Python Job: Software Engineer

The Garvan Institute of Medical Research brings together world-leading clinicians and basic and translational researchers to break down barriers between traditional scientific disciplines and find solutions to disease.

Garvan’s 2030: Discoveries to Impact Strategy is designed to galvanise Garvan’s researchers, professional staff, partners, donors and community around our vision of Global leadership in discoveries to impact, and to enable us as an Institute to deliver on that vision – such that Garvan becomes an institute where research discoveries are taken through to patient impact (new treatments, tests and prevention approaches), on a global scale.

Garvan’s Data Science Platform (DSP) brings together computational experts working in: system administration/DevOps, software engineering, production bioinformatics and computational biology. The DSP works closely with teams across Australia, establishing national infrastructure for genomics and medical research. Our teams collaborate with leading genomics researchers at Garvan and beyond, providing computational expertise, building infrastructure and processing large datasets

The Opportunity

We’re looking for a Senior Software Engineer (or a Mid-seniority one ready for the challenge of a Senior role) to join the DSP's growing Software Engineering team. The Software Engineer will be responsible for the design, implementation, integration, testing, documentation, deployment and support of software and systems that enable genomics research. Most of our work involves free and/or open source software that Garvan either officially maintains or actively contributes to. This role will involve close collaboration with stakeholders from different research groups at Garvan, from our partner organisations and from the genomics research and software development community.

A snapshot of the projects we are currently working on includes the development and integration of eConsent platforms, the customisation and deployment of genomic data exploration portals and the design and implementation of software infrastructure suitable to support national genomics research. In particular, our team is the official maintainer of the dynamic consent platform CTRL, which is being extended with new integrations (e.g. the REDCap database and the data sharing tool elsa) and new use cases, based on our stakeholders’ needs. We are also co-developers of elsa, a tool that, together with CTRL, aims at automating the genomics data sharing process, allowing future collaborative research to easily and securely scale. Additionally we have recently performed the first deployment of gnomAD (a web application to explore large genomics datasets) at the Garvan Institute and are actively working on customising the deployment and data import process, with the goal of contributing relevant patches upstream. For details about these software packages see:

• https://github.com/Australian-Genomics/CTRL

• https://github.com/umccr/elsa-data

• https://github.com/broadinstitute/gnomad-browser

Because of the constantly evolving nature of the research community needs and of our collaborations, we are seeking someone curious and dynamic, who has a keen interest in exploring and learning new technologies and who enjoys finding solutions to complex new problems.

Key Responsibilities

• Design, implement, integrate, test, document, deploy and support software of various types, including data pipelines, REST APIs and web applications.

• Perform deployments/DevOps tasks both for our projects and for additional open source tools needed at Garvan (e.g. research tools for genomic variant filtration and interpretation).

• Engage stakeholders to help understand their needs and provide expert advice on software design and development for research projects.

• Help improve the team’s developer tooling, practices and automations.

• Contribute code and features to open source bioinformatics tools.

• Mentor junior developers and help the whole team grow professionally by sharing own special interests and findings.

Snap shot of benefits

• This is a 2 year full time maximum term contract with a salary of up to $120,000 + 10% super + salary packaging

• Generous salary packaging ($15,900 for general household expenses and $2,650 for meal/entertainment expenses)

• On going training and development

• Flexible work arrangements

• 18 weeks paid parental leave

• Additional day’s leave as Garvan Day

• Employee Assistance Program

• Discounted Health Insurance

• Lifestyle discounts with our community partners

About You

Here are some skills relevant to the role. If you don’t tick all the boxes, we’d still like to hear from you – we value attitude and diversity over things that can be learned:

• Excellent knowledge of one or more among JavaScript/TypeScript, Ruby on Rails, React, Vue.js, Clojure, Python, R, Bash

• Full-stack development experience (or a keen interest in learning the missing half stack)

• Experience in developing, documenting and testing REST APIs and in using REST APIs to integrate applications

• Knowledge of SQL and experience developing applications that use relational databases (including dealing with migrations and data consistency)

• Experience with Big Data tools and frameworks (e.g. Spark, Elasticsearch and Redis)

• Experience with GNU/Linux system administration and/or with DevOps on public cloud services

• Experience with widespread developer tooling, in particular Git beyond the basics (e.g. Git workflows, use of pull requests, rebasing)

• Excellent written and oral communication, representation and interpersonal skills essential for interaction with internal and external stakeholders.

Additional desirable skills and experience:

• Experience with Docker and Kubernetes

• Experience with configuration as code (e.g. Ansible or Terraform)

• Extensive experience with different levels/techniques of software testing and with various software testing frameworks.

• Experience with software and standards used in genomics research, like REDCap, gnomAD, hail, seqr, GA4GH standards (e.g. Passport, DUO), genomic file formats (e.g. SAM, VCF).

• Experience setting up/maintaining CI/CD.

• Knowledge of NoSQL databases/datastores.

• Knowledge of or interest in functional programming, in particular the application of functional design patterns and techniques to languages that are not strictly functional.

How to Apply

To apply for this position, please submit your application with a CV and cover letter as one document, stating why you are interested in this role. We are reviewing applications as they are received. If you think you’re the right person for this role, we’d love to hear how your capabilities, achievements and experience set you apart, including any contributions to public open source projects.

For any additional information about the role please contact the DSP Software Engineering Lead Dr Filippo Ammazzalorso (he/him) at [email protected]

Job Type: Full-time

Salary: Up to $120,000.00 per year