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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

Tuesday
Jun132017

Bioinformatics Research Officer

We are seeking an experienced and highly motivated bioinformatics researcher who will contribute to an exciting research study involving the genomic analysis of neuroendocrine tumours (NET). NET is a heterogeneous collection of tumours with a complex genetic makeup that often display unpredictable clinical behaviour. As leaders of a new international research study based at Peter Mac and with involvement of the University of Melbourne Centre for Cancer Research we aim to identify the genetic determinants of NET including associations with clinical outcome, response to therapy and functional imaging properties. The research will involve high-level bioinformatics analysis of a large series of tumour samples involving engagement with an international consortium and employing a range of genomic methods including whole genome DNA sequencing, RNA-sequencing, DNA methylation and proteomic analysis. The position will also have scope for development of new bioinformatic methods and leading novel research projects.

Candidates who wish to apply for this position MUST:

Have a PhD or Masters degree in a relevant field OR a bachelors degree and at least three years experience in a quantitative discipline such as mathematics, statistics, physics or computer science
Have >2 years experience in the application of bioinformatics to genomics data.
Have excellent skills in R and Unix programming
Possess excellent organization, communication, reporting and time management skills


For further information about this opportunity, please see here

 

Wednesday
Apr122017

Postdoctoral Scientist (Bioinformatics & Computational Biology) 

An excellent opportunity is available for a highly motivated and skilled bioinformatician or computational biologist to work on prostate cancer genomics within the Research Division at the Peter MacCallum Cancer Centre. The role will involve analysis of DNA and RNA sequencing data to investigate the drivers of metastasis and therapy failure in prostate cancer.

Suitable applicants will have a PhD in Bioinformatics, Computational Biology, Statistics, Computer Science, Genetics or related discipline. Additional requirements include expertise in genomics, statistics and the analysis of next generation sequencing data, advanced skills in at least one of R, Python or Perl and experience working on high performance computing clusters.

The research environment will be highly collaborative, with regular interactions with cancer biologists from the Prostate Cancer Research Laboratory and bioinformaticians from the Computational Cancer Biology Program and the Bioinformatics Core Facility. The candidate will work on joint initiatives but will also be responsible for driving own specified projects.

These position will be initially offered for a fixed term duration of 12 months with the possible opportunity to extend. Remuneration will be commensurate with qualifications and experience.

Peter Mac offers its employees the following benefits:

  • Salary packaging 
  • Employee Assistance Program 
  • Central City location 
  • Training and Development program

Further details, complete position description and application can be viewed here.

Saturday
Nov262016

Postdoctoral Fellow (Cancer genomics/bioinformatics) - UNSW Sydney

A postdoctoral fellow position is available within the lab of Dr Jason Wong to work on projects relating to the study of mechanisms of mutation formation in cancer and the impact of these mutations on cellular function. These projects build on recent research from the team described in Nature (https://doi.org/10.1038/nature17437). The successful applicant will carry out computational and bioinformatics data analyses, write research manuscripts and co-supervise research students. There will also be opportunities to undertake experimental research to generate data and test hypotheses, and therefore researchers with experience in laboratory-based research will be highly regarded. The position will be based within the Lowy Cancer Research Centre in the Bioinformatics and Integrative Genomics team led by Dr Jason Wong.

Click to read more ...

Saturday
Nov192016

Research Associate: Bioinformatics, Adelaide

We are seeking a bioinformatician to join the bioinformatics group of the Centre for Cancer Biology (CCB).  This position, available for two years in the first instance, will be primarily associated with the Gene Regulation Laboratory (Prof. Greg Goodall) and the new ACRF Cancer Discovery Accelerator of the CCB. Specific interests of the Gene Regulation Laboratory include the study of the mechanisms and functions of transcriptional and post-transcriptional regulation of gene expression, especially in relation to the epithelial-mesenchymal transition and in cancer metastasis (see http://www.centreforcancerbiology.org.au/research/laboratories/gene-regulation-section/ for further information).

 

The CCB’s bioinformatics group, headed by Dr. Andreas Schreiber, consists of around 10 bioinformaticians and is located in the ACRF Cancer Genomics Facility. The group coordinates and carries out the computational analysis component of the research program of the CCB, performs bioinformatic developmental work within for the Genome Facility and it is also closely associated with the NGS diagnostic service of SA Pathology. The group specializes in genome analysis, supporting the discovery of disease causing mutations, analysis of changes in expression and regulatory networks during the development of cancer and development of software aiding the transition from biomedical research to personalized genomics.

 

The successful applicant will be proficient in interpreting large, complex and diverse next-generation sequencing datasets. Previous experience with working with long reads is an advantage, as is a strong statistical background. The applicant will use both available computational tools as well as develop their own. Previous experience in coding in one or more relevant languages (e.g. Perl, Python, Java, shell scripting) is essential, as is familiarity with Unix/Linux.  We will consider applications from candidates with a PhD or substantial experience in bioinformatics, statistical, mathematical & computational or related sciences. Previous experience in molecular biology, genetics and related areas is an advantage but not essential.

 

Closing date for applications is Dec 12, 2016. For further information, and the application form, see "Research Associate: Bioinformatics (Level ARAS)" (Job Ref - HSC_0282_R_E)  at
https://workingatunisa.nga.net.au/cp/index.cfm?event=jobs.listJobs&jobListid=e227d5fe-d40f-4582-91b6-9bc901269f43