ACCEPTED PAPERS

GLBIO/CCBC 2016 accepted papers that have been published in PLOS ONE
http://collections.plos.org/glbio-ccbc-2016

The PLOS ONE blog about the conference
http://blogs.plos.org/collections/great-lakes-bioinformatics-and-the-canadian-computational-biology-collection/

top

INVITED SPEAKERS

Rob Beiko Dalhousie University

Guillaume Bourque McGill University and Genome Quebec Innovation Center

Carlos Camacho University of Pittsburgh

Sheelagh Carpendale Department of Computer Science University of Calgary, Canada > Click here for biography <

Amy Caudy University of Toronto

Belinda Chang University of Toronto

Dannie Durand Associate Professor Biological Sciences and Computer Science Carnegie Mellon University (CMU) > Click here for biography <

Brendan Frey President & Chief Executive Officer Deep Genomics Toronto, Ontario, Canada > Click here for biography <

Igor Jurisica Professor Departments of Medical Biophysics and Computer Science University of Toronto Toronto, ON Reducing Bias in Network-Based Analyses > Click here for biography <

Mads Kaern University of Ottawa > Click here for biography < Model Discrimination and Inference in Quantitative Combinatorial Perturbation Analysis Genome editing provides a powerful tool to identify gene function and to characterize genetic interactions. This talk presents a theoretical framework to determine how genes and signals influence one another. It is shown how this framework enables the unbiased inference of causality and order within gene networks from quantitative genetic interaction data. Such inference methods will become increasingly important as genome editing technologies transition from single genes to large-scale systematic analyses.

Alexey Nesvizhskii Associate Professor Departments of Computational Medicine & Bioinformatics and Pathology University of Michigan, Ann Arbor  > Click here for biography <

Sushmita Roy Assistant Professor Biostatistics and Medical Informatics Systems Biology Wisconsin Institute for Discovery University of Wisconsin, Madison Computational Inference of Regulatory Network Dynamics on Developmental and Evolutionary Lineages > Click here for biography <

James Wasmuth Assistant Professor Ecosystem & Public Health (EPH) University of Calgary, Canada > Click here for biography <

Matt Weirauch Cincinnati Children’s

BIOGRAPHIES

Sheelagh Carpendale Sheelagh Carpendale is a Professor in Computer Science at the University of Calgary where she holds a Canada Research Chair in Information Visualization and NSERC/AITF/SMART Technologies Industrial Research Chair in Interactive Technologies. She has many received awards including the E.W.R. NSERC STEACIE Memorial Fellowship; a BAFTA (British Academy of Film & Television Arts Interactive Awards); an ASTech Innovations in Technology award; and the CHCCS Achievement Award, which is presented periodically to a Canadian researcher who has made a substantial contribution to the fields of computer graphics, visualization, or human-computer interaction. She leads the Innovations in Visualization (InnoVis) research group and initiated the interdisciplinary graduate program, Computational Media Design. Her research on information visualization, large interactive displays, and new media draws on her dual background in Computer Science (BSc. and Ph.D. Simon Fraser University) and Visual Arts (Sheridan College, School of Design and Emily Carr, College of Art). She is an internationally known for both information visualization and multi-touch interaction research.

- top -

Dannie Durand Dannie Durand is an associate professor in Biological Sciences and Computer Science at Carnegie Mellon University. Her research focuses on the emergence of new genes via gene duplication, domain shuffling, and horizontal transfer. She is the author of the Notung software package, an integrated suite of phylogenetic reconciliation methods for analyzing gene family evolution. She holds a BS degree in physics from MIT and MS and PhD degrees in computer science from Columbia University. Durand is a David and Lucile Packard Foundation Science and Engineering fellow.

- top -

Brendan Frey Brendan Frey is the CEO and Co-Founder of Deep Genomics and a Professor at the University of Toronto. He has made fundamental contributions in the areas of machine learning and genome biology, and is widely known for his work on using machine learning to understand how genetic variation leads to disease. Dr. Frey has received numerous distinctions and is a Fellow of the Royal Society of Canada and a John C. Polanyi Fellow. He recently co-founded a University of Toronto spinoff, Deep Genomics, which is using machine learning to change the course of genomic medicine. Dr. Frey has consulted for several industrial research and development laboratories in Canada, the United States and England, and has served on the Technical Advisory Board of Microsoft Research. His former students and postdoctoral fellows include professors, industrial researchers and developers at universities and industrial laboratories from across Canada, the United States and Europe.

