Software Developer I

Position: Software Developer I
Site: MaRS Centre, Toronto
Department: Genome Sequence Informatics
Reports To: Manager, Infrastructure & Software Development
Salary: Commensurate with level of experience
Hours: 35 hours/week
Status: Full-time, Permanent

We are looking for a passionate software developer to join the Genome Sequence Informatics (GSI) team!

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 three sub-teams:

• Infrastructure: Includes laboratory tracking, pipeline and data management, and reporting. This team develops the open source MISO LIMS (https://miso-lims.github.io) and associated applications, workflow systems like Vidarr and Cromwell (https://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, immune detection, cfMeDIP, and others. 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. You will develop and improve our production system within a research environment.

New employees who may be required to work on-site are required to be fully vaccinated for COVID-19 subject to the duty to accommodate on the basis of protected grounds pursuant to the Ontario Human Rights Code.

Fully vaccinated is defined as having received all of the required doses of a Health Canada approved vaccine and having received the final dose at least 14 days before your employment start date.

As described above, the requirement to be fully vaccinated is subject to the Ontario Human Rights Code. If the candidate is unable to receive the COVID-19 vaccine for a reason protected by the Code, requests for accommodation from the vaccine policy will be assessed on a case-by-case basis.

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

Your responsibilities will include:

• 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.
• Writing clean code, using source code control, unit testing, regression testing, and continuous integration, and creating developer documentation and user guides.

Qualifications:

• You have hands-on experience in end-to-end software development, responding to and diagnosing feature requests and bugs.
• You have experience with a variety of programming languages such as Java, Python, Perl, Javascript, or R.
• You have strong experience working in a Linux environment and using the shell.
• You have acute attention to detail and rigour, required for developing clinical testing applications.
• You have 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.
• You have strong verbal and written communication skills.
• You are able to understand complex problems and develop solutions.
• Knowledge of HPC environments is desirable.
• Experience with production analysis systems is an asset.
• Experience with cancer genomics, bioinformatics, science, healthcare, or related fields is desirable but not required.