Digital research infrastructure
High Performance Computing (HPC) involves the use of supercomputers, parallel computing and/or computer clusters for advanced computing tasks including modelling, batch data processing and analysis.
The University runs a local cluster called Artemis. The Sydney Informatics Hub provides complementary support, training, and consultation for conducting your research on Artemis, HPC.
Artemis was upgraded in 2018 and hosts:
- 7636 compute cores
- 108 NVIDIA V100 GPUs
- 56 Gbps FDR Infiniband networking
- A high-performance Lustre filesystem
- Three high memory nodes with 6 terabytes of RAM per node
To get access to Artemis you simply need to fill out a Research Data Management Plan on Dashr and request HPC access.
- Artemis user guide
- Technical information
- Request technical support (unikey required)
- Artemis HPC Terms and Conditions (pdf, 160KB)
Acknowledgement
Please acknowledge the use of Artemis and Sydney Informatics Hub services to ensure the sustainability of our facility. Suggested wording:
- "The authors acknowledge the Sydney Informatics Hub and the use of the University of Sydney’s high performance computing cluster, Artemis."
The University’s ‘Argus’ Virtual Research Desktops (VRDs) deliver on-demand, GPU powered, computing resources. It accesses HPC for solving large-scale computational problems and data processing, facilitates fast access to storage of large datasets, and enables graphical processing and visualisation within a graphical user interface.
You can get access to a small dedicated virtual machine (VM) computing environment useful for hosting websites, applications, or databases.
The University offers secure unlimited storage for all your research data. To get access simply fill out a Research Data Management Plan and request RDS access.
The National Computational Infrastructure (NCI) is Australia's national research computing service providing researchers with access to high performance computing, cloud, data, visualisation, and research platform services. We support merit based access to NCI through the SIH HPC Allocation Scheme and provide technical and computation assistance and guidance for National Computational Merit Allocation Scheme (NCMAS) applications.
NCI facilities:
- HPC (Gadi)
- GPU computing (Gadi)
- Cloud computing (Tenjin)
- Remote Visualisation (Massive)
- Data Storage
Acknowledgement
Please acknowledge the use of NCI resources and Sydney Informatics Hub services to ensure the sustainability of our facility. Suggested wording:
- "This research was undertaken with the assistance of resources from the National Computational Infrastructure (NCI Australia), an NCRIS enabled capability supported by the Australian Government and the Sydney Informatics Hub, a Core Research Facility of the University of Sydney."
The Pawsey Supercomputing Facility is free for academic research users. Access is gained via NCMAS and additional shares can be obtained time through various access schemes.
Pawsey facilities:
- HPC (Magnus, Galaxy)
- Cloud computing (Nimbus)
- Remote Visualisation (Zeus)
- Data Storage
The University has collaborations and affiliations with many commercial computing services. Most services offer some free-tier level of compute. Many are looking for research workloads to test their facilities, and you can always purchase additional time and resources, to scale rapidly for your needs.
We provide support with accessing:
- Microsoft Azure – free access is available by merit through AI for Earth, Good, Accessibility, Humanitarian Action Grants or paid access can be arranged through the University of Sydney
- Amazon Web Services (AWS) – free access is available by merit through Cloud credits for Research or paid access can be arranged through the University of Sydney
- Ronin – is a web application for easily launching AWS computing services
- Google Cloud Platform – free access is available by merit through GCP Research Credits. For more information about accessing Commercial Cloud please contact sih.info@sydney.edu.au.
Research data management platforms
The University offers a suite of tools to assist researchers in managing their research data. These platforms and best data management practices enable researchers to preserve the context and continuity of their research. Our online tools enable simple and secure collaboration, and allow alignment of research practice with requirements in University and national policy.
The Researcher Dashboard (DashR) is a centralised tool for researchers to register research data planning information and to request/manage associated data and computing services.