- top -

Igor Jurisica Igor Jurisica is Tier I Canada Research Chair in Integrative Cancer Informatics, Senior Scientist at Princess Margaret Cancer Centre, Professor at University of Toronto and Visiting Scientist at IBM CAS. He is also an Adjunct Professor at he School of Computing, Pathology and Molecular Medicine at Queen's U,Computer Science at York University , and an Honorary Professor at Shanghai Jiao Tong University. Since 2015, he has also served as Chief Scientist at the Creative Destruction Lab, Rotman School of Management. His research focuses on integrative computational biology and the representation, analysis and visualization of high-dimensional data to identify prognostic and predictive signatures, drug mechanism_of_action and in-silico repurposing of drugs. Interests include prediction and analysis of protein interactions networks, modeling signaling cascades and high-throughput protein crystallography. He has published extensively on data mining, visualization and cancer informatics, including multiple papers in Science, Nature, Nature Medicine, Nature Methods, J Clinical Oncology, and has over 8,932 citations since 2011. He has been included in Thomson Reuters 2015 & 2014 list of Highly Cited Researchers, and The World's Most Influential Scientific Minds: 2015 & 2014 Reports.

- top -

Mads Kaern Dr. Mads Kaern is a Principal Investigator at the Ottawa Institute of Systems Biology, an Associate Professor of Cellular & Molecular Medicine at the University of Ottawa, and an Affiliate Scientist with the Cancer Therapeutics Program at the Ottawa Hospital Research Institute. With expertise in synthetic biology, dynamical systems and computational biology, Dr. Kaern's research focuses on gene regulatory processes and networks, and their implications. He has authored numerous studies including one of the first characterizations of “bursts” in gene transcription, and the model-based design of viruses that kill cancer.

- top -

Alexey Nesvizhskii Dr. Alexey Nesvizhskii is a tenured Associate Professor in the Departments of Computational Medicine & Bioinformatics and Pathology at the University of Michigan, Ann Arbor. His research laboratory (www.nesvilab.org) is working in the area of bioinformatics, proteomics, and systems biology. The computational tools previously developed by Dr. Nesvizhskii and his colleagues, such as Trans-Proteomic Pipeline (including PeptideProphet and ProteinProphet), PeptideAtlas, SAINT, CRAPome, and DIA-Umpire are among the most cited proteome informatics tools and used by hundreds of laboratories worldwide. His lab actively collaborates with technology developers, biologists, and clinical scientists on a variety of projects, including analysis protein interaction networks, integrative modeling of multi-omics data to reconstruct targetable pathways in cancer, and biomarker discovery. Since 2015 Dr. Nesvizhskii serves as the Director of the Proteomics Resource Facility at the University of Michigan which aims to provide cutting-edge proteomics capabilities to the University-wide research community. As an enthusiastic educator, Dr. Nesvizhskii directs the NIH funded T32 Proteome Informatics of Cancer Training Program at the University of Michigan, and teaches graduate-level courses in the area of bioinformatics, proteomics, and systems biology.

- top -

Sushmita Roy Sushmita Roy is an assistant professor at the Biostatistics and Medical Informatics department and in Systems Biology at the Wisconsin Institute for Discovery, University of Wisconsin, Madison. She got her PhD in 2009 from the University of New Mexico and a post-doctorate at the Broad Institute of MIT and Harvard. Sushmita's research focuses on the development and application of statistical machine learning methods to problems in regulatory network inference and analysis. Sushmita is a recipient of an Alfred P. Sloan Foundation fellowship and an NSF CAREER award.

- top -

James Wasmuth Dr. Wasmuth obtained his BSc in Biochemistry at Imperial College London and then moved to the University of York to complete an MRes degree in Bioinformatics.  He undertook PhD studies at the University of Edinburgh, where he worked in parasite genomics.  Dr. Wasmuth moved to Toronto to carry a postdoctoral fellowship at the Hospital for Sick Children for four years.

top

ACCOMMODATIONS

CHELSEA HOTEL
The headquarters hotel for GLBIO/CCBC 2016, the Chelsea Hotel is Canada's largest hotel with 1,590 guest rooms, is centrally located and just steps from the city's best shopping districts, world-class theatres, vibrant nightlife and exciting attractions. This full-service urban resort offers four restaurants and lounges, separate adult and family recreation areas and pools - including the "corkscrew" - downtown Toronto's only indoor waterslide. Complimentary in room WiFi and use of the fitness Centre are included with your stay.
The room block is now closed.  If you are interested in booking a room at our conference rate, please email Bel Hanson at This email address is being protected from spambots. You need JavaScript enabled to view it. and we will attempt to accommodate your request.

BURWASH B&B
These University of Toronto Dormitories are located just steps away from the GLBIO/CCBC 2016 venue. These basic rooms can be booked as a single or double, have a shared bathroom and include breakfast. Complimentary WiFi is available in the common areas and internet in your room but you must bring your own Ethernet cable.

