The Computational Biologist will participate in the analysis of sequencing data by developing, refining and adapting bioinformatics tools for a high-throughput processing pipeline. They will also participate in the development and maintenance of our production databases, which provide tracking of all of the laboratory and bioinformatics analysis pipelines at the GSC. Packaging and distribution of developed tools and analysis results to the scientific community and contribution to preparation of scientific publications are expected.
- Develops 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 (eg merging, reheadering)
- Dissemination of data to collaborators
- New analyses pipelines as required.
- Develops 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.
- Maintains and develops 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 IS27001 certification 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.
- Designs and builds database solutions taking performance into consideration.
- Coordinates production problem resolution for assigned applications, including working with other technical teams.
- Evaluates third-party software and incorporate new systems into legacy systems
- 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 (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 a 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.
- Previous experience in a bioinformatic setting, though not required, would be considered an asset
Please send your resume with cover letter to firstname.lastname@example.org.
Internal (HEU and HSA union members) applicants please visit internaljobs.phsa.ca to apply online for internal job postings.