Position: Software Developer
Site: MaRS Centre, Toronto
Department: Computational Biology (Genome Sequence Informatics)
Reports To: Senior Manager
Compensation: Competitive salary commensurate with level of experience
Hours: 35 hours/week
Status: Full-time, Permanent

We’re looking for a passionate developer to join the Genome Sequence Informatics (GSI) team. The Software Developer will develop, maintain, fix and upgrade production systems and bioinformatics pipelines required for production analysis. Our production pipeline handles the data from eight Illumina sequencers, producing terabytes of data each week.

GSI, together with the Genomics team, are responsible for sequencing and analysing all data generated at OICR (https://genomics.oicr.on.ca/). GSI designs 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, OpenStack, Open Grid Engine, Apache Oozie, MySQL and PostgreSQL.

The main areas covered by GSI are:
• Lab tracking: We develop the open source MISO LIMS augmented by internally developed applications;
• Pipeline/Data management: We use workflow systems like SeqWare (http://seqware.io) to automate and streamline data analysis, tracking, and workflow management;
• Data release: Archiving data for long term storage and releases data to public archives;
• Reporting: We maintain 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 and explore new technologies and systems to take us into the future. Many of GSI’s software projects are open-source and available on Github: https://github.com/oicr-gsi/.

Your responsibilities will include:
• Designing and crafting software pipelines and applications to meet cancer research needs;
• Improving existing applications with new features and enhancements;
• Ensuring that the sequencing software pipelines are consistently, reliably, efficiently and correctly processing data;
• Deploying applications for production and development as required;
• Suggesting improvements and working with other team members to implement them;
• Supporting production by troubleshooting bugs and preventing outages;
• Building APIs and web services that link our systems together and facilitate reporting;
• Documenting and communicating pipeline processes, building the team knowledge base, and creating developer documentation and user guides; and
• Writing clean code, using source code control, unit and integration testing, and continuous integration.

• You have experience in end-to-end software development, responding to and diagnosing feature requests and bugs;
• You have strong experience working in a Linux environment and using the shell;
• You are competent with a general purpose software development language such as Java or C++;
• You want to contribute to all parts of the development process;
• You understand software engineering principles;
• You communicate clearly;
• You can understand complex problems and develop solutions;
• You have some knowledge of biology, genetics or sequencing;
• You have an open source account (e.g. Github) that contains examples of your code. Please provide this in your application.

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 www.oicr.on.ca.

CLOSING DATE: Until Filled


Software Developer – Ontario Institute for Cancer Research

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