• Please use the following link to book your reservation: Burwash B&B
• On Campus Parking is available at an additional charge. Information available at Victoria University Parking

top

KEYNOTE SPEAKERS

	MATHIEU BLANCHETTE Associate Professor School of Computer Science McGill University Montreal, Quebec, Canada > Click here for biography < Know Thy Ancestors to Know Thyself: Improving Our Understanding of the Human Genome Using Paleogenomics I will first discuss how the genomes of ancestral mammalian species can be reconstructed with surprisingly high accuracy from the genomes of extant species. I will then present how inferred ancestral sequences can be used to improve the detection of ancient evolutionary events such as transposable element and pseudogene insertions that have shaped mammalian genomes. This information can be exploited by statistical and machine learning algorithms to improve the accuracy of transcription factor binding site and micro-RNA target site prediction.
	JANE CARLTON Professor Department of Biology New York University, USA > Click here for biography < Harnessing Genomics to Study the Global Public Health Burden of Malaria Malaria is a devastating disease that caused 0.5 million deaths and ~214 million cases in 2015, and more than half the world’s population is at risk of the disease. In the Center for the Study of Complex Malaria in India, one of ten Centers that form a network across the malarious world, we harness the tools of genomics and bioinformatics to study which species and their genotypes infect subjects temporally and spatially, and how this variation causes changes in disease phenotype and transmission. Our research provides insights into the phylogeography of different malaria parasite species, as well as improved methods for their control.
	ALED EDWARDS Professor, Molecular Genetics CEO, Structural Genomics Consortium (SGC) Uniersity of Toronto, Canada > Click here for biography < Open Science: From Computational Biology to the Real World
	ELIZABETH EDWARDS Professor Dept. of Chemical Engineering and Applied Chemistry University of Toronto > Click here for biography < Metagenomics of Microbial Dechlorinating Consortia Groundwater contamination is a serious threat to global health and prosperity. Petroleum hydrocarbons, industrial solvents and metals are some of the most frequent culprits. Some microbes have evolved and adapted to transform or detoxify contaminants in the environment. Chlorinated solvents such a trichloroethene and tetrachloroethene are widely used as industrial degreasers, dry-cleaning agents and precursors in chemical synthesis – and thus very common groundwater contaminants. Owing to their toxicity, even small spills render groundwater unsuitable for use, and cleanup is typically a costly and long-term undertaking. A fascinating group of subsurface microorganisms, collectively referred to as organohalide-respiring bacteria, are significant players in the global halogen cycle. Certain species, such as Dehalococcoides, can dechlorinate the major dry-cleaning solvent tetrachloroethene and the common industrial solvent trichloroethene to the benign product ethene. Remarkably, these organisms obtain energy for growth from dechlorination and several successful demonstrations of bioaugmentation, where an aquifer is inoculated with culture, have lead to the development of a commercial market for such dechlorinating cultures. Through metagenome investigations in our own lab and elsewhere, we are shedding light on these dynamics and function of these remarkable, ubiquitous, microbial communities.
	JENNIFER GARDY Assistant Professor School of Population and Public Health University of British Columbia, Canada Infectious Disease Genomics: Bioinformatics Challenges In the last five years, genome sequencing has completely changed how public health agencies investigate outbreaks and epidemics of infectious disease. Real-time sequencing of pathogens is being used for everything from rapid diagnostics to inferring individual transmission events, and while the sequencing is straightforward, the associated bioinformatics and interpretation is not. In this talk, I will cover some of the ways genomics is being used in public health and the informatics challenges that this new field of “genomic epidemiology” is facing.
	TIMOTHY R. HUGHES Professor Donnelly Centre for Cellular and Biomolecular Research University of Toronto, Canada > Click here for biography < Decoding Gen Regulation Understanding how regulatory sequence works is one of the greatest challenges facing molecular biology, and the next major hurdle in human genetics. There is now a wealth of data on individual genome sequences, chromatin profiles, and expression outputs, but the details of how cells identify regulatory sequences, or how their functions are exerted, are surprisingly difficult to decipher. We aim to solve this problem by determining and compiling motifs for transcription factors and RNA binding proteins, and developing computational models of regulatory sequence identity and function.
	STEVEN J.M. JONES Professor, FRSC, FCAHS BC Cancer Agency, Canada > Click here for biography < Genomic Analysis of Cancer Genomes to Aid in Clinical Decision Making We are using genomic and transcriptomic analysis of patient tumours to support cancer treatment decision-making. This involves a large number of computational analysis to be conducted and consolidated. Ultimately, these analyses will need to indicate the sensitivity or resistance to therapies of the tumour that could be considered by a clinician. I will discuss the computational pipeline that has been established to move toward this goal.
