Opportunities

We are always looking for self-motivated and friendly students (summer intern and graduate) and postdoctoral fellows to join our diverse team. Students with a background or interest in public health, infectious diseases, bioinformatics, genomics, microbiology, and computer science are encouraged to apply. We accept students through the Faculty of Health Sciences and the Faculty of Science (Dept. of Molecular Biology and Biochemistry) at Simon Fraser University. See our Research Page for a list of ongoing projects and check out our GitHub for the tools and applications we have developed.

Please send a cover letter (introduce yourself, your academic background and interests) and a CV to [email protected] (addressed to Dr. William Hsiao). For undergraduate students applying for internships or graduate studentships, please also include your unofficial transcripts so we can see what courses you’ve taken. We will do our best to get back to you in a timely fashion but please email us again if you don’t hear back within two weeks.

Periodically, we will have grant-funded research associate (post-doctoral) and other staff positions (computer programmers, project coordinators, etc) available. Please check out the current opportunities below. Applicants should follow the specific instructions in the ADs to apply. Only qualified applicants will be contacted. Thank you.

Open Positions

Job Title: IT Analyst and Cloud Computing Developer

Start Date: July 1, 2021

Job 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

Job ID: Summer21CIDGOH

Job Summary

Are you interested in applying your system administration and software development skills to public health infectious disease challenges? The Hsiao Laboratory (https://www.sfu.ca/fhs/about/people/profiles/william-hsiao.html) at Simon Fraser University has an immediate opening for an IT analyst position.

The successful candidates will have close interaction with other researchers and scientific programmers in the IRIDA project (http://www.irida.ca/) – a Canada-wide collaboration with international partners to develop bioinformatics resources for genomic epidemiology. The candidate will also work with public health professionals (our end users and stakeholders) to ensure the tools we develop can directly benefit health care research and operations. IRIDA is the primary platform used in Canada’s National Microbiology Laboratories for infectious disease investigations.

The primary responsibilities of the candidate will be to work with scientists at SFU to help administer the cluster and cloud computing environments necessary for performing data analysis and to make the IRIDA platform and associated bioinformatics resources further “cloud-compatible and deployable”. Secondary responsibilities include helping to design and develop new bioinformatics analysis workflows and troubleshooting system errors. The candidate, as part of a research group, will participate in scientific conferences, presentations, and publications. In collaboration with other members in the Hsiao laboratory, semantic web based solutions will be explored. Knowledge of biology is not essential but interest in applying computer science and statistics to solve health care and biological problems is required. Technologies currently used by the group include SQL, python, JAVA, Workflow development frameworks e.g( Snakemake, Nextflow), RDF (resource description framework), OWL, JSON, Javascript, virtualization (docker and VM), Galaxy (https://galaxyproject.org/), OpenStack, REST API, SPARQL, GitHub version control, Conda, Django framework, and the Java Spring framework.

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). During the current pandemic, the candidate will work remotely until further notice.

Work Performed:

– Facilitate the setup and maintenance of scientific computing environments

– Develop cloud and semantic web enabled applications as part of the core IRIDA development team

– Design and implement new data analysis pipelines using the IRIDA framework

– Package the analysis pipelines using container technologies

– Test and deploy analysis workflows on computing clusters

– Setup bioinformatics software and other software packages needed for the research team

– Document installation of workflows and containers

– Participate in scientific discussions and presentations

Qualifications:

– BSc or MSc in computer science, computer engineering, bioinformatics, computational biology, or relevant experience or certification. Recent University graduates are eligible to apply for this job.

– Documented experience with software development (minimal 2+ years of experience).

– Documented experience with Linux system administration (minimal 2+ years of experience).

– Proficiency in at least one of: C++, Java, Python (preferred), JavaScript (preferred) and ability to write shell scripts to automate tasks.

– Must have excellent communication skills and be fully fluent in spoken and written English.

– Familiarity with cloud computing systems (Compute Canada Cloud, Amazon Web Services, MS Azure, and Google Cloud Platform) and containerization technologies (Docker)

– 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 genomics data is an asset.

– Experience in designing and building robust computational pipelines in a Unix-like environment.

– Familiarity with Django web development framework.

– Familiarity with next generation sequencing technologies such as Illumina and Oxford

Nanopore sequence platforms and the associated computational analysis tools.

– Familiarity with semantic web technologies and ontology development.

Contact:

Please apply through Indeed and send your cover letter, CV and names of two referees to Dr. William Hsiao with the subject line: Position-IT 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.

Reference ID: Summer21CIDGOH

Expected start date: 2021-08-01

Job Type: Full-time

Benefits:

  • Extended health care

Schedule:

  • Monday to Friday

Work remotely:

  • Temporarily due to COVID-19

Company name:  Simon Fraser University

Contact: 

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

Canada

Tel: 604-707-2561

Fax: 604-707-2603

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.

Qualification/Experience/ Skills:

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!