Python Job: Production Bioinformatician

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

The Production Bioinformatician will oversee the development, implementation and support of software and computational pipelines for different sequencing data, specifically whole genome/exome, single cell and RNA data. We are open to candidates with a minimum of 6 months experience. The Production Bioinformatician will deploy and support tools to assist researchers and clinicians with their genomic research.

SNAP SHOT OF BENEFITS

• This is a 2 year term contract with possibility to extend.

• 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. location, start / finish times etc

• 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

The key responsibilities include:

• Develop, implement and maintain the computational infrastructures required to support the analysis of high-throughput genome and single cell sequencing data.

• Support the translation of new computational techniques from a research setting to production scale tools.

• Design and implement pipelines to run on the internal and external high performance compute infrastructure and commercial clouds (AWS, GCP, Azure).

• Deploy and support research tools for genomic variant filtration and interpretation.

• Contribute code and features to open source bioinformatics tools.

• Ensure secure and efficient delivery of data and results to collaborators and customers

• Assist collaborators in data analysis and to check the validity of experimental results.

• Create computational solutions to generate automated reports from raw high-throughput sequence data

• Establish and maintain excellent records of the computational analysis and techniques for all projects in the Data Science Platform.

ABOUT YOU

The desirable skills and experience include:

• Bachelor degree (or higher) in Bioinformatics, Computer Science or related fields

• Demonstrated strong skills in Linux command line and scripting languages (Python, Bash, R or other)

• Demonstrated experience in the development and implementation of new and cutting-edge bioinformatics tools and pipelines using workflow languages such as nextflow, Workflow Description Language (WDL) or snakemake.

• Expertise in computational bioinformatics techniques, with a special focus on genomics, transcriptomics and single cell transcriptomics.

• Experience with source code management tools (git preferred)

• Experience in analysing large scale genomic data using open-source libraries such as Hail

• Experience in deploying and running pipelines in cloud infrastructure, such as Google Cloud, Terra, AWS or Basespace.

• Experience in using high performance computers (HPC) and job schedulers (e.g. PBS pro or SGE).

• Experience in SQL and NoSQL based Databases.

• Experience in containerisation using Docker and/or Singularity.

• Knowledge of web frameworks: Django, Flask etc is a plus.

• Experience with laboratory information management systems (LIMS).

ABOUT GARVAN

The 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.

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.

Job Type: Full-time

Salary: Up to $15,900.00 per month