Appendix III: Assessment of Systems Biology potential in Canada

While a national Systems Biology funding strategy is yet to be developed, Canadian researchers have been active in launching Systems Biology-related initiatives both nationally and internationally. An example of international leadership in Systems Biology is the Canada-led International Regulome Consortium (IRC). Noticeably, the Canadian component of the IRC, in contrast to the international partners, the Welcome Trust Sanger Institute, the Erasmus Medical Center and Genomics Institute of Singapore and other research institutions in continental Europe and Australia, has yet to secure funding. In addition, investments made through the Genome Canada program have created significant Systems Biology-related research capacity, particularly in infrastructure supporting genomics and proteomics research. If utilized appropriately, this infrastructure provides Canada with the potential to become one of the world-leading Systems Biology nations. In the sections below, we provide further evidence for the potential of Systems Biology in Canada by highlighting exiting initiatives across the country.

Atlantic Canada has several initiatives under development to promote integrative and systems level understanding of biological phenomena and biomedical conditions. The North Atlantic Resource for Molecular, Cellular, Integrative and Network Sciences (NARIS) is expected to provide a major addition to high-throughput experimental and computational capacity in Newfoundland, and act as a hub for Systems Biology-related research in this region. Additionally, Dalhousie University recently started a graduate program in Bioinformatics and Computational Biology based on a tradition of strength in the area of evolutionary biology. Dalhousie researchers are spear-heading one of this countries oldest interdisciplinary Systems Biology-related initiatives, the Canadian Institute of Advanced Research’s program in Evolutionary Biology, which aims at providing new understanding of organisms and ecosystems by combining molecular biology, genetics, population biology, bacteriology, protozoology, botany, zoology, chemistry, biochemistry, mathematics, and computer science.

Quebec has a long tradition of integrative and quantitative research and has held a strong international position for many years through the interdisciplinary, multi-university Centre for Nonlinear Dynamics in Physiology and Disease (CND) hosted by McGill University. The CND runs a summer school entitled “Systems Biology: from Genes to Organisms”. In addition to this international flagship for Systems Biology and interdisciplinary education, McGill University’s Department of Anatomy and Cell Biology will soon introduce a graduate track in Human Systems Biology. Moreover, the University of Montreal’s Institute for Research in Immunology and Cancer (IRIC) is starting a new graduate course in Systems Biology as a first step in setting up a new graduate training program, and the Institut de recherches cliniques de Montréal (IRCM) have made significant effort towards the implementation of Systems Biology as a new research theme. École Polytechnique de Montréal has also numerous Systems Biology-related initiatives in the areas of functional genomics, metabolomics and biological pathway analysis and the opening of a new Genomics Centre in Québec City is expected to accelerate the formation of a virtual Systems Biology group with participation from Montreal, Québec City and Sherbrooke. Additionally, Genome Québec has made significant investments to improve genomics and proteomics infrastructure through the McGill University and Genome Québec Innovation Centre, and is sponsoring Systems Biology-related research programs, such as, for example, the multi-university project “Regulatory Networks in Gene Expression: From the Genome to the Organism” and the “Montreal Network for Pharmaco-Proteomics and Structural Genomics”.

Ontario has several emerging Systems Biology-specific initiatives that include the establishment of the Centre of Cellular and Biomolecular Research at the University of Toronto to stimulate unconventional interactions among disciplines; the founding, by the University of Ottawa and the National Research Council, of the Ottawa Institute of Systems Biology; and the launch of a program in Integrated Systems Biology and of the Sun Centre of Excellence in Systems Biology at Mount Sinai Hospital's Samuel Lunenfeld Research Institute in Toronto. Additionally, the Centre for Computational Biology at Toronto’s Hospital for Sick Children is dedicated to the advancement of Systems Biology research. Another example of a Systems Biology-related initiative is University of Ottawa’s recently established Centre for Advanced Research in Environmental Genomics (CAREG), which seeks to integrate the fields of eco-toxicology, genetics, physiology and bioinformatics to develop novel genomics-based solutions to environmental problems. Genome Canada, through the Ontario Genomics Institute, has made significant investments in genomics and proteomics infrastructure as well as Systems Biology-related research programs such as the Stem Cell Genomics Project, the Biomolecular Interaction Network Database project, the Proteomics and Functional Genomics: An Integrated Approach program, and the Dynactome Project seeking to map spatio-temporal dynamic systems in humans.

The Prairie Provinces interdisciplinary include the Manitoba Centre for Proteomics and Systems Biology, dedicated to the promotion and practice of Systems Biology and Proteomics, and the Institute for Biocomplexity and Informatics at the University of Calgary, which, in collaboration with the Alberta Ingenuity Centre for Machine Learning, focuses on the structure, dynamics and evolution of genetic regulatory networks and their behaviours. In addition, the Institute for Biomolecular Design at the University of Alberta, which is an interdisciplinary research and platform technology centre, is an international contributor to in silico technology innovation through its Project CyberCell. Genome Prairie is also supporting Systems Biology-related research programs, such as the development of an integrated and distributed bioinformatics platform, and the Sun Centre of Excellence for Visual Genomics at the University of Calgary. In addition, the University of Manitoba’s Mammalian Functional Genomics program is involved in Systems Biology-related research, for example, through the Genome Canada funded NorCOMM project and the International Knockout Mouse Project. Genome Canada also supports the Human Metabolome Project at the University of Alberta.

British Columbia has a strong presence in Systems Biology through a formal affiliation of the world-leading Institute of Systems Biology in Seattle with the University of British Columbia. Significant existing strengths, particularly in genomics, proteomics, bioinformatics and mathematical biology, provide a solid foundation for further developments. For example, in proteomics, the University of British Columbia recently launched a new life science institute, the Canadian Laboratories in Integrated Proteolysis. Moreover, the nationally and internationally renowned Bioinformatics Training Program for Health Research, offered through a partnership between Simon Fraser University, the University of British Columbia, and the BC Cancer Agency, and the Canadian Genetic Disease Network’s Canadian Bioinformatics Workshop series housed at the bioinformatics.ca resource, which is the portal to bioinformatics activities in Canada, are some of the examples of the strong capacity and expertise in Systems Biology-related research. Additionally, the University of British Columbia has a pan-Canada program in Biomedical Models of Cellular and Physiological Systems and Disease, which is a full project under the auspices of the Mathematics of Information Technology and Complex Systems Network of Centres of Excellence housed at Simon Fraser University.

The National Research Council is traditionally strong in integrative multi-disciplinary research and technology development and transfer. Its investments through the Genomics and Health Initiative (GHI) have lead to a significant genomic and proteomic infrastructure in several regions across the country. The GHI, established in 1999 in order to bring the benefits of genome and health sciences to all Canadians, funds focused inter-disciplinary programs combining elements of genomics, proteomics, bioinformatics and convergence technologies to address health-related issues in a Systems Biology-related manner. Examples of NRC-based Systems Biology-related programs include Cancer Genomics; Genomics for Enhanced Crop Performance; Human Pathogens and their Host Interactions; and Systems Biology of Brain Cell Interactions. The NRC also has considerable expertise and strength in Information Technology and has developed a number of tools for data mining of large datasets and the integration of diverse datasets. Additionally, the program in Genomics-Based Approach to Enhancing Bioremediation through Microbial Identification and Community Profiling could provide a cornerstone for the development of Environmental Systems Biology in Canada. Innovation and expertise in instrumentation is critical for Systems Biology and the NRC could become an important partner in Canadian Systems Biology by developing and providing cutting-edge technology platforms and facilitating interactions among scientific and industry communities.