Junior Software Engineer

at  The Garvan Institute of Medical Research

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 Junior Software Engineer to join the DSP’s Software Engineering team and be part of the DSP’s long-term strategy for growing and fostering software engineering excellence within Garvan. We are interested in applicants at all levels, ranging from fresh graduates (or even students close to completion of their degree) to mid-level software engineers. Remote applicants from across Australia and New Zealand are welcome.
The Junior Software Engineer will be involved in 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 development of scalable cloud-based image analysis tools, the development and deployment of solutions to manage and share large medical datasets and the customisation and deployment of genomic data exploration portals. This work also overlaps with our involvement in designing and implementing the software infrastructure that will support the future of national genomics research.
In particular, our team is the official maintainer of the dynamic consent platform CTRL, currently used in multiple clinical studies across Australia. We are also co-developers of the related tool elsa, enabling safe sharing of genomics data for collaborative research. In the medical imaging domain, we’ve been developing new cloud-based tools in collaboration with Garvan microscopy facilities (e.g. FLIM motion correction). Last but not least, we manage Garvan’s internal deployments of gnomAD and seqr (web applications to explore large genomics datasets), providing internal customisations and contributing relevant patches upstream.
For details about these software packages see:
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https://github.com/Australian-Genomics/CTRL
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https://github.com/umccr/elsa-data
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https://github.com/Garvan-Data-Science-Platform/motion-correction
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https://github.com/broadinstitute/gnomad-browser
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https://github.com/broadinstitute/seqr
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).
• Proactively participate in the requirements collection and design process. Help supporting our scientific partners with technical issues, progressively taking ownership for relevant projects and areas of expertise.
• Help improve the team’s developer tooling, practices and automations.
• Contribute code and features to open source bioinformatics tools.
• Actively participate in the team’s professional growth by sharing one’s special interests and findings.

Snap shot of benefits

• This is a 2 year full time maximum term contract with a salary range of $85,000 - $120,000 + 11% super + salary packaging (dependent on experience)
• Generous salary packaging (up to $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 or if you’re looking for your first job and have no professional experience, we’d still like to hear from you – we value attitude and diversity over things that can be learned:

• A Bachelor degree (or higher) in Computer Science/Bioinformatics or a related field or in an unrelated field paired with demonstrable computing skills. (Note: candidates nearing the completion of their degree will also be considered.)
• 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, testing and using REST APIs
• Knowledge of SQL and experience developing applications that use relational databases
• Experience with GNU/Linux system administration and/or with DevOps on public cloud services
• Experience with widespread developer tools and understanding of their purpose (e.g. revision control, linting, auto-formatting)
• Excellent written and oral communication, representation and interpersonal skills essential for interaction with internal and external stakeholders.

Additional desirable skills and experience:

• Experience with Big Data tools and frameworks (e.g. Spark, Elasticsearch and Redis)
• Experience with Docker and Kubernetes
• Experience with configuration as code (e.g. Ansible or Terraform)
• Experience with software testing techniques and 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/BAM, 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
f.ammazzalorso@garvan.org.au

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).
• Proactively participate in the requirements collection and design process. Help supporting our scientific partners with technical issues, progressively taking ownership for relevant projects and areas of expertise.
• Help improve the team’s developer tooling, practices and automations.
• Contribute code and features to open source bioinformatics tools.
• Actively participate in the team’s professional growth by sharing one’s special interests and findings

Here are some skills relevant to the role. If you don’t tick all the boxes or if you’re looking for your first job and have no professional experience, we’d still like to hear from you – we value attitude and diversity over things that can be learned:

• A Bachelor degree (or higher) in Computer Science/Bioinformatics or a related field or in an unrelated field paired with demonstrable computing skills. (Note: candidates nearing the completion of their degree will also be considered.)
• 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, testing and using REST APIs
• Knowledge of SQL and experience developing applications that use relational databases
• Experience with GNU/Linux system administration and/or with DevOps on public cloud services
• Experience with widespread developer tools and understanding of their purpose (e.g. revision control, linting, auto-formatting)
• Excellent written and oral communication, representation and interpersonal skills essential for interaction with internal and external stakeholders