Research Programmer - Ryan Morin Lab

Institution/Company:
Canada's Michael Smith Genome Sciences Centre (GSC)
Location:
Vancouver, BC, Canada
Job Type:
  • Programmer/Developer
Degree Level Required:
Bachelor's
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Research Programmer - Ryan Morin Lab

Job Summary

The Genome Sciences Centre at BC Cancer is looking for a highly motivated programmer with bioinformatics expertise to work in a fast-paced and highly rewarding research environment with a group of scientists and students who are at the bleeding edge of lymphoid cancer research. The successful candidate will work closely with all laboratories in the Centre for Lymphoid Cancer, namely Drs. David Scott, Christian Steidl, Leandro Venterutti and Ryan Morin. We are seeking a highly organized and motivated individual who will take a leadership role in conceptualizing, designing and implementing pipelines for standardizing and automating high-throughput analyses of cancer genome data. The position will support a growing diverse team including trainees and clinical researchers with expertise in bioinformatics, biostatistics and molecular biology. As a member of this group, you will be tasked with ongoing implementation, documentation, improvement, and testing of analytical tools and pipelines and will be required to follow best practices in software engineering. This will include ensuring proper handling, quality assurance and versioning of experimental data and metadata. You will also actively participate in routine code review and maintain robust version control of analytical pipelines using GitHub and continuous integration. As these pipelines typically begin with terabyte-scale inputs and require hundreds to thousands of concurrent processes, part of your job will involve ensuring efficient parallelization using a high-performance cluster with an emphasis on compatibility, reproducibility, ease of installation, and interoperability with various cloud-like computing environments.

Organizational Status

Reports to Dr. Ryan Morin, Senior Scientist, Genome Sciences Centre and Bioinformatics Lead, Centre for Lymphoid Cancer.

Responsibilities:

Specific Duties

As a scientific programmer you will work with our team members to: •Design, implement, and maintain pipelines for cancer genomic analyses based on the needs of the team, mostly using Snakemake, Python, and R •Suggest, and implement, improvements within our existing code base to increase efficiency and reduce the burden of large temporary files •Design and implement testing suite to ensure robustness, scalability, and reproducibility of existing and new bioinformatic pipelines •Review pull requests and ensure internal and external contributors adhere to best practices and ensure compatibility with existing features •Assist trainees and staff with converting non-production code (R and Python) into reusable, documented, modular code •Implement a testing framework using continuous integration to ensure the functionality of existing and new code is consistently maintained •Evaluate third-party software for new applications and integrate into new or existing pipelines •Build on existing databases and expand on existing application programming interfaces

Qualifications:

Qualifications •Bachelor’s Degree in Computer Science completed

Required Skills: •1+ years of Python programming experience and demonstrated track record in contributing to open-source software •Demonstrated proficiency in R (including tidyverse) •Excellent problem solving and troubleshooting skills •Organization and ability to produce results while maintaining multiple tasks •Experience developing software in a Linux or UNIX-like environment including shell scripting and common command-line tools •Experienced using Git for source control and willingness to assist a diverse team with its proper use •Demonstrated interpersonal skills including the ability to work effectively with others in a team environment

Preferred Skills: •Experience with basic Linux systems administration •Effective use of high-performance computing environment using the Slurm workload manager •Expertise with automated software testing •Package/dependency management expertise (e.g. conda) and/or experience with Docker, Singularity, or Kubernetes •Experience with mySQL or similar databases •Working knowledge of a combination of Awk and Perl and experience with databases would be beneficial

  • How to Apply

    Please submit a detailed cover letter and resume to bcgscjobs@bcgsc.ca, using Job Reference No: RP_R00008_RDMorin Lab_2011_11_05 in the subject line of your email. This posting will remain online until filled. Due to current COVID-19 restrictions, the position would require working remotely on a temporary basis. This restriction would be re-evaluated upon re-contracting.

Additional Information

We believe that equity, 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.

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