	CHRISTINA LESLIE Computational Biologist Memorial Sloan Kettering Cancer Center New York, USA > Click here for biography < Decoding Gene Regulatory Programs in Cellular Differentiation In order to differentiate into distinct lineages, multipotent cells must undergo large-scale remodeling of chromatin and orchestrate dramatic gene expression changes. How do multipotent cells encode the potential for multiple cell fates, and how can we decipher the transcriptional programs that carry out cell state transitions in commitment to specific fates? To address these questions, we carried out an integrative computational analysis of enhancer landscape and gene expression dynamics in hematopoietic differentiation using DNase-seq, histone mark ChIP-seq, and RNA-seq. We examined how early establishment of enhancers and complex regulatory locus control together govern gene expression changes in cell state transitions. We found that high complexity genes – i.e. those with a large total number of DNase-mapped enhancers across the lineage – differ architecturally and functionally from low complexity genes, achieve larger expression changes, and are enriched for both cell-type specific and “transition” enhancers, which are established in hematopoietic stem and progenitor cells (HSPCs) and maintained in one differentiated cell fate but lost in others. We then developed a quantitative model to predict gene expression changes from the DNA sequence content and lineage history of active enhancers. Our method accurately predicts expression changes for high complexity genes during differentiation, suggests a novel mechanistic role for PU.1 at transition peaks in B cell specification, and can be used to improve assignment of enhancers to genes. We are using these methods to decode normal cell state transitions in T lymphocyte differentiation and aberrant cell states in cancer.
BIOGRAPHIES
MATHIEU BLANCHETTE After completing his Ph.D. (U. of Washington, 2002) and postdoc (UC Santa Cruz, 2003), Mathieu joined the School of Computer Science at McGill and founded the Computational Genomics Lab. His team and him have published in more than 70 publications in the fields of genome evolution, sequence analysis, and gene regulation. Recently elected member of the College of Scholar of the Canadian Royal Society, he was a Sloan Fellow (2009), and received the Outstanding Young Computer Scientist Researcher Prize from the Canadian Association for Computer Science (2012), and the Chris Overton prize (2006). top
JANE CARLTON Jane Carlton is a Professor of Biology and Director of the Center for Genomics and Systems Biology at New York University. She received her PhD in Genetics at the University of Edinburgh, and has worked at several genomics institutions in the U.S., including NCBI at the National Institutes of Health (NIH) in Bethesda, and the sequencing center TIGR, founded by J. Craig Venter. Professor Carlton is passionate about genomics and the power it has to revolutionize the study of parasites. Her research involves comparative genomics of different species of malaria parasites, and the sexually transmitted protozoan Trichomonas vaginalis. She has a keen interest in global public health through her collaborations with scientists in India, first as the PI of a Fogarty Global Infectious Disease training and research grant, with exchange of trainees between New Delhi and New York, and now as Program Director of a 7 year “Center for the Study of Complex Malaria in India”, one of 10 International Centers of Excellence in Malaria Research funded by NIH. In 2013 she was awarded an NYU Grand Challenge project “Mapping the New York City Metagenome”, which uses next generation sequencing to characterize, map and ultimately track microbes on paper currency, bicycles and sewage circulating in the city. She has published more than 100 articles and reviews, and her work has been profiled by CNN, BBC, The Economist, USA Today and the Wall Street Journal. She received the American Society of Parasitologists’ Stoll-Stunkard Memorial Award in 2010, and was elected a Fellow of the American Association for the Advancement of Science in 2012. Professor Carlton’s ultimate goal is to cultivate and expand the science and use of genomics to improve global health. top
ALED EDWARDS Aled Edwards is CEO of the Structural Genomics Consortium (SGC), a public-private partnership that generates open-source research tools to support drug discovery. Over the years, Al and his teams at the SGC have contributed ~15% of all the available structural information for human proteins in the public domain. The SGC and its collaborators in the pharmaceutical industry are using this structural information to generate and make available chemical probes for members of several human protein families. These probes are being tested in patient derived cells and tissue within an expanding open source network of clinical institutions. At least 20 clinical trials of first-in-class medicines have been launched based on SGC research. Al did his undergraduate and graduate work at McGill University and did his post-doctoral work at Stanford University with Roger Kornberg, where he initiated the structural biology of RNA polymerase II. top
ELIZABETH A. EDWARDS Elizabeth A. Edwards, PhD, P. Eng., Professor, Department of Chemical Engineering and Applied Chemistry, and Cell and Systems Biology (Status only), University of Toronto. Dr. Elizabeth Edwards holds Bachelor’s and Master’s degrees in Chemical Engineering from McGill University, Montreal, and a PhD degree (1993) in Civil and Environmental Engineering from Stanford University. She is internationally known for her work on anaerobic bioremediation, the application of molecular biology and metagenomics to uncover novel microbial processes, and the transition of laboratory research into commercial practice to develop bioremediation and bioaugmentation strategies for groundwater pollutants. She has received several prestigious awards including an NSERC Synergy Award for Innovation with Geosyntec Consultants (2009), a Killam Research Fellowship (2008), a Premier’s Research Excellence Award (2003), and an NSERC Women’s Faculty Award (1995). She is a fellow of the AAAS (2011), and was inducted into the Canadian Academy of Engineering (2011) and the Royal Society of Canada (2012). She is also the founding director of BioZone, a Centre for Applied Bioscience and Bioengineering Research and a Tier 1 Canada Research Chair in Anaerobic Biotechnology. top
