Infrastructure_
Research project support
Supporting data and compute intensive research
Supporting research in statistics, machine learning, natural language processing, geospatial analysis, Bayesian approaches, software engineering, data processing, modelling and simulation, bioinformatics and data management.
Many of our services are available free of charge to University researchers, research students, and affiliates. While project support may be considered to customers external to the University, a fee-for-service arrangement may apply. Please contact us (sih.info@sydney.edu.au) for more information.
Areas of expertise
Data science
We have a team of data scientists and software engineers to connect the best data science methods to your research problem.
Our team can provide support in data science, including solutions with:
- machine learning and probabilistic modelling
- data collection, transformation, analysis, and visualisation
- image & natural language processing
- software engineering
- automation
We deliver:
- short consultations and data transformation projects
- longer engineering and analysis projects in milestones of 2-12 weeks effort
- assistance with scoping and estimating work for grant proposals
- development of open-source software for data-driven research, with a focus on Python and R
- advanced training for researchers in data science technologies
Statistical consulting
We provide tailored statistical advice to higher degree by research (HDR) students. We can also advise academics, researchers, affiliates and partners of the University.
Our team can provide:
- advice on experimental design
- support with data analysis and interpretation
- support with reviewing statistics in your project or grant application
- support with calculation of sample size and experimental power that will be needed in your grant application
We have a range of services available to support your research project, including access to global best practice bioinformatics pipelines, support with analyses and grant applications, training courses, and access to a researcher community.
Pipelines and analysis support
We develop global best practice data processing and bioinformatics pipelines and execute these for researchers on their datasets, at scale, on National HPC facilities, University of Sydney’s Artemis HPC, and on Commercial Cloud. We engineer bioinformatics pipelines to maximise the efficiency and minimise run times and costs for HPC and Cloud facilities. Our high-throughput pipelines for model and non-model organisms include:
- small germline variant calling
- somatic variant calling
- structural variant and indel calling
- transcriptome assembly
We assist with bioinformatics analyses such as:
- Read and assembly quality checking
- Metagenomics (WGS and 16S)
- Metatranscriptomics
- Genome wide association studies
- Single cell
- Differential expression
- Comparative genomics
- Phylogenetics
- Short and long read de novo assembly
- Genome annotation
We also assist with
- sensitive/protected and big data management lifecycles
- best practices and advise on the experimental design for next generation sequencing studies.
- Data visualisation and quality control.
- How to effectively use the University’s Artemis HPC and Research Data Storage systems for large datasets.
- Specialist software and online platforms including QIAGEN’s CLC Genomics Workbench. Ingenuity Pathway Analysis and Galaxy Australia.
- Popular open source software
Grant support
We assist with:
- developing budgets and draft University in-kind contribution estimates for computing, data storage, and data analysis services for grant applications.
- preparing and reviewing project proposals for computing resources grants, including the National Computational Merit Allocation Scheme, Intersect HPC Allocation Scheme, Microsoft Azure and AWS Cloud Research grants.
Training courses
We deliver a range of bioinformatics training courses open to University of Sydney research staff, students and affiliates, with some courses open to all researchers.
Genomics and bioinformatics community
Our mailing list provides a platform for all researchers to actively engage with other genomicists and bioinformaticians.
Modelling, simulation and visualisation
Access assistance with modelling, simulation, scientific visualisation and informatics.
Our team can assist with:
- data-intensive and computationally-intensive modelling, simulation, visualisation, and informatics executed on National HPC facilities University of Sydney’s Artemis HPC and Argus VRDs, and Commercial Cloud. This includes support for accelerating, parallelising and scaling up algorithms, developing portable and reusable code, workflow management and automation, optimising code for, and transitioning code between HPC and Cloud services.
- analyses – including computational chemistry, molecular dynamics, computational fluid dynamics, finite element analyses, mathematical modelling, machine learning, computer vision, image analyses, scientific visualisation, GPU programming.
- preparing and reviewing project proposals for computing resources grants, such as the National Computational Merit Allocation Scheme, Intersect HPC Allocation Scheme, and Commercial Cloud research grants. We assist with resource benchmarking and demonstrating code scalability as required by these schemes.
Research data management
Our experts are available to provide training and support to help manage your research data and use research data platforms effectively.
Our team provides researchers with :
- assistance from expert research data consultants to help effectively manage research data
- support to follow best-practice in research data management, including sensitive data and managing collaborations
- training and workshops that cover a variety of platforms to manage research data
- RDM online module
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