Bioinformatics Specialist

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Note: Applications will be accepted until 11:59 PM on the Posting End Date.

Job End Date

At UBC, we believe that attracting and sustaining a diverse workforce is key to the successful pursuit of excellence in research, innovation, and learning for all faculty, staff and students. Our commitment to employment equity helps achieve inclusion and fairness, brings rich diversity to UBC as a workplace, and creates the necessary conditions for a rewarding career.

Job Summary
UBC established the Sequencing and Bioinformatics Consortium (SBC) to help make sequencing affordable and accessible to the largest number of researchers on campus.  Data analysis, data management and systems administration are essential components of all SBC activity, as the environment is one of rapid change and emerging technologies and methods, each requiring customized and novel data solutions.

The Bioinformatics Specialist is responsible for overseeing the UBC Sequencing and Bioinformatics Consortium's (SBC) analysis pipelines as well as compute and data management systems.  This individual researches, analyzes and implements solutions to support and enhance Consortium activities and provides excellent service to its users.
Organizational Status
Reports to the VPRI Shared Research Platform Manager – Operations, and works in collaboration with the Scientific Advisor of the SBC, VP Research & Innovation Office, the Advanced Research Computing (ARC) team, UBC IT, the users of the SBC (researchers, staff, students or industry clients) as well as collaborators at affiliated organizations.
Work Performed

• Acts as the lead analyst/programmer for bioinformatics data analysis and software development projects and lead architect for data management and database solutions.
• Provides design input and strategic technical suggestions in these areas to maintain an end-to-end system that efficiently houses, analyzes and disseminates high-quality data and results.
• Designs solutions to resolve system-related problems, meet user requirements, and streamline system workflows.
• Monitors and analyzes systems issues and provides recommendations for all systems supported infrastructure as part of regular operations.
• Writes and maintains systems documentation including user and technical manuals.
• Understand customer needs and requirements to develop, implement and monitor effective quality control processes; devise and review specifications for laboratory outcomes.
• Create and enforce standards in accordance with industry standards and customer expectations.
• Responsible for implementing and executing inspection, testing, and evaluation methods to ensure that products adhere closely to SBC quality expectations.
• Clearly defines all workflows, communicates documentation requirements for processes (SOPs), and ensures all practices are being followed and refined as required based on new learnings.
• Inspect intermediary and final outputs and compare to quality requirements; approve or reject output as require.
• Ensures internal department workflow and tracking documents exist and are up to date; authority to pause internal processes until pipelines/processes are approved and documented appropriately.
•  Acts as a liaison between technical groups and stakeholders to coordinate the system's installation and ensure technical compatibility and satisfaction.
• Develops tests for all software developed by creating test data and inputs and testing code. 
• Implements data management tools including relational database management applications for efficient storage and retrieval of all results from all samples used in the research work.
• Conducts and supports bioinformatic and statistical analysis and interpretation of DNA and RNA sequencing data in internal and collaborative research projects using appropriate software tools and custom-written programs and scripts.
• Documents and communicates analysis results in written and oral form.
• Contributes to team interactions by consultation, collaboration, teamwork and task sharing.
• Works to ensure that experimental design includes data management and analysis considerations.
• Ongoing professional development in bioinformatics data management and analysis.
• Offers guidance to researchers for project-specific protocol adaptations. Evaluates technology through vendor collaborations.
• Maintains appropriate professional designations and up-to-date knowledge of current information technology techniques and tools.
• Develops and implements innovative strategies as technology evolves
• Works with SBC partners at other local sequencing centres to address client needs, as required.
• Performs tasks as needed not described above in consultation with the Shared Research Platform Manager – Operations or Scientific Advisor.

Consequence of Error/Judgement
Errors would have significant impact to the integrity and reputation of the Consortium, the research of its users and the development of the genomics community in British Columbia. Errors in judgement would affect UBC's ability to create a nationally recognized Consortium, and recruit and retain talented researchers, staff and students. Errors would have a significant impact on the university's ability to receive grant funding and on the Scientific Advisor's ability to carry out his/her mission and functions.
Supervision Received
Works independently under the supervision of the Associate Director, under broad goals and objectives developed in conjunction with the Scientific Advisors of the Sequencing and Bioinformatics Consortium. Responsible for independently developing and implementing projects based on the goals and objectives of the Sequencing and Bioinformatics Consortium.
Supervision Given
Expected to assist and advise other SBC team members and users including students. May supervise or participate in supervision of more junior personnel such as non-union technical staff, undergraduate research assistants or Co-op students.
Minimum Qualifications

Undergraduate degree in a relevant discipline.  Minimum of three years of related experience, or the equivalent combination of education and experience. 

- Willingness to respect diverse perspectives, including perspectives in conflict with one’s own
- Demonstrates a commitment to enhancing one’s own awareness, knowledge, and skills related to equity, diversity, and inclusion
Preferred Qualifications

• Master’s degree preferred.
• Three years of related bioinformatics experience, or the equivalent combination of education and experience.
• Experience working in Linux/UNIX operating system environment. Proficiency in one or more of bash scripting, Python, and R.
• Familiarity with Git or other code versioning management software.
• Familiarity with bioinformatics tools for sequence analysis e.g. QC suites, aligners, assemblers,  gene expression
• Experience working with high performance computing or other Linux cluster environment or cloud computing systems.
• An understanding of parallelization using job schedulers such as PBS Pro or  SLURM.
• Eager to learn new things and contribute to a dynamic research environment. Demonstrates strong technical, analytical and problem-solving skills.
• Ability to plan and carry out multiple tasks and projects, to prioritize and organize effectively, to work under pressure and to meet established timelines.
• Ability to work independently and in a team environment.
• As this position also involves extensive personal interaction as well as via phone and email, excellent written and verbal English communication skills are critical.
• Familiarity with sequencing instrumentation hardware and software requirements for data collection.
• Familiarity with the following is an asset:
  • Commercial cloud computing environments e.g. Google, Amazon
  • UBC ARC’s Sockeye high-performance computing platform
  • Software architecture and design skills such as UML
  • Experience with C/C++ or Java.
  • Knowledge of RDBMS systems MySQL or Oracle, experience in database administration
  • Web application configuration experience with PHP, Tomcat, and Apache
  • Continuous integration systems such as Bamboo, Jenkins, and OpenShift
  • Experience with statistical and computational approaches to the analysis of genomic and genetic data sets, including conducting and publishing biological research including experimental design and/or domain-specific knowledge including human genetics, microbial ecology and immunology