JENNIFER GARDY Dr. Jennifer Gardy is an Assistant Professor in the School of Population and Public Health at the University of British Columbia, where she holds a Canada Research Chair in Public Health Genomics. Based at the British Columbia Centre for Disease Control, her lab uses microbial genomics, phylogenetics, and bioinformatics to understand the transmission and epidemiology of infectious diseases, including tuberculosis, influenza, and measles. Her group was the first to use genome sequencing to reconstruct a large outbreak of tuberculosis and she is continuing to apply this novel technique to other outbreak scenarios and to routine public health microbiology. Her group is also interested in how information visualization techniques can be used in public health to better communicate complex data to stakeholders. Before joining BCCDC in 2009, Jennifer’s graduate training was in computational biology. She completed her PhD in 2006 under Fiona Brinkman at Simon Fraser University, where she developed the PSORT-B tool for bacterial protein subcellular localization prediction. She then spent three years as a postdoctoral fellow at UBC in Bob Hancock’s lab, where she developed the Cerebral Cytoscape plugin for network visualization and where she contributed to InnateDB, a data warehouse for systems biology investigations of the innate immune system. Infectious disease genomics: bioinformatics challenges: Advances in DNA sequencing technology are dramatically changing public health microbiology. Sequencing-based diagnostics can give us a complete picture of a patient’s infection in just a few hours, while genomic investigations of disease outbreaks are allowing us to reconstruct transmission events and understand the movement of a pathogen through a population to a degree never before possible. This new era isn’t without its informatics challenges, though, from understanding how much we can trust the genomic results to accreditation of software pipelines for clinical use. This talk will introduce some the ways in which genomics is being used in public health, along with the bioinformatics issues facing the medical microbiology genomics community. top
TIMOTHY R. HUGHES Timothy R. Hughes is a Professor in at the at the University of Toronto. He studied engineering and music at the University of Iowa, and received his Ph.D. in Cell and Molecular Biology from Baylor College of Medicine, working on telomere replication. He did his postdoctoral work at Rosetta Inpharmatics (now Merck) working on microarray technology and its applications, including the development of ink-jet arrays now available from Agilent. Since moving to Toronto in 2001, Dr. Hughes has been the recipient of a Canada Research Chair in Genome Biology, the Ontario Premier’s Research Excellence Award, the Terry Fox Young Investigator award, and an HHMI foreign scholarship. He has authored or co-authored over 100 manuscripts, and is a scholar of the Canadian Institutes For Advanced Research. His laboratory has worked in gene regulation, systems biology, RNA processing, genome sequencing, and computational biology, and has a fundamental goal of understanding how the genome sequence is interpreted by the cell. top
STEVEN J.M. JONES Dr. Jones gained his PhD at the Sanger Institute, Cambridge, UK in 1999, where he was involved in the C. elegans genome project. Currently, he is Head of Bioinformatics and Associate Director of the Genome Sciences Centre at the BC Cancer Agency in Vancouver. Dr. Jones has played a role in numerous other genome projects, including that of the human, mouse, rat, bovine, fruitfly and the SARS coronavirus. Dr. Jones major research focus is in the computational analysis of DNA sequence and the analysis of genomic and transcriptomic data. In healthcare research, he has applied next generation DNA sequencing technology to detect mutations arising in both patient samples and in cancer cell lines in various cancer types and under the influence of different therapeutics. A key goal is to develop bioinformatic approaches to predict the most efficacious therapies from patient tumour samples to help guide clinical decision making. Amongst Dr. Jones many and varied honours and awards he is a Fellow of the Royal Society of Canada as well as the Canadian Academy of Health Sciences. He has been invited to give over 120 presentations, nationally and internationally, is an author on over 300 peer reviewed publications and is Principal Investigator and co-applicant on grants totaling over $97 million. top
CHRISTINA LESLIE Christina Leslie did her undergraduate degree in Pure and Applied Mathematics at the University of Waterloo in Canada. She was awarded an NSERC 1967 Science and Engineering Fellowship for graduate study and did a PhD in Mathematics at the University of California, Berkeley, where her thesis work dealt with differential geometry and representation theory. She won an NSERC Postdoctoral Fellowship and did her postdoctoral training in the Mathematics Department at Columbia University in 1999-2000. She then joined the faculty of the Computer Science Department and later the Center for Computational Learning Systems at Columbia University, where she began to work in computational biology and machine learning and became the principal investigator leading the Computational Biology Group. In 2007, she moved her lab to the Computational Biology program of Memorial Sloan Kettering Cancer Center, where she is currently an Associate Member. Dr. Leslie's research group uses computational methods to study the regulation of gene expression in mammalian cells and the dysregulation of expression programs in cancer. She is well known for developing machine learning approaches – algorithms for learning predictive models from data – for analysis of high-throughput biological data, especially from next-generation sequencing. Focus areas in the lab include dissecting transcriptional and epigenetic programs in differentiation, microRNA-mediated gene regulation, alternative cleavage and polyadenylation, and integrative analysis of tumor data sets.

