About OICR

OICR is Ontarios cancer research institute. We bring together people from across the province and around the world to improve the lives of everyone affected by cancer. We take on the biggest challenges in cancer research and deliver real-world solutions to find cancer earlier and treat it more effectively. We are committed to helping people living with cancer, as well as future generations, live longer and healthier lives.

Launched in December 2005, OICR is an independent institute funded by the Government of Ontario through theMinistry ofColleges, Universities, Research Excellence and Security.

Job Details

Position: Software Developer II

Location: MaRS Centre, Toronto

Department: Computational Biology (Genome Sequence Informatics)

Reports To: Manager, Infrastructure & Software Development

Salary: Commensurate with level of experience; total compensation includes a competitive benefits plan, plus a defined benefit pension plan (HOOPP)

Hours: 35hours/week

Job Type: Hybrid

Status: Full-time, permanent

Position Summary

The Ontario Institute for Cancer Research (OICR) is seeking a Software Developer II to join the Genome Sequence Informatics (GSI) team.

GSI designs applications to streamline and automate analysis for the Genomics program (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, Python, JavaScript, MySQL, PostgreSQL, and MongoDB and we use technologies like Docker, OpenStack, Prometheus, Loki, Promtail, and Altair Grid Engine, and are expanding into Cloud environments. Many of GSIs software projects are open-source and available on GitHub: github.com/oicr-gsi and github.com/miso-lims.

GSI has three sub-teams:

• Infrastructure: Includes laboratory tracking, pipeline and data management, and reporting. This team develops the open source MISO LIMS (miso-lims.github.io) and associated applications, workflow systems like Vidarr and Cromwell (cromwell.readthedocs.io) to automate and streamline data analysis, tracking, and workflow management, and maintains a suite of specialized reports for quality control, forecasting, and lab operations.
• Analysis: Bioinformatics analysis and data release. Develops the analysis techniques and pipelines used by OICR Genomics for alignment, de novo assembly, variant detection, quantification of tumour heterogeneity and purity, RNAseq analysis, variant significance prediction, structural variant calling and any other specific project requirements. This team also archives data for long-term storage and releases data to collaborators and public archives.
• Cancer Genome Interpretation: Validates pipelines for accreditation, analyzes and interprets genomic data using accredited pipelines and processes, and drafts reports for clinical cases.

Software developers in GSI are enthusiastic and autonomous. As part of the team, you will be involved in 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. Your role will involve developing and adapting our software and infrastructure to leverage remote HPC infrastructure and cloud-based environments.

Position Responsibilities

• 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.
  

Qualifications

• A bachelor's degree in Computer Science, or recognized equivalent
• Hands-on experience in end-to-end software development, responding to and diagnosing feature requests and bugs
• Experience with a variety of programming languages such as Java and Python
• Strong experience working in a Linux environment and using the shell
• Strong experience working in an HPC environment
• Familiarity with one or more cloud service providers and experience working with cloud-based infrastructure
• Acute attention to detail and rigour, required for developing robust applications
• Strong relationship skills including the ability to discover real requirements hidden in bug and feature requests, recommend alternative approaches, and contribute to team development efforts
• Strong verbal and written communication skills
• Ability to understand complex problems and develop solutions
• Some familiarity with production analysis systems
• Some familiarity with cancer genomics, bioinformatics, science, healthcare, or related fields

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

To learn more about working at OICR, visit our career page.

POSTED DATE: May 7, 2025
CLOSING DATE: Until Filled

OICR is committed to fostering a climate of equity, diversity, inclusion, and accessibility. This commitment is central to, and mutually supportive of, our research excellence mandate. We welcome and respect the diversity of all members of our community and we support an inclusive culture for all. We welcome all applicants, and encourage applications from racialized persons, Indigenous Peoples, women, persons with disabilities, LGBTQ2S persons, and others who may contribute to furthering a diversity of ideas within our community. OICR is committed to fair assessment of a candidates abilities, and consideration for diversity of thought, method, and experience. Providing an accessible workplace and recruitment process is important to us, as described in our Accessibility Plan (https://oicr.on.ca/accessibility/). Should you require accommodation during any stage in the recruitment process, please complete the form at the bottom of page https://oicr.on.ca/careers/. Information received related to accommodation will be handled confidentially.

Resume Format:If you elect to apply, please click on the Apply for this Job button below. You will be required to enter contact details, and to attach your resume to your application.Please attach your resume as a .pdf or .doc file.

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