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About the Role
Garvan’s Data Science Platform (DSP) is seeking a Senior Software Engineer to lead the design, development, and deployment of a research data sharing and analysis platform for the AllClear program. This platform will make single-cell omics and matched clinical information accessible to researchers studying breast cancer metastasis and relapse mechanisms.
Responsibilities
- Lead the deployment, customisation, and ongoing operation of a Gen3-based research data platform on Google Cloud Platform.
- Coordinate data curation and ETL workflows for single-cell omics and patient clinical data.
- Design and implement integrations between Gen3 and analysis and visualisation tools.
- Contribute to the architecture and design decisions of the platform, including creating implementation plans and driving execution.
- Perform DevOps tasks such as Kubernetes deployment, infrastructure-as-code with Terraform/OpenTofu, and CI/CD for the AllClear platform and related tooling.
- Engage stakeholders to understand their data and workflow needs, translate them into technical requirements, and provide updates.
- Contribute to and improve the team's developer tooling, practices, and automations.
- Mentor other team members and share expertise across the DSP.
- Contribute code and features to open-source data-platform and bioinformatics tools.
Requirements
- A PhD in Computer Science, Bioinformatics, or a related field, or equivalent industry experience.
- Excellent working knowledge of Python and Bash.
- Strong experience with TypeScript, React, and Next.js.
- Strong experience deploying and operating applications on Google Cloud Platform, including cloud architecture, IAM, security, and cost management.
- Demonstrated experience deploying and operating containerised applications on Kubernetes, including familiarity with Helm charts.
- Infrastructure-as-Code experience with Terraform / OpenTofu.
- Experience developing applications that use relational databases (PostgreSQL preferred), including schema design and data-model reasoning.
- Comfort with GNU/Linux system administration in a server / cloud context.
- Fluency with git and GitHub in a team collaboration context.
- Ability to take a high-level project objective, break it into an implementation plan, seek team feedback, and drive execution.
- Excellent written and oral communication in English, including with non-technical stakeholders.
- Prior experience with Gen3 or another research data commons platform (Desirable).
- Experience with single-cell omics data formats and workflows (Desirable).
- Experience working with clinical or patient data, including awareness of ethical considerations and data security requirements (Desirable).
- Experience setting up and maintaining CI/CD pipelines (Desirable).
- Familiarity with genomics standards and bioinformatics tools (Desirable).
- Experience with columnar storage formats or big-data frameworks (Desirable).
- Full working rights in Australia.
Skills
- Python
- Bash
- TypeScript
- React
- Next.js
- Google Cloud Platform
- Kubernetes
- Helm
- Terraform
- OpenTofu
- Infrastructure-as-Code
- DevOps
- CI/CD
- Relational Databases
- PostgreSQL
- GNU/Linux
- System Administration
- Git
- GitHub
- Gen3
- Research Data Commons
- Single-cell omics
- h5ad
- AnnData
- Scanpy
- CellxGene
- Clinical Data
- Genomics Standards
- SAM/CRAM/VCF
- GA4GH
- Bioinformatics Tools
- gnomAD
- hail
- seqr
- REDCap
- Columnar Storage Formats
- Parquet
- Big Data Frameworks
- Spark
- Elasticsearch
Location
- Australia
Work Type
- Fixed-term
Experience Level
- Senior
Education Level
- PhD in Computer Science, Bioinformatics, or a related field, or equivalent industry experience.
Salary/Compensations
- Dependent on candidate skills and experience
Benefits
- Generous salary packaging
- Ample opportunities for on-going training and development
- Stimulating, diverse and highly international research environment
- Flexible work arrangements
- 18 weeks paid parental leave for both parents including paid superannuation
- A range of additional leave types
- Discounted Health Insurance
- Lifestyle discounts with community partners
About the Company
- Garvan Institute of Medical Research is an independent Medical Research Institute in Sydney, delivering scientific and clinical impact on a global basis.
- Garvan is one of Australia’s largest and most highly regarded Medical Research Institutes.
- The institute's vision is global leadership in discoveries to impact human health by harnessing information encoded in our genome.
- Garvan promotes a diverse workplace and is committed to equity, diversity, inclusion and belonging.
Equal Opportunity
- Garvan promotes a diverse workplace and is committed to the principles of equity, diversity, inclusion and belonging. We are always looking for culture ‘add’, not culture ‘fit’ and are building diverse teams with great sets of complementary styles and skills to help deliver our important work effectively.