top

ABOUT THE CANADIAN COMPUTATIONAL BIOLOGY CONFERENCE (CCBC)

Over the past 18 months, the Bioinformatics/Computational Biology (B/CB) Advisory Committee has worked closely with research funders to develop a strategic framework with a view to building a fully integrated Canadian B/CB capacity across the life sciences. One of the key items that has already emerged from this consultative process was the interest and strong willingness to organize a regularly scheduled Canadian Computational Conference. Given the fortuitous planning of the ISMB-sponsored regional GLBIO2016 conference in Toronto, select members of the B/CB advisory group were delighted to be invited to co-organize the first Canadian Computational Biology Conference with the Great Lakes Bioinformatics (GLBIO) conference for 2016.

This first Canadian Computational Biology conference will offer Canadians the opportunity to bring stakeholders together to explore the possibility of an action plan for the formation of a national network, including how it needs to be structured and funded to ensure its sustainability. By establishing a Canadian B/CB conference the research community and stakeholders have the opportunity to build an integrated community that is linked to International initiatives. We look forward to the meeting serving as a platform upon which like-minded individuals will inform others on the potential benefits that such a meeting would bring to the B/CB community in Canada.

In addition to gathering the National and US/Canadian great lakes community in this inaugural Canadian Computational Biology conference, we have the opportunity to put together an exciting scientific program and venue that will benefit students, scientists and managers at all level of people through the proceedings at this conference. As the first launch of the Canadian conference, the organizers are grateful for the considerable organizational support and experience of the International Society of Computational Biology and the local chapter of the Great Lakes Bioinformatics conference, who have done much to assist the Canadian meeting.

Since the beginning of this initiative, both Genome Canada and the Canadian Institutes of Health Research (through the Institute of Genetics and its B/CB sub-committee) have been steadfast in their support of this community. While it is clear that there remains much work to be done, both organizations have participated in a vision that brings the Canadian community together. Without their sponsorships, support and assistance the Canadian conference would not have been possible.

Keeping up with the needs of the life sciences community for innovative and increasingly complex algorithms, tools and databases is surpassing existing researcher capacity. There is a pressing need to coordinate and integrate what is currently being done in Canada to be able to meet the demands of the user community. The establishment of this national conference is the first step in coordinating our efforts within the B/CB community, in collaboration with research funders, infrastructure providers, users and other stakeholders. Finally, this first conference will provide the Canadian community with a pivotal forum for discussions as to how best to bring all stakeholders together in support of a sustainable national network.

More details on the Canadian Bioinformatics and Computational Biology community will always be available from the bioinformatics.ca website.

top

GETTING AROUND

The conference will be held at Victoria College, University of Toronto. 

Gooderham Building Photo courtesy of Toronto Tourism & Visitors Association

1. By Toronto Transit Commission (TTC): With four lines and 69 stops, Toronto’s subway system is easy to navigate. Maps are displayed on all subway cars and are available at station ticket booths. Subway stops connect to streetcar or bus routes that weave throughout the city and extend to the GTA (hold on to your paper transfer for free connections). Single fare is $3 for adults, $2 for students/seniors and 75 cents for children; keep in mind that drivers don’t provide change. You can save money by buying multiple tokens or tickets or a one-day or one-week transit pass. Single-day passes cost $11 and allow unlimited rides from the start of service until 5:30 the following morning. On weekends and statutory holidays, the $11 day pass provides unlimited travel for a group of up to six people, with a maximum of two adults. Weekly passes, valid from Monday to Sunday, cost $39.25 for adults and $31.25 for students/ seniors. Visit ttc.ca or call 416-393-INFO for more information.

2. By GO Transit: For routes out of Toronto into neighbouring suburbs, check GO Transit bus and train schedules at gotransit.com.

3. By regional transit: Visiting Mississauga? Go to the Click n’ Ride route planner on mississauga. ca, type in your origin and destination, and the website will map out your best route. For route information in Brampton, visit Brampton Transit at brampton.ca.

4. By taxi: Toronto has numerous cab companies, and all charge the same base rate of $4.25, plus $1.75 per kilometre ($1.09 per mile) or 52 cents a minute. The easiest cab number to remember is 416-TAXICAB, which connects you to all taxi and airport-limo companies.

5. By bike: Renting a bike is easy. Keep an eye peeled for automated bike stands throughout the city. Bike rentals are ideal for shorter rides and are a great alternative to taxi jaunts. Grab a bike at one stand, then return it to another. Visit toronto.ca for a Toronto cycling map.

6. By foot: Toronto is a safe and walkable city. Look for trails throughout the parks, gardens and beaches; routes are outlined at toronto.ca. Explore the PATH, an easy-to-navigate system of underground walkways and shopping arcades that runs beneath the downtown core. The 30-km x subway stations, major hotels and several attractions, including Union Station, Roy Thomson Hall, The Air Canada Centre, CN Tower, Toronto Eaton Centre, Queens Quay and City Hall. Maps are available at toronto.ca.

Source: Toronto Tourism & Visitors Association

top

TRAVEL & ACCOMMODATIONS

• Accommodations
• Getting Here
• Getting Around
• Exploring Toronto
• VISAs
  

NEW TRAVEL INFORMATION (See the VISAS tab for more information)

As of March 15, 2016, visa-exempt foreign nationals are expected to have an Electronic Travel Authorization (eTA) to fly to or transit through Canada. Exceptions include U.S. citizens, and travellers with a valid Canadian visa. Canadian citizens, including dual citizens, and Canadian permanent residents are not eligible to apply for an eTA.

However, from March 15, 2016 until fall 2016, travellers who do not have an eTA can board their flight, as long as they have appropriate travel documents, such as a valid passport. During this time, border services officers can let travellers arriving without an eTA into the country, as long as they meet the other requirements to enter Canada.  Find answers to your questions about the leniency period.

For more information, explore the University of Toronto interactive map (click here).

top

WORKSHOPS

--- CAREER SESSION, Monday, May 16, 2016 ---

Career Ready: Elevator Pitch and Interview Skills
Date: Monday, May 16, 2016
Time: 12:30pm - 1:30pm
Location: VC 115
Instructors:
Part 1: Dr. Nana Lee, Director and Lecturer Graduate Professional Development, Faculty of Medicine, University of Toronto
Part 2: Dr. Michael Brudno, Associate Professor & Canada Research Chair in Computational Biology, Hospital for Sick Children and University of Toronto

Description:
Part 1: Improving your elevator pitch. You’ve just bumped into the person who could decide your next career move. They are about to head to their next meeting and you have two minutes to convince them that your science is worthy. Can you do it? In this session you will learn the theory behind how to deliver a great elevator pitch. You will then get the opportunity to put this theory to the test, honing and practicing your pitch with other audience members so that the next time you hop in an elevator, you will be ready.

Part 2: Witness a live interview for a faculty position. Ever wondered what it is like to interview for a faculty position? In this session, you will find out! One brave soul will participate in a “mock” faculty position interview, revealing to the audience the rigors of the interview process. Following the interview, the audience will be asked to participate in a critique of both the interviewee and interviewer.

Postdocs, graduate students and undergraduate students interested in learning communication skills useful for getting a job will benefit form this career session.

Prerequisites: Think about your best 3 line elevator pitch!

GLBIO/CCBC 2016 WORKSHOPS

--- Monday, May 16, 2016 ---

Workshop 1
Microbiome Analysis: 16S and Metagenomics
Date: Monday, May 16, 2016
Time: 10:30am-12:30pm, continuing 1:30pm-3:30pm
Location: VC 213
Instructors: Morgan Langille, Rob Beiko, & Mike Hall (Dalhousie University)

Description: We present a high-level overview of the major steps in analyzing microbiome data including 16S profiling and shotgun metagenomics. In addition, attendees will have hands on time to walk through a tutorial with an example dataset that provides suggestions for best practices in the field.

Prerequisites: Some basic UNIX experience (Newbies can walk through Part 1 and Part 2 of this tutorial: www.dropbox.com/s/9d4q6oxxmg7pq0i/Unix_and_Perl_course.zip?dl=1)

> Return to Agenda
.................................................................................

Workshop 2
Jupyter Notebooks for Performing and Sharing Bioinformatics Analyses
Date: Monday, May 16, 2016
Time:  10:30am-12:30pm
Location:  VC 101
Instructors:  Jonathan Dursi (University of Toronto)

Description:  In this workshop, we will learn:

• The basics of Jupyter notebooks - what they are and how they work
• How to install and run Jupyter notebooks on their laptop, in R and Python
• How to perform interactive analyses in a web browser using Jupyter
• Using markdown and latex to
• How to "Port" an R bioinformatics workflow from some scripts into a Jupyter notebook
• How to share a Jupyter notebook online, using three different approaches
  • SageMathCloudGit
  • Hub and git
  • mybinder.org

Prerequisites:  Participants will need to have some familiarity with R (or python), and be comfortable entering commands on the command line, but need not be an expert at either

Setup instructions: The data files will be downloaded day of event:

https://github.com/ljdursi/glbio-jupyter-workshop/blob/master/README.md

> Return to Agenda
................................................................................

Workshop 3
Quick Guide to Best Practices in Software Carpentry
Date: Monday, May 16, 2016
Time:  10:30am-12:30pm, continuing 1:30pm-3:30pm
Location:  VC 215
Instructors:  Marcelo Ponce and Erik Spence (SciNet, U. Toronto)

Description:  At the end of this workshop, participants will be able to put projects under version control with git, and will be able to apply basic best coding practices such as using comments, documentation, and modularization. They will have an overview of other basic software tools that can further improve their productivity. See http://software-carpentry.org/

Scientists at all levels who would like to become more productive by learning (or re-learning) basic computing skills like best practices in coding, version control, and related skills will benefit from this workshop.

