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Current Opportunities

Software Developer II - Toronto, Ontario

Position: Software Developer II
Site: MaRS Centre, Toronto
Department: Genome Sequence Informatics, Genomics
Reports To: Director, Genome Sequence Informatics
Salary: Commensurate with level of experience
Hours: 35 hours/week
Status: Full-time, Permanent

The Ontario Institute for Cancer Research (OICR) looking for an experienced and passionate Software Developer II to join the Genome Sequence Informatics (GSI) team.

Learn more about working at OICR here.

GSI designs applications to streamline and automate analysis for the Genomics program (https://genomics.oicr.on.ca), controls the data life cycle, and creates useful and dynamic reports at scale. We ensure data flows smoothly, securely, and correctly from the lab through to the clinicians and researchers who use it. Our primary languages are Java, R, Python, Javascript, MySQL, PostgreSQL, and MongoDB and we use technologies like Docker, OpenStack, Prometheus.IO, Loki, Promtail, and Univa Grid Engine, and are expanding into Cloud environments like Microsoft Azure. Many of GSI’s software projects are open-source and available on GitHub: https://github.com/oicr-gsi/ and https://github.com/miso-lims.

GSI has six focus areas:

  • Lab tracking: Develop the open source MISO LIMS (https://miso-lims.github.io) and associated application
  • Pipeline/Data management: Develop and run workflow systems like Vidarr and Cromwell (https://cromwell.readthedocs.io) to automate and streamline data analysis, tracking, and workflow management.
  • Data release: Archive data for long-term storage and release data to collaborators and public archives
  • Reporting: Maintain a suite of specialized reports for quality control, forecasting, and lab operations
  • Bioinformatics support: Perform project-specific analysis for collaborators, including alignment, de novo assembly, variant detection, quantification of tumour heterogeneity and purity, RNAseq analysis, variant significance prediction, and structural variant calling and any other specific project requirements.
  • Cancer Genome Interpretation: Analyze and interpret genomic data using accredited pipelines and processes and draft reports for clinical cases.

Software developers in GSI are enthusiastic and autonomous. As part of the team, you will take the lead on all aspects of development of new applications for high-impact cancer research and clinical reporting, as well as monitoring, diagnosing, and pushing fixes to improve stability and performance of existing applications. You will bring your experience and expertise to developing and improving our production system within a research environment.


  • Designing and crafting databases, web services, and software applications to meet cancer research and clinical reporting needs, working closely with other software developers and laboratory and IT personnel;
  • Building APIs and web services that link our systems together and facilitate reporting;
  • Improving existing applications with additional features and enhancements;
  • Ensuring that the sequencing software pipelines are consistently, reliably, efficiently, and correctly analyzing genomic data;
  • Deploying software applications for production, staging, and development as required;
  • Suggesting improvements and working with the team to implement them;
  • Supporting production by troubleshooting bugs and preventing outages; and
  • Writing clean code, using source code control, unit testing, regression testing, and continuous integration, and creating developer documentation and user guides.


  • Bachelor’s degree or equivalent experience in computer science, software engineering or similar;
  • 2+ years software development experience, particularly in science, healthcare, or related fields;
  • 2+ years experience with a variety of programming languages such as Java, Python, Perl, Javascript, or R;
  • Excellent design and architecture knowledge, especially with production analysis systems;
  • Deep hands-on technical expertise and excellent analytical abilities;
  • Acute attention to detail and rigour required for developing clinical testing applications;
  • Exceptional relationship skills including the ability to discover real requirements hidden in bug and feature requests, recommend alternative approaches, and lead development efforts;
  • Experience mentoring and training less experienced developers;
  • Strong verbal and written communication skills;
  • Strong experience working in a Linux environment;
  • Ability to understand complex problems and develop solutions; and
  • Experience with cancer genomics or bioinformatics is desirable but not required.

OICR is a collaborative, not-for-profit research institute accelerating the development of new cancer research discoveries for patients around the world while maximizing the economic benefit of this research for the people of Ontario. We are dedicated professionals who bring expertise to each of our roles. We are looking for individuals who share our values of excellence, innovation, collaboration, impact, responsibility and community.

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