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Entries in genomics (2)

Monday
Jul172017

Postdoctoral Fellow in Bioinformatics - Data61, CSIRO


•An outstanding opportunity to launch your research career at CSIRO
•Work in the largest innovation group in Australia
•Join Data61 at CSIRO - Australia's premier science & technology research organisation

The Position

The Postdoctoral Fellow will be based in Data61's EcoSciences Precinct office in Brisbane and will work closely with experimental research scientists and technical staff from the National Research Collections of Australia, including the Australian National Insect Collection (ANIC), the Australian National Herbarium, Australian Fish Collection and the Australian Algal Collection.
  
The appointee will work primarily with the Environomics FSP project "High-throughput Collection Genomics". This project is seeking to unlock the genomic resources held within the millions of historical biological specimens in the National Research Collections Australia. Its success depends on surmounting numerous technical and analytical challenges.  This position will focus on developing tools for assembling and analysing whole genomes from historical specimens of insects, lichen, flowering plants and fish and deal with the many challenges of working with degraded low-coverage genomes. This work will contribute to an analysis pipeline that will be used to generate genomic reference sequences from many thousands of individuals in the National Collections for the molecular identification of specimens, with subsequent applications in, e.g., eDNA-based biodiversity surveys, conservation, biodiversity discovery, and biosecurity.

Location:      Dutton Park, QLD

Salary:          $78K - $88K pa plus up to 15.4% superannuation

Tenure:        specified term of 3 years

Reference:  42486

To be successful you will need:
•A doctorate (or will shortly satisfy the requirements of a PhD) or equivalent research experience in a relevant discipline area, such as genetics, bioinformatics or information science.
•Demonstrated knowledge and skills in advanced bioinformatics research, specifically high-throughput DNA sequence data analysis and a deep understanding of the underlying molecular biology.
•Proficiency in at least one of R, Python or Perl as well as experience in utilising high-performance computing environments.
•The ability to work effectively as part of a multi-disciplinary, regionally dispersed research team, plus the motivation and discipline to carry out autonomous research.
•Experience in the effective communication of scientific findings in written and verbal form, and a solid record of publication in quality, peer reviewed journals.
•A record of science innovation and creativity, plus the ability & willingness to incorporate novel ideas and approaches into scientific investigations.

Owing to terms of the fellowship, candidates must not have more than 3 years of relevant Postdoctoral experience.

Who we are: The Commonwealth Scientific and Industrial Research Organisation (CSIRO) 

AT CSIRO WE INVENT THE FUTURE
 We do this by using science and technology to solve real issues. Our solutions make a difference to industry, people and the planet.

As Australia's national science agency, we've been pushing the edge of what's possible for almost 90 years. Today we have thousands of talented people working across Australia and internationally. Our people work closely with industry and communities to leave a lasting legacy. Collectively, our innovation and excellence places us in the top ten applied research agencies in the world.

WE COLLABORATE TO INNOVATE

We work flexibly at CSIRO, offering a range of options for how, when and where you work. Talk to us about how this role could be flexible for you. 

Find out more here!: Balance

Our commitment to you
CSIRO's Data61 offers an open and supportive workplace, where employee wellbeing is a top priority. We are committed to providing a diverse and inclusive workplace by focusing on gender equality, support and development of women in leadership, increasing the employment of Australian Aboriginal and Torres Strait Islanders whilst supporting the LGBTI community and other diverse backgrounds.


CSIRO's Data61 offers a range of flexible working opportunities, including part-time and job share arrangements, to provide you with work/life balance. We emphasise an individual's growth and development which is supported by interacting and learning from world leading scientists and engineers, who provide the opportunity to challenge, transform and innovate new ideas.


CSIRO's Data61 is committed to sourcing the brightest and best talent to become part of the Data61 family that contributes to creating Australia's data driven future.


How to Apply: Please upload one document only containing your CV/Resume, cover letter and statement addressing the selection criteria.


Before applying please view the full position details and selection criteria here: Position Details

Applications Close:  10:00pm AEST, 6 August 2017

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