Senior Software Engineer

Garvan Institute of Medical Research; Sydney; Hybrid; AUD 140,000 - 190,000; Full time

Benefits offered by this job

Generous salary packaging

Training and development

International research environment

Flexible work arrangements

18 weeks parental leave

Leave types (cultural, conference, etc

Discounted Health Insurance

Lifestyle discounts

Job summary

Garvan Institute of Medical Research seeks a Senior Software Engineer to lead a Gen3-based data platform on Google Cloud Platform, serving the AllClear program. You will handle data curation, ETL, and integration with analytics tools while shaping architecture and driving delivery in a collaborative, international research setting.

The role requires deep expertise in Python, TypeScript/React, cloud infra, Kubernetes, and data security for clinical datasets, within a dynamic biomedical research

Qualifications

• PhD in CS/Bioinformatics or equivalent industry experience.
• Excellent Python and Bash skills.
• Strong TS/React/Next.js experience.
• GCP deployment and cloud architecture expertise.
• Kubernetes deployment experience with Helm.
• IaC experience with Terraform/OpenTofu.
• Relational DB design with PostgreSQL.
• GNU/Linux server/cloud administration.
• Fluent English communications in cross-functional teams.
• Gen3 or research data commons experience.
• Single-cell omics data formats/workflows knowledge.
• Experience handling clinical data with security considerations.

Responsibilities

• Lead deployment, customization, and operation of a Gen3-based platform on GCP.
• Coordinate data curation and ETL for single-cell omics and clinical data.
• Design and implement Gen3 integrations with analysis/visualisation tools.
• Contribute to architecture plans and drive execution.
• DevOps tasks: Kubernetes via Helm, IaC with Terraform/OpenTofu, CI/CD.
• Engage stakeholders to translate data/workflow needs into requirements.
• Improve developer tooling, practices, and automation.
• Mentor team members and share expertise across the DSP.
• Contribute code to open-source data-platform tools used by the team.

Skills

Python

Bash

TypeScript

React

Next.js

Google Cloud Platform

Kubernetes

Helm

Terraform/OpenTofu

PostgreSQL

Git/GitHub

Gen3

Single-cell omics

Data security/compliance

Education

PhD in Computer Science or Bioinformatics

Tools

Gen3

Kubernetes

Terraform/OpenTofu

Helm

PostgreSQL

Job description

THE OPPORTUNITY

Garvan Institution of Medical Research brings together world leading scientists and clinicians, collaborating locally and globally, to advance our understanding of disease, particularly cancer, autoimmunity and genetic disorders. Garvan is a global leader in fundamental biomedical research and its translation. Our mission is to make discoveries that will improve health for all

Garvan’s Data Science Platform (DSP) brings together computational experts working in system administration, DevOps, software engineering, production bioinformatics, computational biology and AI. The DSP works closely with various collaborators at Garvan, across Australia and internationally. The Senior Software Engineer will be based in the National Scale Genomics Infrastructure team and will lead the design, development, and deployment of a research data sharing and analysis platform for the AllClear program — a National Breast Cancer Foundation Collaborative Research Accelerator Grant studying breast cancer metastasis and relapse mechanisms. The platform will make single-cell omics and matched clinical information accessible to the AllClear consortium of researchers and facilitate exploration and analysis. This is a 2-year fixed-term position with salary dependent on candidate skills and experience.

SNAPSHOT OF BENEFITS

• Generous salary packaging to save you income tax on your wages thereby boosting your monthly take home pay (max. $15,900 general expenses + $2,650 meals/accom)
• Ample opportunities for on-going training and development
• Stimulating, diverse and highly international research environment
• Flexible work arrangements e.g. start / finish times
• 18 weeks paid parental leave for both parents including paid superannuation
• A range of additional leave types to meet your personal needs including cultural leave, conference leave, community service and study leave
• Discounted Health Insurance
• Lifestyle discounts with our community partners

WHAT YOU WILL DO

This is a senior position. The details of the duties and responsibilities will be set in the individual goals based on experience. In general, the key responsibilities include:

• Lead the deployment, customisation, and ongoing operation of a Gen3-based research data platform for the AllClear program on Google Cloud Platform.
• Coordinate data curation and ETL workflows for single-cell omics and patient clinical data, working directly with AllClear researchers and clinical data custodians.
• Design and implement integrations between Gen3 and analysis and visualisation tools.
• Contribute to the architecture and design decisions of the platform: produce implementation plans, seek team review, and drive execution.
• Perform DevOps tasks — Kubernetes deployment via Helm, infrastructure-as-code with Terraform / OpenTofu, CI/CD — for the AllClear platform and for related tooling used across the team.
• Engage stakeholders — AllClear researchers, clinical partners, and internal Garvan collaborators — to understand their data and workflow needs, translate these into technical requirements, and share updates with them through presentations or other means.
• Contribute to and improve the team's developer tooling, practices, and automations.
• Mentor other members of the team and share expertise across the DSP.
• Contribute code and features to open-source data-platform and bioinformatics tools where the team uses them.

ABOUT YOU

• 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, with a clear understanding of cloud architecture, IAM, security, and cost.
• 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: branching model, code review, issue tracking, and clean commit history.
• Ability to take a high-level project objective, break it into a reviewable implementation plan, seek team feedback, and drive execution.
• Excellent written and oral communication in English, including with non-technical stakeholders (clinical researchers, program managers, data custodians).
• Prior experience with Gen3 or another research data commons platform.
• Experience with single-cell omics data formats and workflows (h5ad / AnnData, Scanpy, CellxGene).
• Experience working with clinical or patient data, including awareness of the associated ethical considerations and data security requirements.
• Experience setting up and maintaining CI/CD pipelines.
• Familiarity with genomics standards (SAM/CRAM/VCF, GA4GH) and bioinformatics tools (gnomAD, hail, seqr, REDCap).
• Experience with columnar storage formats (Parquet) or big-data frameworks (Spark, Elasticsearch).

ABOUT GARVAN

Garvan Institute of Medical Research is an independent Medical Research Institute (MRI) in Sydney, delivering scientific and clinical impact on a global basis and in partnership with organisations that share our vision. We are proud to be one of Australia’s largest and most highly regarded MRI’s.

Our vision is global leadership in discoveries to impact and our enduring purpose is to impact human health, by harnessing information encoded in our genome.

We seek to see our world-class discovery research achieve life-changing impacts, not only for individual patients with rare diseases, but for the many thousands affected by complex, common disease.

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.