Bioinformatician

Institution/Company:
Ontario Institute for Cancer Research
Location:
Toronto, ON, Canada
Job Type:
  • Staff
Degree Level Required:
Masters, Bachelor's
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Bioinformatician

Position: Bioinformatician Site: MaRS Centre, Toronto Department: Computational Biology (Genome Sequence Informatics) Reports To: Senior Manager Salary: Commensurate with level of experience Hours: 35 hours/week Status: Full-time, Permanent

The Ontario Institute for Cancer Research (OICR) is seeking an experienced and passionate Bioinformatician to join the Genome Sequence Informatics (GSI) team. The Bioinformatician functions in an intermediate technical role that requires an individual with proven skills in both biology and computing, and who is dedicated to supporting a multi-disciplinary team of scientists, laboratory technicians, and informatics professionals.

Learn more about working at OICR here.

GSI is part of the Genomics program at OICR (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: Develop the open source MISO LIMS (https://miso-lims.github.io) augmented by other applications; Pipeline/Data management: Develop and run 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: Archive data for long term storage and release data to public archives; Reporting: Maintain a suite of specialized reports for quality control, forecasting, and lab operations; Bioinformatics support: Perform project-specific analysis for collaborators, including 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; and Cancer Genome Interpretation: Analyze and interpret genomic data using accredited pipelines and processes and produce for clinical purposes.

Responsibilities:

Performing initial stage analysis on next-generation sequencing data transforming data from sequence to information meaningful for biologists; Ensuring that data is managed efficiently, securely, and without loss or corruption through its lifecycle; Providing bioinformatics support and training to end-users (research laboratory staff, remotely located collaborative users); Responsibility for researching, planning, implementing, and testing bioinformatics software tools that meet the analysis needs for specific collaborative projects; Development and support of protocols and workflows for standard analysis tasks; Continuous interaction with the production development team to ensure that the NG sequencing software pipeline is consistently, reliably, efficiently and correctly processing data; Interaction with collaborative research groups to explain next-generation sequencing capabilities and limitations, advise on experimental design, and present findings tools, techniques; Work with 3rd party software vendors to characterize and resolve problems with production software systems; and Responsibility for documenting and communicating pipeline processes and building the team knowledge base.

Qualifications:

Bachelor’s or master’s degree in related discipline, with demonstrated experience in the skill set. Advanced skills in Linux shell programming environment; Proficiency with some Linux based scripting language (Perl, Python etc.) required; Competence with general purpose software development languages such as C, C++, Java preferred; Experience with statistical and graphical software packages (R, Matlab) and associated bioinformatics libraries; Must have excellent communications and interpersonal skills; Willingness to be accessible and respond to production pipeline issues outside of normal working hours; Experience supporting a high availability production software environment; Experience providing end-user software support, diagnosing and resolving end-user issues; Experience working in a multidisciplinary team environment; and Experience working with data from the Illumina, Nanopore or other sequencing platforms is highly desirable.

Additional Information

OICR is a collaborative, not-for-profit research institute accelerating the development of new cancer research discoveries for patients around the world while maximizing the economic benefit of this research for the people of Ontario. We are dedicated professionals who bring expertise to each of our roles. We are looking for individuals who share our values of excellence, innovation, collaboration, impact, responsibility and community.

Launched in December 2005, OICR is an independent institute funded by the Government of Ontario through the Ministry of Colleges and Universities.

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

CLOSING DATE: Until Filled

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.

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

Resume Format: If you elect to apply, you will need a text or HTML version of your resume so that you can cut and paste it into the application box provided. Before you submit the completed application, you will be asked to attach one or two files to your application. Please attach your resume as a .pdf or .doc file.