University of Queensland.
  Contact:  s.bollmann -at - uq.edu.au - After obtaining a Master degree in Biomedical Engineering at the Ilmenau University of Technology, Steffen 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, where he pioneered the application of deep learning methods for quantitative susceptibility mapping, in the group of Prof Markus Barth. In 2019 Steffen joined the Siemens Healthineers collaborations team at the MGH Martinos Center in Boston during a 1 year industry exchange where he worked on the translation of deep learning reconstruction techniques into clinical applications. Since joining the School of Information Technology and Electrical Engineering at the University of Queensland in 2020 Dr Bollmann develops computational methods to process quantitative magnetic resonance imaging data. As part of the ARDC platform grant AEDAPT, Steffen is developing the NeuroDesk platform - a flexible, scalable, and browser-based data analysis environment for reproducible neuroimaging..

• Audrey Stott, Bioinformatics Platform Specialist, Pawsey
  Contact:  audrey.stott -at- pawsey.org.au - Audrey comes from a mixed background of podiatric medicine, wet lab and bioinformatics. From working bedside, to bench, and DevOps, her experience in these fields have led her to the area of increasing accessibility for bioinformaticians in a data-driven world. She works at the Pawsey Supercomputing Research Centre as a systems administrator to provide development and support for improving services and user experience for researchers.

Talk 16 - 25 August 22, 2.00pm AEST - Making AuScope's Portal Play FAIR

In this talk I will describe the steps being taken to improve the conformance of the datasets displayed on AuScope Portal to the FAIR Data Principles (Findable, Accessible, Interoperable, Reusable). This spans a range of actions including:

(1) augmenting the display of metadata on the Portal, (2) upgrading geonetwork records to a newer standard and (3) maintaining a high standard of metadata in a geonetwork catalogue while minimising the maintenance burden. (Slides | Video)

Speaker

• Vincent Fazio, Senior Engineer, CSIRO Minerals.
  Contact:  vincent.fazio -at- csiro.au - Vincent Fazio is a software developer with a broad range of interests including: implementing metadata standards, geospatial information systems, displaying 3D geospatial datasets, website development and open source software.

Talk 14 - 26 May 2022, 12.30pm AEST - Implementing the OHDSI OMOP Common Data Model for Medical Research 

The Common Data Model allows data consolidation of Electronic Medical Records (EMR) from diverse hospital and GP sources, enhancing research breadth. The Observational Health Data Science and Informatics, Observational Medical Outcomes Partnership common data model (OHDSI OMOP or OMOP) has a very large international community working towards open source research tools and capabilities. The ARDC is investing to accelerate research in the medical domain through the conversion of key hospital and general practice EMR datasets to this model, through an EMR to OMOP public sector bridges project. In this talk, we shall present the rationale for converting data to this model and the challenges and lessons learnt in converting datasets to this model. Project DOI:10.47486/PS014 | (Slides | Video below)

Speaker

• Prof Dougie Boyle, Academic Specialist in Clinical Data Analytics, University of Melbourne

Prof Boyle is a founding lead of the Australian Health Research Alliance, Transformational Data Collaboration (AHRA TDC) working towards health data quality, terminology standardisation and common data model implementation for Australia. Prof Boyle is leading an ARDC project to advance convergence of the OHDSI OMOP common data model.
Contact dboyle -at- unimelb.edu.au

Talk 9 - 25 October 2021 - CILogon: Integrated Identity and Access Management Platform

"CILogon enables researchers to log on to cyberinfrastructure (CI) by providing an integrated open source identity and access management platform for research collaborations, combining federated identity management (Shibboleth, InCommon) with collaborative organization management (COmanage). Federated identity management enables researchers to use their home organization identities to access research applications, rather than requiring yet another username and password to log on. Collaborative organization management enables research projects to define user groups for authorization to platforms." 

Speakers 

• AU Support - AAF - Patrick Carnuccio, Solutions Analyst

• John Scullen, AAF, Head Projects & Managed Services
  Contact patrick.carnuccio -at- aaf.edu.au
  This is a pre-recorded talk by CILogon.

Talk 9 - 25 October 2021 - CILogon: Integrated Identity and Access Management Platform

"CILogon enables researchers to log on to cyberinfrastructure (CI) by providing an integrated open source identity and access management platform for research collaborations, combining federated identity management (Shibboleth, InCommon) with collaborative organization management (COmanage). Federated identity management enables researchers to use their home organization identities to access research applications, rather than requiring yet another username and password to log on. Collaborative organization management enables research projects to define user groups for authorization to platforms." 

Speakers 

• AU Support - AAF - Patrick Carnuccio, Solutions Analyst

• John Scullen, AAF, Head Projects & Managed Services
  Contact patrick.carnuccio -at- aaf.edu.au
  This is a pre-recorded talk by CILogon.

  Talk 8 - 3 September 2021 - Scalable Data Processing on Nectar using Apache Airflow

In this webinar, we demonstrate how to create distributed workers and micro services on Nectar using Apache Airflow technology. We have used Airflow to enable Data CO-OP capability in analysis and synthesising big datasets. This work is funded by ARC Linkage Infrastructure, Equipment and Facilities grant for the project "Data Co-operative Platform for Social Impact and Wellbeing", an infrastructure project across Swinburne, Griffith, ANU, Melbourne and UTAS.

Speakers 

• Amir Aryani, Soda Lab, Swinburne. Amir Aryani is the Head of the Social Data Analytics (SoDA) Lab in the Social Innovation Research Institute. The Lab applies contemporary and emerging co-op data analytics techniques to provide insight into health and social problems.

• Jan Hettenhausen, Griffith. Jan is the tech Lead and software developer in the eResearch & Specialised Platforms team at Griffith University. In his 8 years in the eResearch team he’s worked on a range of bespoke research application and national platforms, is a vocal advocate of continuous delivery and DevOps and has authored and co-authored a number of conference and journal papers. 

• Duong Nhu, Soda Lab, Swinburne. Duong is a Research Assistant at Soda Lab, Swinburne. He is also doing a Ph.D. at Monash University, specializing in machine learning. Before Soda Lab, Duong worked as a data scientist/data engineer at various startups and IT consultancies.

Talk 6 - 17 June 2021 - CI/CD - Continuous Integration/Continuous Deployment

CI (Continuous Integration) and CD (Continuous Deployment) offer software development teams enhanced services for making code changes more easily and reliably. In Tech Talk 6, we hear how two teams do their flavour of CI / CD. See Slides below.

Speakers 

• James Tocknell, Software Developer/Data Scientist, Macquarie AAO. Australian Astronomical Observatory (AAO) is building the FAIMS software, and has extensive experience with data services/platforms for astronomy.
  James Tocknell works within the Research Data and Software (RDS) team at the AAO (Australian Astronomical Optics), Macquarie University. The RDS team provides the Data Central science platform for astronomers and research teams, software development for cutting edge optical astronomical instrumentation, and is developing the latest version of the FAIMS data acquisition app. When not finishing up his PhD on outflows from protoplanetary discs, James maintains a number of open source projects, including the h5py package.
  James will cover how the AAO (as a software team), h5py (as an open source project), and I (as an individual and researcher) use CI/CD, and compare and contrast the use of self-hosted vs commercial CI/CD hosted services.

• James Dempsey, Senior Software Developer, CASDA CSIRO. CASDA is the data archive and services for the CSIRO ASKAP project - the pathfinder for the Square Kilometre Array project, "the world's largest and most powerful radio telescope".
  James works in CSIRO Information Services Application team. He specialises in scientific data management, particularly astronomy data, and led the development of CSIRO's Data Access Portal (DAP) and CSIRO ASKAP Science Data Archive (CASDA).
  Successfully releasing software is hard to do. So, the approach CSIRO take is to automate it and do it often. This is where continuous integration and continuous delivery come in. I’ll walk you through what CSIRO do with DAP and CASDA to keep our releases easy.

Talk 4 - 15 Apr 2021 - Platforms for Sensitive Data Analysis -  Slides | Chat | Video now available and see below.

The purpose of this workshop is for developers to share experiences and learn from each other the particular problems, solutions, technical challenges and architectural decisions that have been made in their projects in order to address the unique needs of developing this type of platform.  Slides | Chat | Videos now available and see below plus Intro | Discussion.

Platforms: Speakers - Org: (see 8 Bios below Platform Descriptions)

• SeRP: Anitha Kannan and Jerico Revote - Monash - The Secure eResearch Platform (SeRP) software is an application suite developed by Swansea University to underpin health data research in the UK. It delivers a secure, trusted and scalable environment for data governance, linkage, control and management services for data custodians, and secure remote data analysis environments for research users. Monash SeRP, the Monash University deployment of SeRP, enables the automation of research data governance at scale. Monash data custodians can manage governance over their research data with full control and visibility over who accesses the data, where/when the data is used and how it is being used. Approved researchers, including Monash, national and international collaborators, who access data in SeRP have pre-configured tools that support SAS, SPSS, STATA, R, Python, Machine Learning/Natural Language Processing etc. (VIDEO)

• AIS: Chris Albone, Fang Xu, and Ryan Sullivan - Uni Sydney - The Australian Imaging Service (AIS) is a national federation for secure imaging data management and analysis. It consists of a number of core nodes with auditable access controls and a planned fleet of edge devices for standardized de-identification and encryption of data before leaving the clinical site. (VIDEO)

• SDE: Amr Hassan - Monash - Secure Data Enclaves (SDE) is a software-defined, secure, and centralised private cloud infrastructure that aims to give Monash researchers a safe environment to host, process, and analyse their sensitive data. From inception, the design was focused on creating a capability with security at its core, that did not require the user to sacrifice their overall experience. The platform architecture and design enable the team to offer each workload its dedicated enclave with well defined and monitored traffic routes to ensure that only authorised access is allowed. (VIDEO)

