Software Developer

Institution/Company:
Ontario Institute for Cancer Research
Location:
Toronto, ON, Canada
Job Type:
  • Programmer/Developer
Degree Level Required:
Bachelor's, Masters, PhD
Apply Now

Software Developer

The Ontario Institute for Cancer Research (OICR) is seeking an experienced and passionate developer to join the Genome Sequence Informatics (GSI) team. The Senior Software Developer will develop, maintain, fix and upgrade production systems and bioinformatics pipelines required for production analysis. Our production pipeline handles the data from seven Illumina sequencers, producing terabytes of data each week.

GSI is part of OICR’s Adaptive Oncology, specifically the Genomics, program (https://genomics.oicr.on.ca/) and supports all three sequencing teams: the Translational Genomics Laboratory for clinical samples, the Genomics Resources Program for high-throughput research projects, and the Princess Margaret Genome Centre for functional genomics. 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 clinicians and researchers who use it. We use languages and software tools like Java, Perl, Python, Javascript, OpenStack, Open Grid Engine, Univa, MySQL and PostgreSQL.

The main areas covered by GSI are:

  • Lab tracking: We develop the open source MISO LIMS (https://miso-lims.github.io) augmented by internally developed applications;
  • Pipeline/Data management: We use workflow systems like Niassa (https://oicr-gsi.github.io/niassa/) and Cromwell (https://cromwell.readthedocs.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 550 node, 9600+ hyperthread cluster and 12 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/ and https://github.com/miso-lims.

Responsibilities:

  • Designing and crafting software pipelines and applications to meet cancer research needs;
  • Building APIs and web services that link our systems together and facilitate reporting;
  • 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;
  • Documenting and communicating pipeline processes, building the team knowledge base, and creating developer documentation and user guides;
  • Writing clean code, using source code control, unit and integration testing, and continuous integration.

Qualifications:

  • You have 2+ years of experience in software development;
  • 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 applicatio

Additional Information

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.

Keywords: