Positions

Honours undergrad research students, and graduate students interested in any of our projects should contact Fiona Brinkman directly at brinkman@sfu.ca. For other positions listed below, see the instructions associated with each position. See also further information below for applicants.

Current lab openings

Graduate student positions available for 2017!

This Fall 2016 we were successful in securing three of the 16 Genome Canada bioinformatics grants awarded across Canada – all building on our large IRIDA (www.irida.ca) infectious disease analysis platform project. Graduate student projects will now be available starting in 2017 (January, May or September start) that are suitable for students with a range of computer science and microbiology/genomics backgrounds. Specific projects include the following – please inquire by emailing brinkman@sfu.ca if you are interested:

- Improving prediction of antimicrobial resistance genes/phenotypes from metagenomics data, in collaboration with researchers at McMaster University who are expanding the Comprehensive Antibiotic Resistance Database (CARD) and computer science researchers at Dalhousie University developing faster algorithmic approaches for sequence searching.

- Expanding aspects of our web-based microbial genome visualization tool (improves on IslandViewer for viewing many genomes at once) – and using this to analyze select infectious disease outbreak datasets. Analyses will capitalize on integrated ontology information thanks to our new international GenEpiO (Genomic Epidemiology Ontology) consortium. See www.irida.ca/data-integration and github.com/GenEpiO/genepio.

 

Web Application Software Developer:

Would you like to play a key role the development of web-based bioinformatics applications to be used internationally for infectious disease research and public health outbreak investigations? The Brinkman Laboratory at Simon Fraser University (Metro Vancouver, BC) has an opening for a member of our team: a software developer who would further develop tools aiding microbial genome analysis for the national IRIDA.ca project and related international initiatives. This person will work with the support of infectious disease researchers in our group, developing new visualizations for our IslandViewer software, and associated tools. The successful candidate will work as part of an interdisciplinary team of software/database developers, bioinformaticians, data curators and biologists/microbiologists, including our national and international collaborators. Tasks will focus on development of these select web-based bioinformatics tools, and providing some support to researchers in our group with related software development needs.

The qualified applicant will have Bachelor’s degree in the computer sciences, strong knowledge of Linux and MySQL, and demonstrated experience designing web-based interfaces and visualization tools using Javascript libraries/frameworks and CSS.  Some Perl and/or Python experience is desired, with additional knowledge of web frameworks including Django or Catalyst being an asset. Bioinformatics experience is beneficial but not essential for this position.

Salary is based on experience and is competitive. Please quote “position WASD2016-1S” in the subject line of your email if you are interested in this position and email your resume to: brinkman-jobs (at) sfu.ca

We thank all applicants and regret that only those selected for an interview may be contacted further. Note: In accordance with immigration requirements, preference will be given to Canadian citizens, landed immigrants and permanent residents of Canada.

Database Developer:

Do you enjoy integrating data, enabling insights not possible before, and working with an interdisciplinary team of researchers? The Brinkman Laboratory at Simon Fraser University (Greater Vancouver, B.C., Canada) has a unique opening for a database developer position as part of a national project involving the integration of select data for the Canadian Healthy Infant Longitudinal Development (CHILD) Study (http://www.canadianchildstudy.ca/) and AllerGen Network Centre of Excellence (http://allergen-nce.ca/). The successful candidate will work as part of an interdisciplinary team of software/database developers, bioinformaticians, data curators and biologists, including our national and international collaborators. Tasks will include maintenance of the existing database, updating data from external databases, improving the user interface and the integration of additional rich data as part of a newly funded project.

The qualified applicant will have Bachelor’s degree in the computer sciences with web/database development experience. Biology/Bioinformatics experience is preferred but not essential. The applicant should have strong knowledge of MySQL and experience with Linux and Javascript is an asset.

Salary is based on experience and is competitive. Please quote “position ABDB2016-2D” in the subject line of your email if you are interested in this position and email your resume to: brinkman-jobs (at) sfu.ca

We thank all applicants and regret that only those selected for an interview may be contacted further. Note: In accordance with immigration requirements, preference will be given to Canadian citizens, landed immigrants and permanent residents of Canada.


Aerial view of SFU facing north

 

More information for potential applicants

The Brinkman Laboratory comprises an interdisciplinary computer lab and molecular microbiology lab environment, with access to notable additional resources, including our Computing Cluster (“Buster the Cluster”) and File Server, WestGrid, and departmental facilities. The Department of Molecular Biology and Biochemistry (MBB) at Simon Fraser University is housed in one of the newer buildings on campus, the South Science Building. MBB and the institute it formed from has produced a significant number of prominent bioinformaticists/genomicists who have gone on to become a coordinator of NCBI’s Genbank, coordinator or instructor of the Canadian Bioinformatics Workshop, or play leadership roles in international pharmaceutical companies, genome sequence centres and other genomics/bioinformatics facilities. In addition to the department’s interest in genomics and bioinformatics, the university has also indicated its strong interest in fostering interdisciplinary health-related research: It formed an interdisciplinary Faculty of Health Sciences, the IRMACS (Integrated Research in the Mathematics and Computing Sciences facility (part of our research group is located there) and SFU recently further strengthened its mandate to support interdisciplinary, engaged research through its strategic vision.

Simon Fraser University is located within wonderful greenspace within the Burnaby Mountain Conservation Area in Greater Vancouver, British Columbia, Canada, 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 by respected national surveys, such as Maclean’s, as one of Canada’s top three comprehensive universities for almost 20 years. In the past few years SFU was listed among Canada’s top 100 employers (Mediacorp Canada); named one of Canada’s top 10 family-friendly employers (Today’s Parent magazine) and has won the YWCA’s Innovative Workplace of the Year award, among others. Note that Vancouver has been chosen as the world’s “Most Liveable City” the majority of times in the past decade by the Economist Intelligence Unit (EIU).

Please see Student Central, the MBB website and SFU Bioinformatics for more information regarding graduate student admissions, M.Sc./Ph.D. degree requirements, etc. For those interested in interdisciplinary work, note that the MBB graduate program is flexible, allowing (with permission) students to take courses for their degree from other departments and even other institutions. Students interested in bioinformatics have a few options including getting accepted in the competitive SFU/UBC bioinformatics graduate program (which includes a rotation program). Another option, suitable for those interested in starting on thesis work right away with a specific thesis supervisor, involves completing bioinformatics training through the MBB graduate program or newly forming Bioinformatics program, which several very high caliber students have successfully done (like Jennifer Gardy, Brinkman Lab Ph.D. student, Governor General’s Gold Medal winner for top graduate student across all SFU faculties in 2006, and now a Research Scientist at the BC Centre for Disease Control and occasional host of major science shows like The Nature of Things – yeay Jenn!).

The city of Vancouver