• AusCAT: Matthew Field - UNSW. (VIDEO)

• ERICA: Tim Churches - UNSW. ERICA (E-Research Institutional Cloud Architecture) is a framework which allows institutions and organisations to rapidly establish public-cloud-hosted, secure, remote access data analysis facilities for sensitive data entirely under their own control and governance, while sharing software development, maintenance and security accreditation costs with other ERICA sites. Currently there are three ERICA sites in operation, with three more to be established during 2021. This talk will cover the motivations for, capabilities and technological underpinnings of the ERICA framework. (VIDEO)

• AARNet: Frankie Stevens and Robert Pocklington. The AARNet Sensitive Data service will provide researchers across the Australian university sector with a rich collaboration and analysis environment coupled with the requisite controls needed for working with sensitive data. Workflows and audit trails will enable controlled collaboration across institutions, and compliance with legislation and funding body requirements. All stages of the research lifecycle will be supported through the provision of tools for the analysis, management and storage of sensitive research data. The service will enable cross-disciplinary advances, innovation and faster research results to bring economic, commercial, environmental, social or cultural benefits to the Australian community. AARNet is a not-for-profit company that provides ultra high-speed Internet and communications services exclusively to Australia's research and education sector. (VIDEO)

• OMOP PSB: Dougie Boyle and Roger Ward - Uni Melbourne (VIDEO)

AIS - Ryan Sullivan (U Sydney)

Ryan is the product manager for characterization research technology at the University of Sydney and head of the Australian Imaging Service. He has a background in microscopy and neural implant fabrication.

AIS - Fang Xu (U Sydney)

Fang Xu is the senior Devops engineer who co-designs, builds and supports Sydney University's research IT infrastructure including XNAT, CTP and Omero. Fang has a background in software development and system administration in both on-premise and cloud environments. 

AIS - Chris Albone (U Sydney)

Christopher Albone is an enterprise architect at the University of Sydney. His areas of focus include research administration and research technology. He has long been involved in the implementation of XNAT and related systems at the University

SeRP - Jerico Revote (Monash)

Jerico is the lead Research Devops Systems Engineer at Monash eResearch Centre, Monash University. He has led the technical deployment of Monash SeRP in partnership with Swansea University. Jerico is also leading the technical devops for the ARDC Secure eResearch Platform project.

SeRP - Anitha Kannan (Monash)

Anitha is the Director, Research Platform Data Strategy in the Office of the Senior Vice-Provost and Vice-Provost (Research) at Monash University. 

She is leading the ARDC Secure eResearch Platform project that will deploy and run the SeRP software stack as a managed, nationally consistent service via deployments and multi-tenancy arrangements at Monash eResearch Centre, Monash University. 

SDE - Amr Hassan (Monash)

Amr Hassan is the Delivery leader for Technology Services and eResearch at Monash University. He leads the infrastructure platforms team at eSolutions. He holds an interdisciplinary PhD in Computational Sciences, an M.Sc in Scientific Computing, and a B.Sc. in Computer Science.

ERICA - Tim Churches (UNSW)

Tim Churches is a medically-trained epidemiologist and health data scientist, with nearly three decades of experience in designing and implementing large-scale public health and clinical research data systems, including the SURE secure data analysis facility at the Sax Institute. He is the co-founder of the ERICA project.

AARNet - Rob Pocklington

Rob is Senior Developer for AARNet's sensitive data platform.

AARNet - Frankie Stevens

Frankie is AARNet Associate Director, eResearch. She has 20 years experience in higher education / research, and is a former cancer researcher.

Talk 2 - 3 Dec 2020

Building Serverless Web Applications for Researchers.
This talk will discuss the advantages, limitations and architecture of building serverless web applications in the research domain. Further, this talk will explore 2 existing research web applications Data Mosaic and Geophysical Processing Toolkit, how they take advantage of serverless technologies and the reasoning behind the architecture. Subscribe to get access to the Zoom meeting.

Sam Bradley CSIRO - A software engineer and full stack developer working in the CSIRO Mineral Resources Business Unit for the last 2 years. Sam has 12  years of experience delivering all types of software projects from production web applications to experimental scientific prototypes. Slides.

Talk 9 - 25 October 2021 - CILogon: Integrated Identity and Access Management Platform

"CILogon enables researchers to log on to cyberinfrastructure (CI) by providing an integrated open source identity and access management platform for research collaborations, combining federated identity management (Shibboleth, InCommon) with collaborative organization management (COmanage). Federated identity management enables researchers to use their home organization identities to access research applications, rather than requiring yet another username and password to log on. Collaborative organization management enables research projects to define user groups for authorization to platforms." 

Speakers 

• AU Support - AAF - Patrick Carnuccio, Solutions Analyst

• John Scullen, AAF, Head Projects & Managed Services
  Contact patrick.carnuccio -at- aaf.edu.au
  This is a pre-recorded talk by CILogon.