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!
The Centre for Infectious Disease Genomics and One Health, led by Dr. William Hsiao and located at Simon Fraser University (https://cidgoh.ca/), is seeking a software developer to contribute to the application development to support a number of projects, ranging from text mining and ontology mapping applications to data validation and visualization systems to increase data interoperability between agencies. The position will provide experience in a new era of software development focused on the standardization of data elements and structures using semantic web technology such as Web Ontology Language (OWL) ontology, the OBOFoundry.org suite of ontologies, and SPARQL querying.
What do you bring (Qualifications and Experience) :
Candidates must demonstrate within the content of their application that they meet the following criteria:
- Bachelors or Masters’s degree in Computer Science, or related computational field, with minimum 3 years of working experience in Linux application server environment (e.g. Ubuntu, CentOS) and Apache or NGINX server.
- Web development experience in setting up interactive websites with user authentication in for example Django or WordPress.
- Familiarity with the OBOFoundry.org ontology family, OWL 2.0 ontology curation, and Stanford Protégé editor will be an asset.
This is a one-year position with the possibility of extension depending on the availability of funds and performance. Salary will be commensurate with education and experience. The successful candidate, as part of a research group, will participate in scientific conferences, presentations, and publications.
How to apply:
Please send your cover letter, CV, and names of two referees in a single PDF to Dr. William Hsiao ([email protected]) with the subject line: Position-Onto-2023.