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  • Software Developer, Bioinformatics

    Position: Software Developer, Bioinformatics
    Site: MaRS Centre, Toronto
    Department: Informatics and Biocomputing
    Reports To: Senior Manager
    Salary: Commensurate with level of experience
    Hours: 35 Hours per Week
    Status: Full-Time, Permanent


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

    The GSI team 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, OpenStack, Open Grid Engine, Apache Hadoop, Apache Oozie and PostgreSQL.

    The main areas covered by GSI are:

    Lab tracking : OICR uses a commercial LIMS augmented by internally developed applications.
    Pipeline/Data management: We use SeqWare (http://seqware.io) 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.

    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.
    QUALIFICATIONS:

    You have experience in end-to-end software development, responding to and diagnosing feature requests and bugs;
    You have experience working in a Unix/Linux environment, using the shell;
    You are competent with a general purpose software development language such as Java;
    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; and
    You have some knowledge of biology, genetics or sequencing.

    For interested candidates, please apply here:

    https://www.recruitingsite.com/csbsi...bNumber=776156

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