Bioinformatician

Institution/Company:
Ontario Institute for Cancer Research
Location:
Toronto, ON, Canada
Job Type:
  • Staff
Degree Level Required:
Bachelor's
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Bioinformatician

The Ontario Institute for Cancer Research (OICR) is seeking a talented Bioinformatician to join the Data Curation and Bioinformatics team under the Data Coordination Centre (DCC) of the International Cancer Genome Consortium (ICGC) Accelerating Research in Genomic Oncology (ARGO) (https://icgc-argo.org/). To ensure the success of reaching ARGO’s ambitious goal of uniformly analyzing the genomes of more than 100,000 participants and linking these data to high-quality clinical information, the Software Engineering group led by Dr. Yung is tasked to build robust and scalable solutions used by the DCC and Regional Data Processing Centres (RDPCs) for data management and analysis. The candidate will join our efforts by contributing to developing bioinformatics analytic pipelines, exploring and integrating open source data resources, supporting external collaborators including ARGO members and cancer researchers, and internal team members such as business analysts and software engineers.

We are looking for a talented individual with a passion for bioinformatics in computational cancer genomics. If you are passionate about the field and want to become part of a team building cutting-edge solutions from the ground up, just get in touch.

Responsibilities:

  • Develop scalable, portable and reproducible computational workflows to perform uniform analyses;
  • Develop technical plan and implement tools for data quality control, validation and reporting;
  • Perform routine workflow execution, monitoring and debugging for ARGO RDPC in the Collaboratory OpenStack environment;
  • Perform benchmarking tests to evaluate different solutions and suggest optimizations;
  • Develop fully automated workflows for routine data handling processes, such as data transfer from EGA to ICGC data repository;
  • Participate code review collaboratively with peers to improve code quality;
  • Explore public biological databases and open source bioinformatics tools, suggest integration approaches and build prototype to evaluate/fine-tune integration plan;
  • Interact with business analysts to assist the translation of bioinformatics needs into software functional requirements and specifications;
  • Provide technical support to ICGC ARGO program members resolving data submission issues and other ARGO RDPC members to ensure smooth data processing;
  • Provide helpdesk support for external users with wide range of requests including data accessibility, data download and portal functionality etc;
  • Contribute to preparing and maintaining documentation for user guides, SOPs and data processing pipelines;
  • Maintain and update ARGO dictionary and metadata schemas to enhance data validation, and support for new data types and data elements;
  • Other assigned scripting and data handling tasks.

Qualifications:

  • Undergraduate degree or higher in bioinformatics, genomics, computational biology or computer sciences with significant bioinformatics experience;
  • Extensive programming experience with Python or other languages, preferably in large-scale projects;
  • Experience with bioinformatics resources, databases, tools and common standard formats;
  • Working experience in analyzing large genomics datasets (raw sequencing data, gene expression, germline and somatic mutational events, copy number variants, methylation, etc.);
  • Knowledge of software development best practices, eg, modular design with clean decoupling, source code version control, unit test, continuous integration etc;
  • Knowledge of or experience using existing scientific workflow systems, such as CWL / WDL / Nextflow / Snakemake etc is an asset;
  • Experience with user support is an asset;
  • An interest in cancer research and knowledge of cancer genomics and biology/genetics;
  • Experience in designing relational database schema and good knowledge of big data No-SQL solutions (e.g. Elasticsearch, MongoDB) is an asset;
  • Be highly self-motivated and detail-oriented;
  • Strong verbal and written communication skills.

Additional Information

OICR is an innovative cancer research institute located in the MaRS Centre in the Discovery District in downtown Toronto. OICR is addressing significant challenges in cancer research with multi-disciplinary, multi-institutional teams. New discoveries to prevent, detect and treat cancer will be moved from the bench to practical applications in patients. The OICR team is growing quickly. We are innovative, dedicated professionals who bring expertise to each of our roles. We are looking for individuals interested in being part of a culture of excellence that will result in Ontario being recognized internationally as a leading jurisdiction for cancer research.

Launched in December 2005, OICR is an independent institute funded by the Government of Ontario through the Ministry of Training, Colleges and Universities.

For more information about OICR, please visit the website at www.oicr.on.ca.

CLOSING DATE: Until Filled

OICR is an inclusive employer dedicated to building a diverse workforce. We encourage applications from all qualified candidates and will accommodate applicants’ needs throughout all stages of the recruitment and selection process. Please advise the Recruiter to ensure your accessibility needs are accommodated throughout this process. Information received relating to accommodation will be addressed confidentially.

The Ontario Institute for Cancer Research thanks all applicants. However, only those under consideration will be contacted.

Resume Format: If you elect to apply, you will need a text or HTML version of your resume so that you can cut and paste it into the application box provided. Before you submit the completed application, you will be asked to attach one or two files to your application. Please attach your resume as a .pdf or .doc file.

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