Prerequisites:  Some basic command line and python experience will be assumed. Participants should bring a laptop with the following software installed:
1. A linux-like environment
For Windows this could be MobaXTerm (http://mobaxterm.mobatek.net/) or Cygwin (www.cygwin.com/)
2. Python (www.python.org/) or a python Integrated Development Environment such as Enthought Canopy (https://www.enthought.com/products/canopy/) or Anaconda (https://www.continuum.io/downloads),
3. Git (git-scm.com/).

Make sure to do this ahead of time, because there will not be enough time to get this installed on everyone's laptop during the session.

> Return to Agenda
................................................................................

Workshop 4
Network visualization and analysis with Cytoscape
Date: Monday, May 16, 2016
Time:  1:30pm-3:30pm
Location:  VC 101
Instructors:  Ruth Isserlin, Jeff Liu, Veronique Voisin (Bader lab)

Description:  This workshop will cover general concepts in network visualization and analysis and will teach a pathway enrichment analysis workflow useful for analyzing and interpreting large gene lists from various types of genomics data, including gene expression and genomic mutations.  Scientists at all levels interested in learning the basics of network visualization and analysis with Cytoscape will benefit from this workshop.

Prerequisites:  A laptop with the most recent version of Cytoscape installed (instructions will be provided before the workshop)

> Return to Agenda

................................................................................

--- Tuesday, May 17, 2016 ---

Workshop 5
Hands-on workshop on Machine Learning with Applications to Bioinformatics
Date: Tuesday, May 17, 2016
Time:  5:30pm-9:30pm
Location:  VC 215
Instructors:  Ivan Kryukov and Jeff Wintersinger

Description:  This workshop will cover how to employ Machine Learning toolbox; including Classification, Clustering, Regression, and Dimensionality Reduction; to explore and analyze biological datasets.

This is an introductory workshop for anyone with basic programming skills who is interested to have a hands-on experience with machine learning techniques.

Prerequisites:  Familiarity with Python; Laptop with Python and scikit-learn
installed. A GitHub page for the workshop with instructions on how to
install necessary packages will be provided prior to the event.

> Return to Agenda

................................................................................

Workshop 6
Exploring and Refining Core Competencies for Bioinformatics (ISCB Curriculum Task Force)
Date: Tuesday, May 17, 2016
Time:  5:30pm-7pm
Location:  VC 213
Instructors:  Lonnie Welch, Michelle Brazas, Russell Schwartz

Description:  Participants in this workshop will explore the draft competencies and guidelines of the Curriculum Task Force of the ISCB Education Committee, learn how they are being used to shape training programs in different contexts, and work together to provide input into a refined and updated set of core competencies and guidelines.

Prerequisites:  None

> Return to Agenda
................................................................................

--- Wednesday, May 18, 2016 ---

Workshop 7
Next generation sequencing - From Sample to Sequence
Date: Wednesday, May 18, 2016
Time: 3:30pm-5:30pm
Location: VC 115
Instructor: Adam Rosebrock

>>Sign up here<<

Description: Over the past decade, the development and large-scale deployment of multiple “next generation” technologies has revolutionized the process of sequencing nucleic acids. Since the turn of the millennia, sequencing throughput has evolved from megabases to terabases of information per machine*week and has diversified from one dominant technology to a half-dozen fundamentally different measurement techniques and sample preparation approaches. Although sequence analysis begins for most computational biologists at the common currency of the FASTA/FASTQ file, understanding how these reads were generated is an important part of interpreting sequencing data.

In this two-hour tutorial, I will present the theory and practical considerations of several classic and next-generation sequencing technologies with a specific focus on issues relevant to computational biologists. Participants will gain a mechanistic understanding of next-generation sequencing and biological sample preparation and build a core vocabulary to enable communication across the “wet-dry” divide. Students will be exposed to outstanding problems and caveats of current sequencing approaches and will hopefully be inspired to consider new computational approaches to identify, circumvent, and ultimately correct extant issues with state-of-the-art approaches.

Mirroring how many wet-lab biologists view informatics tools as an impenetrable black box, many computational biologists view sequencing as closed, idealized process. The goal of this session is to provide computational biologists with a working knowledge of the biology and technology underlying sequencing and take the lid off of the black box!

Prerequisites: None

> Return to Agenda
................................................................................

Workshop 8
Computational approaches to synthetic biology
Date: Thursday, May 19, 2016
Time: 10:30am-12:00pm
Location: VC 115
Instructors: Cathy Su, Esther Jang, Alexander Sullivan (iGEM Toronto)

>>Sign up here<<

Description: iGEM is an international student competition in genetic engineering founded by MIT. Teams of undergraduate and graduate students around the world execute a synthetic biology project of their own design for entry into each year's competition. The power of iGEM lies in that large groups of students simultaneously collaborate. In recent years, more and more students have chosen to incorporate bioinformatics and computational biology into their work. Here we will discuss some examples from previous projects and why bioinformatics has been valuable, then consider what the future work of iGEM may bring to the field.

Prerequisites: None

> Return to Agenda

top