DashR can be used to:
- Enter and maintain your Research Data Management Planning (RDMP) details
- Request data storage on the Research Data Store Classic (RDS) or Research Computing Optimised Storage (RCOS)
- Request high performance computing (HPC) services on Artemis
- Control and update user access to the above services
The eNotebook provides researchers with a collaborative working tool suitable for both internal and external collaborators. The eNotebook is versatile and can be used in any discipline. It is a great option for curating, storing and sharing working documents, procedures, observations, conclusions, notes, images and data files. Its strengths include the ability to consolidate all sorts of research data along with a rigorous audit trail to maintain integrity of the data.
Research Electronic Data Capture (REDCap) is an online, customisable data capture tool. It provides the ideal means to gather data in a secure environment and avoids the need to enter data into spreadsheets or use paper-based forms and surveys.
REDCap makes it easy to collect standardised, clean data. Researchers and external collaborators can simultaneously access their sensitive data on REDCap in a secure, encrypted manner.
The Research Data Store (RDS) is the University’s primary data store. It is an enterprise grade Network Attached Storage (NAS) device for storing research data, which has a large and expandable storage capacity.
A package of Microsoft programs, both desktop and web-based, for collaborative document editing and data management. OneDrive can be used for data storage, which has a desktop syncing application. OneNote can be used to collate research-based contextual information e.g. research process journals and metadata.
The University’s enterprise edition of GitHub is the Code Repository, a software repository management platform that provides a university-wide resource for code management, code review, and general collaboration. The code repository includes virtually the same set of features as github.com but is self-contained and managed by the University.
The FileSender function of AARNet is a secure, large file sending solution. Files up to 2TB in size can be sent to specified recipients, with the additional option to encrypt files for secure sending of highly protected data.
CLC Genomics Workbench is a comprehensive suite of bioinformatics tools packaged into a user-friendly graphical environment. You can perform a range of analyses on next generation sequencing data and create customisable workflows for studies in genomics, transcriptomics, epigenomics and metagenomics.
Licensing
The University has 5 CLC licenses that are available free of charge to Sydney University students, researchers, and affiliates.
Users are required to book one of 5 university licenses using the Sydney Informatics Hub PPMS. Bookings are essential in order for you to use a license, to ensure fair use amongst CLC Genomics Workbench users.
Please email sih.info@sydney.edu.au for more information on CLC Genomics Workbench.
Ingenuity Pathway Analysis (IPA) is a powerful analysis and search tool that uncovers the significance of ‘omics data and identifies new targets or candidate biomarkers within the context of biological systems.
Licensing
The University has one IPA license that is available free of charge to Sydney University students, researchers, and affiliates. Users are required to book their sessions using the Sydney Informatics Hub PPMS. Please email our Bioinformatics Technician at sih.info@sydney.edu.au to get access to IPA.
Training
The QIAGEN Bioinformatics website has a set of training resources. The most popular webinars are:
Introduction to Ingenuity Pathway Analysis
Formatting and Uploading your Dataset into IPA
Galaxy Australia is a free web-based bioinformatics analysis and workflow platform. It contains thousands of bioinformatics tools to combine, analyse and interpret genomic (DNA), transcriptomic (RNA), proteomic (proteins) and metabolomic (small molecules) data. It provides a simple point-and-click graphical user interface. and aims to make applying bioinformatics approaches on powerful national computing infrastructure easier.
The use of the SIH services including the Artemis HPC and associated support and training warrants acknowledgement in any publications, conference proceedings or posters describing work facilitated by these services.
The continued acknowledgment of the use of SIH facilities ensures the sustainability of our services.
Suggested wording
General acknowledgement:
"The authors acknowledge the technical assistance provided by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney."
Acknowledging specific staff:
“The authors acknowledge the technical assistance of (name of staff) of the Sydney Informatics Hub, a Core Research Facility of the University of Sydney.”
For further information about acknowledging the Sydney Informatics Hub, please contact us at sih.info@sydney.edu.au.