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Meeting Report from the Bioinformatics & Computational Genome Canada Meeting Report from the Bioinformatics & Computational Biology Workshop Toronto, Ontario, Canada – December 5 & 6 2011 This workshop was made possible with the generous support of our sponsors: Genome Canada 2011 Bioinformatics and Computational Biology Workshop ______________________________________________________________________________ The wordle above was created by Guillaume Bourque using the text of this report. It is meant to illustrate the kind of data mining approach that is relevant to bioinformatics. 2 Genome Canada 2011 Bioinformatics and Computational Biology Workshop Table of Contents Executive Summary ......................................................................................................................... 4 Background ..................................................................................................................................... 5 Process ............................................................................................................................................ 6 Presentations .................................................................................................................................. 7 Theme Breakout Groups and Discussion ...................................................................................... 10 Strategy Session ............................................................................................................................ 14 Recommendations ........................................................................................................................ 14 Next Steps ..................................................................................................................................... 16 Appendices Appendix 1 – Workshop Program Appendix 2 – Final List of Participants Appendix 3 – Speaker Biographies Organization Abbreviations CANARIE Canada’s Advanced Research and Innovation Network (www.canarie.ca) CFI Canada Foundation for Innovation (www.innovation.ca) CIHR Canadian Institutes of Health Research (www.cihr.ca) EMBL European Molecular Biology Laboratory (www.embl.org) GC Genome Canada (www.genomecanada.ca) MITACS Mathematics of Information Technology and Complex Systems (www.mitacs.ca) NRC National Research Council (www.nrc-cnrc.gc.ca) OICR Ontario Institute for Cancer Research (www.oicr.on.ca) 3 Genome Canada 2011 Bioinformatics and Computational Biology Workshop Executive Summary On December 5 & 6, 2011, a workshop was held to bring together bioinformaticians and computational biologists, along with researchers from other related disciplines such as biologists, mathematicians, statisticians, application developers, informatics specialists, data visualisation experts and machine learning specialists. This workshop was convened with a view to deriving input from a broad spectrum of stakeholder communities, as a first step in the creation of a multi-year road map for bioinformatics and computational biology in Canada. Led by a selected panel of presenters, participants in the workshop were charged with commenting upon opportunities in informatics-related genome research. The principal recommendations from the workshop are (in priority order): Funding Genome Canada should take a lead-role in coordinating the development of a significant, national, multi-year funding program directed to boinformatics/computational biology. Networking Mechanisms should be established to improve coordination and promote interdisciplinary collaborations within the bioinformatics/computational biology community. Integration The Canadian bioinformatics community should develop and use data standards and best practices as necessary elements for data integration and modelling. High Quality Personnel Programs should be developed to attract, retain and train innovative individuals in the areas of bioinformatics, computational biology, and bio-statistics, who have an interest in working in the life sciences. High Performance Computing A coordinated and well-managed high-performance computing infrastructure that is targeted for life sciences should be supported. Algorithm and Software Development Algorithms and software must be developed with the end user in mind and based on established best practices. Policies The community should work closely with Genome Canada and Government agencies to ensure appropriate policies and legislation are in place to realize the full potential of Canada’s bio-economy. 4 Genome Canada 2011 Bioinformatics and Computational Biology Workshop Background Genome Canada’s Science and Industry Advisory Committee (SIAC) identified the need to advance the area of bioinformatics/computational biology in Canada. The 2011 cross-Canada consultations in connection with Genome Canada’s strategic plan also highlighted the importance of a national effort to address the needs in this area. Therefore, SIAC undertook the planning for a bioinformatics/ computational biology workshop scheduled for the fall of 2011. For many participants, this workshop was a singular opportunity to meet with bioinformaticians, computational biologists and colleagues from other related disciplines. A decade ago, in September 2001, Genome Canada and the Canadian Institutes of Health Research held a jointly sponsored workshop on bioinformatics. At that time, bioinformatics expertise and technology in Canada were just emerging and were variable across the country. Since the 2001 meeting, Genome Canada continued to encourage research in this area, mostly through its Science & Technology Innovation Centres (STICs) and funding competitions focused on technology development. A ten-member steering committee was struck to organize the workshop. Chair: William (Bill) Crosby, SIAC Member Professor of Biological Sciences University of Windsor Members: Guillaume Bourque Francis Ouellette Director of Bioinformatics Associate Director, Informatics and Bio-computing McGill University and Genome Quebec Ontario Institute for Cancer Research Innovation Centre Associate Professor, Cell and Systems Biology University of Toronto Mark Daley Gijs van Rooijen Departments of Computer Science and Chief Scientific Officer Biology, University of Western Ontario Genome Alberta Stacey Gabriel, SIAC Member George Weinstock, GC Board of Directors Director, Genetic Analysis Platform Program Associate Director, The Genome Center Co-Director, Genome Sequence Analysis Prog. Washington University School of Medicine Co-Director, Program in Medical and Population Genetics, Broad Institute Michael Hallett, Advisor John Yates III, SIAC Member Director Department of Cell Biology McGill Centre for Bioinformatics Scripps Research Institute Steven Jones Jacques Simard, SIAC Chair, Committee Observer Associate Director and Head, Bioinformatics Canada Research Chair in Oncogenetics Genome Sciences Centre Director, Endocrinology and Genomics Axis, CHUQ British Columbia Cancer Research Centre Research Centre & Dept. Molecular Medicine, Laval 5 Genome Canada 2011 Bioinformatics and Computational Biology Workshop The Bioinformatics and Computational Biology Workshop was held on December 5 & 6, 2011 in Toronto. Sponsors included the Canadian Institutes of Health Research – Institute of Genetics and Institute for Cancer Research, and IBM Canada. Workshop Objectives Existing tools and approaches have only partially realized the information potential in existing data sets. A pan-national initiative in bioinformatics/computational biology will substantially and positively impact the life science economy in Canada, with benefits in human health, as well as non-health sectors, such as, agriculture, environment, fisheries, and forestry. An emphasis of the workshop was to assemble an interdisciplinary group of biologists, mathematicians, statisticians, application developers, informatics specialists, data visualisation experts, machine learning specialists, and computational scientists dedicated to developing novel approaches to deriving value from genomics-related data, creating user- friendly interfaces, and establishing rich learning environments for the training and development of highly qualified personnel required for this critical aspect of research. The importance of and need for infrastructure was also to be considered. An international dimension to the initiative is expected and encouraged. The specific goals of the workshop were two-fold: To inform Genome Canada during its development of a request for applications set to be launched in 2012. To inform the development of a multi-year roadmap detailing the current state-of-the-art and future challenges and opportunities in bioinformatics. Process The Workshop Steering Committee chose to divide the subject matter into seven themes. An expert speaker for each theme was asked to present to participants an overview of the outstanding issues for the theme and to list the roadblocks, challenges and opportunities. Theme Speaker Title of Talk 1 Information Theory and Lila Kari, University of The Many Facets of Natural Computing Biological Computing Western Ontario 2 Network and Pathway Gary Bader, University of Network and Pathway Analysis – Moving Analysis Toronto Towards Applications 3 Ecology and Evolution Magnus Nordborg, Genomic Approaches to Understanding Gregor Mendel Institut Adaptation 4 Proteomics and Analysis of Andrew Emili, University Deriving Knowledge from Proteomic Data Data Sets of Toronto 5 Clinical Applications John McPherson, OICR The Rise of Personalized Medicine in Cancer: Implications and Challenges
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