Bioinformatics Software Developer

Ontario Institute for Cancer Research
Toronto, ON, Canada
Job Type:
  • Programmer/Developer
Degree Level Required:
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Bioinformatics Software Developer

Position: Bioinformatics Software Developer Site: MaRS Centre Address: 661 University Avenue, suite 510. Toronto, Ontario. M5G 0A3 Department: Genome Sequence Informatics Reports To: Senior Manager, Genome Sequence Informatics Salary: $65,000-75,000 Hours: 35 Hrs/week Status: Temporary, full-time for 3 year term with Benefits

We’re looking for an experienced and passionate developer to join the Genome Sequence Informatics (GSI) team to support the Genome Canada funded Canadian Data Integration Centre (CDIC).

GSI is responsible for the primary analysis of all data generated at OICR. We design applications to streamline and automate analysis, control the data lifecycle, and create useful and dynamic reports at scale. We ensure that data flows smoothly, securely and correctly from the lab through to the researchers who use it. We use languages and software tools like Java, Perl, Python, Javascript, Open Grid Engine, Apache Hadoop, Apache Oozie and PostgreSQL, and in the future, technologies like OpenStack and CEPH.

The main areas covered by GSI are:

• Lab tracking: OICR uses support the Open Source MISO system. • Pipeline/Data management: Our production pipeline handles the data from six Illumina sequencers, producing terabytes of data each week. We use SeqWare ( to automate and streamline data analysis, tracking, and workflow management. • Data release: GSI archives data for long term storage and releases data to public archives • Reporting: The institute has a suite of specialized reports to help forecasting, lab operations and strategy • Bioinformatics support: Includes alignment, de novo assembly, variant detection, quantification of tumour heterogeneity and purity, RNA-seq analysis, variant significance prediction, and structural variant calling as well as any other specific project requirements.

Software developers in GSI are enthusiastic and autonomous, responsible for full stack development and deployment. As part of the team, you will be involved in all aspects of implementation, testing, and deployment of new applications for high impact cancer research. You will use our 8500 core compute cluster and 4 petabytes of storage to create long term solutions to analyze, track and secure big data.

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 Research, Innovation, and Science.

For more information about OICR, please visit the website at


Your responsibilities will include:

• Designing and crafting databases, web services, and software applications to meet the needs of internal and external users of CDIC resources • Improving existing applications with new features and enhancements • Deploying applications for production and development as required • Suggesting improvements and working with the team to implement them • Support production by troubleshooting bugs and preventing outages • Building APIs and web services that link our systems together and facilitate reporting • Writing clean code, using source code control, unit and regression testing, and creating developer documentation and user guides


Required Qualifications:

• You have experience in Java and Python development • You can work in a Unix/Linux environment • You understand software engineering principles • You communicate clearly • You have some experience with cancer genomics or bioinformatics.

Please include a link to an open source repository (e.g. Github) that contains examples of your code.

Additional Information

POSTED DATE: August 21, 2017 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 .doc file.