Computational Biologist, Database Development (Bioinfo/LIMS)

Job Reference No. CBDBDev_P01067_HSA123442_BioApps_2022_03_03

Canada’s Michael Smith Genome Sciences Centre (GSC) is a state-of-the-art, large scale, high throughput, clinically accredited genomics and bioinformatics facility. If you have a computer science degree and experience in database programming and design—along with an interest in research science and motivation to contribute to efforts toward improving the lives of cancer patients—consider joining our team at the GSC!

The GSC’s Computational Biologist provides database planning, development and maintenance to support our core sequence pipelines. Duties include analysis, dissemination, as well as storage management and compression, of over 5Pb of internally generated sequencing data.

The position is anchored within a team of exceptional scientists, computational biologists and programmers, which collaborate directly on the development of robust, cost efficient, and competitive processes for new targeted and precision medicine analytical pipelines. By working within the GSCs bioinformatics facility, you will develop close relationships with world-renown computational and genome science technologists, cancer researchers and medical scientists; have access to one of the most robust computational and next generation genome sequencing technology facilities in Canada, all while living in one of the most beautiful, diverse and eclectic cities in the world. Your work will help to save lives and contribute to a world free from the fear of cancer.

This is an opportunity to work with highly motivated colleagues in a science-oriented, creative and dynamic environment. We offer a competitive salary, excellent benefits and significant career development opportunities. Apply now!

Duties and Responsiblities

• Assists in development and maintenance of 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 development and maintenance of 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 maintenance of 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 designing and building 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.

Education, Training and Experience

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

Skills and Abilities

• Experience in SQL, database programming and database design.
• Demonstrated ability in Python, Javascript, or other high level programming language
• Experience with REST API development.
• Experience with front-end web development (React.js, Javascript). Functional knowledge of distributed version control systems, such as GIT.
• Experience developing software as part of a team and 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.