Summer Coop student
Company name: Simon Fraser University
William Hsiao, PhD
Senior Scientist (Bioinformatics),
Clinical Assistant Professor, Pathology & Laboratory Medicine, UBC
Adjunct Professor, Molecular Biology and Biochemistry, SFU
Rm 2067a, 655 West 12th Avenue
Vancouver, BC, V5Z 4R4
Email: [email protected]
Starts: May 1, 2019
The length of the work term: (4-8 months)
The Hsiao Lab based at BC Centre for Disease Control Public Health Laboratory with academic affiliation at both University of British Columbia and Simon Fraser University develops innovative solutions spanning the entire epidemiology and genomics knowledge generation spectrum from data processing, management, analysis, to knowledge engineering and discovery. We combine bioinformatics techniques (sequence analyses and workflow development) with semantic web technologies (RDF, ontology, big data) to support better genomic epidemiology solutions in public health. Our lab is looking for a Co-Op student (4-8 months) to help with system automation of bioinformatics pipeline software, in support of rapid genomic sequencing, analysis and reporting. The successful candidate will work closely with our team of curators, computational biologists and bioinformatician and will be part of the team at BCCDC. Successful candidate will be supervised by a senior scientific programmer and Dr. Hsiao.
This summer co-op position will primarily help to achieve easy deployment of Galaxy (https://galaxyproject.org/) within a Microsoft Azure cloud computing environment, as well as the development of Galaxy automation scripts (using Ansible). This work is done in association with the consortium IRIDA.ca project, an open-source platform for sequencing that is being deployed in Canadian labs and internationally. Galaxy is used to perform IRIDA workflows, but must vary in configuration depending on provincial health lab or other agency infrastructure.
Undergraduate degree in a relevant discipline. Bachelor’s Degree in bioinformatics, computer science or related field
It would be advantageous to have experience with a mixture of existing software:
- Operating System: Linux (CentOs)
- Bioinformatics: Galaxy
- Automation scripting: e.g. Puppet, Ansible
- Programming languages: Python
- Package management: Conda
- Grid networking: e.g. Slurm, Grid Engine, SOG
- Cloud computing: Microsoft Azure
- Container tech: Docker / python virtual environment
Job duties and Responsibilities:
Create the ansible script(s) needed to create and manage on-demand instances of Galaxy (https://github.com/galaxyproject/ansible-galaxy) in a cloud environment. Create service monitoring / testing, with attention to internet and linux server security issues. Work within a team environment that thrives on code review and a shared, versioned GitHub code base. Provide creative solutions for data transfer issues that arise with the volume of genomics data processed within a cloud environment. Become our Lab’s genomics cloud computing expert!
Bioinformatics Data Analyst
We are seeking a bioinformatics analyst with experience in high-throughput sequencing data analysis to join the research groups of Dr. William Hsiao (https://www.cidgoh.ca) and Dr. Amy Lee (https://sfu-lee-lab.github.io/Lee_Lab_Webpage/) in Vancouver, Canada.
The primary responsibility of the candidate will be to process and analyze next-generation sequencing data, especially in the area of microbial genomics, host transcriptomics and multi-omics integrative analyses. Other responsibilities may include supporting data analysis of trainees in the group and providing technical documentation for grant reports and other reporting needs. The selected candidate will work with a multidisciplinary team of other bioinformatics scientists and molecular biologists, software engineers, data scientists, and data curators.
The primary work location will be Simon Fraser University Burnaby Campus located in Greater Vancouver. Simon Fraser University is surrounded by wonderful greenspace on the Burnaby Mountain Conservation Area approximately 5 km from the edge of the city of Vancouver (and a three-hour drive north of Seattle, Washington, in the U.S.). SFU has been consistently ranked as Canada’s top comprehensive University (Maclean’s ranking no. 1 for 13 of the last 14 years).
– Analysis of microbial genomics and host RNASeq data
–Collaborate with wet-lab scientists and software engineers to design experiments, analyze data, and interpret results
– Design and implement new data analysis workflows using common workflow engines such as Nextflow
– Package the analysis pipelines using container technologies
– Test and deploy analysis workflows on computing clusters and cloud environments
– Participate in scientific discussions and presentations
– BSc or MSc in computer science, bioinformatics, computational biology, or relevant experience or certification.
– Documented prior experience analyzing genomics and high-throughput sequencing data.
– Strong analytical skills and a solid foundation in statistical analysis.
– Demonstrated ability to work in a team environment (references required)
– Demonstrated ability in R or other similar statistical programming languages.
– Willing to work on a variety of bioinformatics and data science-related projects.
– Must have excellent oral and written communication skills and ability to organize, analyze and communicate scientific data.
– Must have good technical writing skills to document code and applications.
– Must have strong self-motivation and be able to work in a multi-tasking and multi-disciplinary environment.
Other Considerations (experience considered an asset but not necessary):
– Experience working with microbial genomics data is an asset.
– Experience in designing and building robust computational pipelines in a Unix-like
– Familiarity with next-generation sequencing technologies such as Illumina and Oxford
Nanopore sequence platforms and the associated computational analysis tools.
– Familiarity with cloud computing systems (Digitial Research Alliance of Canada Cloud, Amazon Web Services, MS Azure, and Google Cloud Platform) and containerization technologies (Docker/APPtainer)
Please send your cover letter, CV and names of two referees to Dr. William Hsiao and Dr. Amy Lee ([email protected]) with the subject line: Bioinformatics_Analyst. We thank all applicants and regret that only those selected for an interview may be contacted further.
We hire on the basis of merit and are committed to employment equity. All qualified persons are encouraged to apply. We especially welcome applications from members of visible minority groups, women, Aboriginal persons, persons with disabilities, persons of minority sexual orientations and gender identities, and others with the skills and knowledge to engage productively with diverse communities. In accordance with immigration requirements, preference will be given to Canadian citizens, landed immigrants and permanent residents of Canada. We are committed to providing employees with a positive working environment supporting growth and flexibility. Simon Fraser is located in a beautiful conservation area in metro Vancouver with access to a wide range of recreational opportunities. Contact us to learn more.
Start Date: June 15, 2023
End Date: Full-term position for 1 year, renewable pending on funding and performance
Closing date: Open until position is filled
Salary: commensurate with experience and competitive