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Thursday
Jul062017

Production Bioinformatics Engineer

About us

The Garvan Institute of Medical Research, renowned for innovation and excellence, is building its next generation data analysis infrastructure to unlock the secrets of the genome and ultimately transform health care. The Kinghorn Centre for Clinical Genomics (KCCG), part of the Garvan’s Genomics and Epigenetics division, aims to advance the use of genomic information in patient care by employing world-leading DNA analysis technology and expertise in genetics, pathology and bioinformatics to deliver and interpret Next Generation Sequencing (NGS) data for research and clinical use.

As part of KCCG’s core strategic aims, the ‘Genomic Technologies Group’ extends and complements Garvan’s capabilities in genomic, transcriptomic, and epigenomic research by implementing, evaluating, and refining new and existing technologies for both clinical and research applications and, where applicable, establish a pathway for translation of new technologies and techniques into commercial products, such as Genome.One. 

The opportunity

We currently have an opportunity for a Production Bioinformatics Engineer to join the Genomic Technologies Group. The Production Bioinformatics Engineer will be responsible for the efficient implementation of analytic workflows and best practices for the generation and processing of NGS data, with particular focus on single cell sequencing protocols.

Specific tasks will include but not be limited to:

  • Transform research-grade bioinformatics analysis workflows into products that are more robust, transparent and reassuring;
  • Responsible for researching, planning, implementing, testing, and optimising bioinformatics software tools for NGS data that meet the analysis needs for laboratory research scientists;
  • Ensure that NGS pipelines are consistently, reliably, efficiently and correctly processing data;
  • Work closely with Garvan’s Data Intensive Computer Engineering (DICE) group regarding the building of software pipelines that will run on DICE’s HPC and OpenStack computing environment, Australia’s supercomputing facility, the National Computational Infrastructure (NCI), as well as on commercial clouds (AWS, Google, and Azure);
  • Responsible for documenting and communicating pipeline processes and building the team knowledge base;
  • Provide bioinformatics support and training to end users (transforming data from sequence to information meaningful for laboratory research scientists);

About you

To be successful in this position, you will be a talented and methodological programmer who is attentive to detail and eager to learn about diverse genomic applications and the associated data ecology. You will be a team player and enthusiastic collaborator who thrives in diverse computational environments.

You will also possess the following key skills and attributes: 

  • Bachelor degree in software engineering, bioinformatics, biomedical engineering, biotechnology, or a related discipline;
  • Experience with high performance computing environments, cloud computing, and workload managers/batch submission/job schedulers;
  • Experience with NGS data analysis;
  • Experience in installation and evaluation of third party software applications and tools;
  • Fluency in programming in several languages (Bash, R, python desirable);
  • Experience with Atlassian tools (Confluence, Bitbucket, etc);
  • Experience with source code management tools (git preferable);
  • Strong analytical, critical thinking, and problem-solving skills;
  • Excellent interpersonal skills and ability to work cooperatively with other team members;
  • Excellent organisational and time management skills;
  • Knowledge of single cell sequencing workflows desirable;
  • Familiarity with flow cytometry desirable;
  • Familiarity with Containers like Docker, and container-orchestration software like Kubernetes and Mesos desirable;
  • Experience with GPGPU computing desirable;
  • Excellent knowledge of statistics and probabilities desirable;
  • Familiarity with workflow management systems such as Toil, Cromwell, Airflow, Nextflow, Arvados, etc desirable.  

How to Apply

All applications must be submitted via Garvan’s careers website: http://www.garvan.applynow.net.au/jobs/GC2048-production-bioinformatics-engineer