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Bioinformatics has become an important part of many areas of health research. Several fields of research such as microbiome, cancer, immunology and clinical research are generating massive amounts of data that need appropriate computational tools for their analysis and interpretation. Moreover, a need for bioinformatics training is more pressing than ever as big data are more and more present in health research.

In order to meet this need in the Canadian health research space, the Université Laval Big Data Research Center (BDRC-UL), in cooperation with the Canadian Bioinformatics Workshop series (hosted at is organizing a summer school in bioinformatics centred on the microbiome. This summer school is in line with the CIHR Strategic Plan “Health Research Roadmap II: Capturing Innovation to Produce Better Health and Health Care for Canadians” as the Strategic Direction 1 “Promoting Excellence, Creativity and Breadth in Health Research and Knowledge Translation” considers trainees to be leaders in the Canadian Health Research Enterprise.

The 2017 Microbiome Summer School is a collaboration between a number of partners and sponsors all of which will contribute to make this course a success. Partners and sponsors include Calcul Québec, the Canada Excellence Research Chair on microbiome, Université Laval, as well as multiple CIHR Institutes such as the Institute of Nutrition, Metabolism and Diabetes, the Institute of Musculoskeletal Health and Arthritis, the Institute of Circulatory and Respiratory Health, the Institute of Genetics, the Institute of Gender and Health, and the Institute of Infection and Immunity.

This summer school will provide an introduction to the use of bioinformatics in microbiome research as well as big data analytics applied to this field. Participants will initially be introduced to a range of basic tools and resources applicable to a range of subject areas. To enable specific exploration of resources in a particular field of interest, participants will be divided into small groups to work on a problem set by the organizers. The course will include training and mentoring provided by experts from the Université Laval Big Data Research Centre (BDRC), Université Laval, and faculty from other Canadian institutions such as University of Toronto, Dalhousie University, Simon Fraser University, and the University of British Columbia (from the faculty/instructors).


The primary objective of this summer school is to meet the needs in bioinformatic training for the Canadian microbiome research community through introductory “state-of-the-art” bioinformatic courses. This is why we will incorporate machine learning approaches.

The secondary objectives include:

  • Provide a nexus for informatics and bioinformatic students to interface to address the big data challenges associated with metagenomics studies.
  • Assemble multiple genomes, map short-read data to sequenced genomes and query the mapping for variation using machine learning algorithms, transcript prevalence (from mRNAseq data), and compare microbiome using software tools.
  • Transferring large data sets between computers;
  • Running extended analyses while asleep;
  • Executing and modifying existing Python and R scripts;
  • Make effective use of basic computational resources such as Compute Canada, through Calcul Québec, the non-profit organization in charge of coordinating Advanced Research Computing efforts throughout Canada.


The fee per participant is $300 and will cover for the course, travel, lodging and meals.

Target audience

This course is aimed at individuals intending to or working in microbiome research with a biomedical/health perspective who want to gain experience in bioinformatics. Applicants are expected to be embarking on bioinformatics related projects or need to use such approaches in their work. We expect a mix of bioinformatic and informatic researchers.

Eligible applicants are:

  • Trainees (master, Ph.D., post-doctoral students);
  • Lab managers;
  • Independent researchers (depending on application pressure, preference will be for early career investigator);
  • Bioinformatician and informatician wanting to gain expertise in microbiome methodologies and big data analytics related to microbiome research.

Place availability

CIHR will support up to 45 trainees.

  • Up to 4 spots will be for registrants whose research activities relate to the mandate of the Institute of Circulatory and Respiratory Health (ICRH).
  • Up to 2 spots will be for registrants whose research activities relate to the mandate of the Institute of Musculoskeletal Health and Arthritis (IMHA).

Selection criteria

All applications will be assessed according to the following selection criteria:

  • The ranking will be adjusted by relevance of the project, computer ability, and the motivation letter.
  • Gender equity and geographical representation will also be taken into account.
  • A number of places should be reserved for staff from the Canadian Food Inspection Agency (CFIA) (2 max).
  • Potential international participants may be accepted if place availability permits. Preference will be for applicants from CIHR recognized institutions.

How to apply

Applications will be received via the website, applicants will fill the application form to be assessed by the selection committee.

Successful applicants will be contacted (see timeline) and asked to register to the event.


Deadline for applications: March 24, 2017
Notification of decision: April 19, 2017
Deadline for registration: April 26, 2017