Senior Software Engineer

The Garvan Institute of Medical Research; Sydney; On-site; AUD 150,000 - 230,000; Full time

Benefits offered by this job

Salary packaging

Training & development

International research environment

Flexible work arrangement

Parental leave (18 weeks)

Additional leave types

Health insurance discounts

Lifestyle discounts

Job summary

Garvan Institute of Medical Research in Sydney is seeking a Senior Software Engineer to lead a Gen3-based research data platform for the AllClear program on Google Cloud Platform. You will coordinate data curation, ETL workflows for single-cell omics and clinical data, and build integrations with analysis tools.

Ideal candidates hold a PhD or equivalent experience, with strong Python, Bash, TypeScript, React, Next.js, Kubernetes, and Terraform/OpenTofu expertise.

Qualifications

• PhD in Computer Science or related field, or equivalent industry experience.
• Strong Python and Bash programming proficiency.
• Experience with TypeScript, React, Next.js, and Kubernetes.

Responsibilities

• Lead deployment, customization, and operation of a Gen3-based data platform on Google Cloud.
• Coordinate data curation and ETL workflows for omics and clinical data.
• Design integrations between Gen3 and analysis/visualisation tools.
• Contribute to architecture decisions and drive execution with CI/CD and IaC.
• Mentor team members and share expertise across the DSP.

Skills

Python

Bash

TypeScript

React

Next.js

Google Cloud Platform

Kubernetes

Terraform

OpenTofu

PostgreSQL

Linux

Git

Education

PhD in Computer Science

Tools

Gen3

CI/CD

Job description

Garvan Institute 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

THE OPPORTUNITY

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).
• Desirable: 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.

Only applicants with full working rights in Australia are eligible to apply for this role.

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