Canada’s Michael Smith Genome Sciences Centre (GSC)

Today’s Research. Tomorrow’s Medicine.

 

The GSC is a department of the BC Cancer Research Institute and a high-throughput genome sequencing facility. We are leaders in genomics, proteomics and bioinformatics in pursuit of novel treatment strategies for cancers and other diseases.

Among the world’s first genome centres to be established within a cancer clinic, for more than two decades our scientists and innovators have been designing and deploying cutting-edge technologies to benefit health and advance clinical research.

Among the GSC’s most significant accomplishments are the first publication to demonstrate the use of whole-genome sequencing to inform cancer treatment planning, the first published sequence of the SARS coronavirus genome and major contributions to the first physical map of the human genome as part of the Human Genome Project.

By joining the GSC you will become part of an exceptional and diverse team of scientists, clinicians, experts and professionals operating at the leading edge of clinical research. We look for people who share our core values—science, timeliness, respect—to join us on our mission to use genome science for the betterment of health and society.

Summary

Job Reference No: CB LIMS HSA # 107100_P01067_2021_04_16

In accordance with the Mission, Vision and Values, and strategic directions of Provincial Health Services Authority, patient safety is a priority and a responsibility shared by everyone at PHSA. As such, the requirement to continuously improve quality and safety is inherent in all aspects of this position.

The Computational Biologist will participate in the analysis of sequencing data by developing, refining and adapting bioinformatics tools for a high-throughput processing pipeline.  The Computational Biologist will also participate in the development and maintenance of the production databases, which provide tracking of all of the laboratory and bioinformatics analysis pipelines at the GSC.  Additionally, the Computational Biologist will assist in the packaging and distribution of developed tools and analysis results to the scientific community, and will be contributing to the preparation of scientific publications. 

Duties

  • Assists in the development and maintains the core sequence analysis pipelines at GSC, including but not limited to:
    • QC of sequencing data;
    • Alignment of sequenced reads;
    • Formatting and manipulation of alignment files for use by downstream pipelines (e.g. merging, reheadering);
    • Dissemination of data to collaborators;
    • New analyses pipelines as required.
  • Assists in the development and maintains GSC laboratory, quality and analysis databases, including:
    • Routine database integrity checks and database maintenance;
    • Development of views and interfaces for data entry;
    • Development of reports for internal users and collaborators;
    • Investigation of new frameworks and designing new schemas and tables.
  • Communicates with stakeholders in the lab, on analysis teams, and with external collaborators to understand and document requirements for development and to respond to questions about collaborator data and data quality.
  • Works with upstream and lab teams generating data to be housed in the database, and with downstream users of the databases to meet requirements, and responds to internal requests for query and API support.
  • Participates in the development and maintains ETL pipelines between GSC production databases.
  • Manages the storage and compression of over 5Pb of internally generated sequencing data as well as the download and storage of external data.
  • Works closely with GSC Systems team and Quality Assurance team to establish and carry out best practices for data security, and ensure compliance with ISO 27001 certification, CAP/DAP clinical accreditation requirements and other data use agreements.
  • Tests and validates new data analysis software for analyses such as alignment, duplicate marking and merging.
  • Participates in code walk-throughs and reviews of solutions.
  • Participates in the design and builds database solutions, taking performance into consideration.
  • Coordinates production problem resolution for assigned applications, including working with other technical teams.
  • Produces thorough but concise written documentation of database tables, applications, validations, SOPs, and other processes and procedures as required.

Performs other related duties as required.

Eligibility

Education, Training and Experience

  • Graduation from a recognized Bachelor of Science Program in Computer Science or equivalent with significant computer science components. 
  • Two (2) years of recent related experience or an equivalent combination of education, training and experience acceptable to the GSC Group Leaders.

Skills and Abilities

  • Demonstrated expertise in database programming and database design.
  • Demonstrated ability in Python.
  • Experience designing and/or maintaining a relational database including knowledge of SQL or PostgreSQL, and with ORMs.
  • Experience with REST API development.
  • Experience with front-end web development (AngularJS, React).
  • Functional knowledge of distributed version control systems, such as GIT.
  • Experience developing software as part of a team, familiarity with Agile development and ticketing systems.
  • Comfortable working in an Unix environment, including experience with shell scripting and common command-line tools.
  • Excellent verbal and written communication skills.
  • Demonstrated interpersonal skills including the ability to work effectively with others in a team environment.
  • Demonstrated ability to efficiently organize work assignments and establish priorities.

Apply

Please submit a cover letter, curriculum vitae and the names of three referees willing to provide letters of reference. The cover letter should include a brief description of your previous research experience and long-term career goals. Please email your application to bcgscjobs@bcgsc.ca.

Important!

We believe that diversity and inclusivity are essential for the advancement of human knowledge and science.

We welcome all applicants and provide all employees with equal opportunity for advancement, regardless of race, colour, ancestry, place of origin, political belief, religion, marital status, family status, physical or mental disability, sex, sexual orientation, gender identity or expression, age, conviction of a criminal or summary conviction offence unrelated to their employment.

All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority.

Due to COVID-19 restrictions, the position would require working remotely on a temporary basis.

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