Workshop

CFIA/C3G/GQ GENOMIC VIROLOGY WORKSHOP

McGill University, Montreal, Canada

Monday, March 6th and Tuesday, March 7th 2017

The Canadian Food Inspection Agency (CFIA), the Canadian Center for Computational Genomics (C3G), Genome Québec (GQ) and the University of Florida (UF) are proud to announce a jointly organized free workshop on bioinformatics approaches for viral characterization using Next Generation Sequencing (NGS) data. The workshop will be held on March 6th and 7th 2017 at McGill’s campus, downtown Montreal, and will host virology and big data mining specialists: Dr. Mattia Prosperi and Dr. Alberto Riva from the University of Florida, Department of Epidemiology. Dr. Levent Albayrak from the University of Texas Medical Branch and Jae Min from the University of Florida, Department of Epidemiology, will also be present as guest instructors.

Although a substantial number of bioinformatics tools exist to analyze sequences generated by NGS platforms and characterize viral entities, their use requires both high expertise and computational resources. The workshop will focus in defining a workflow that anyone with interest in virology can reproduce using the processing power of standard personal computers. We will start with a general overview on NGS technologies and move forward to more complex analysis of full (meta-)genomes and huge dataset with a focus to virology.

The workshop will consist of both lectures and practice sessions. Computers will be provided for each participant with the necessary bioinformatics tools made available throughout the workshop. The maximum number attendees has been reached. Registration is now closed for this year. Thank you for your interest!

Workshop schedule

Locations

Morning lectures + lunch : Salle du parc (C-14) , McGill University New Residence Hall, 3625 Park Ave.
Once inside the residence, walk down the stairs to the last floor (ballroom level) or ask the desk clerk for the elevator (take it down to the lowest level).
Afternoon practices : room TR3090, Trottier building

 

Monday, March 6th

8:15 Welcoming and introduction Guillaume
8:45-9:45 Introduction to next generation sequencing technologies and applications Jae
9:45-10:45 Reference assembly and error correction Mattia
10:45–11:00 Coffee break
11:00-12:00 Metagenomics Mattia
12:00-13:00 Lunch
13:00-14:00 Practice: Introduction to analytic suites Levent
14:00-15:00 Practice: Basic reference assembly and SNP pipeline Alberto
15:00-15:15 Coffee break
15:15-16:15 Practice: Metagenomics classification Alberto
16:15-17:15 Free computer time with instructors Alberto, Emmanuel, François, Jae, Levent, Mattia

Tuesday, March 7th

8:45-9:45 De novo assembly Mattia
9:45-10:45 Phylogenetics applications Jae
10:45-11:00 Coffee break
11:00-12:00 Methylation and viruses Alberto
12:00-13:00 Lunch
13:00-14:00 Practice: De novo assembly with UGENE Levent
14:00-15:00 Practice: Virus-tailored assembly Alberto
15:00-15:15 Coffee break
15:15-16:15 Practice: Phylogenetics with MEGA Jae
16:15-17:15 Free computer time with instructors Alberto, Emmanuel, François, Jae, Levent, Mattia

Guest instructors and hosts

Levent Albayrak University of Texas Medical Branch, Post-Doc, PhD
Guillaume Bourque McGill University & Genome Quebec Innovation Center, Department of Human Genetics, Director of Bioinformatics, Associate Professor, PhD
Emmanuel Gonzalez McGill University & Genome Quebec Innovation Center, Canadian Centre for Computational Genomics (C3G), Bioinformatics consultant, PhD
Francois Lefebvre McGill University & Genome Quebec Innovation Center, Canadian Centre for Computational Genomics (C3G), Bioinformatics Manager
Jae Min College of Public Health and Health Professions & College of Medicine, University of Florida, Department of Epidemiology, PhD student
Mattia Prosperi College of Public Health and Health Professions & College of Medicine, University of Florida, Department of Epidemiology, Preeminence Associate Professor, PhD
Alberto Riva Interdisciplinary Center for Biotechnology Research, University of Florida,Associate Scientist, PhD

Contacts

Registrations are now closed but should you have any question prior or during the workshop, you can contact Francois and Emmanuel here: workshops@computationalgenomics.ca

Life outside the workshop

McGill University

McGill University is located downtown Montreal @ 845 Sherbrooke Street West, Montreal, Quebec. Here is a map! You can reach our downtown campus by public transit (McGill metro station or by bus), by bike, or on foot. If you bring a car, parking on campus is limited. Please be prepared to park off campus.

Getting to Montreal

Plane: You’ll land at Trudeau International Airport (aka Dorval). You can get downtown with either the public transit 747 bus or by taxi (flat rate to downtown zone). You can also pick-up a rental car at the airport.
Train: You’ll arrive at the Gare Centrale with either VIA Rail or Amtrak. This station is linked to public transit.
Bus: You’ll arrive at the Gare d’autocars de Montréal. Take either public transit or a taxi to campus.

Accomodations

The Downtown area has a plenty of accommodation: hotels, bed & breakfast, and youth hostels. A quick internet search should help provide you with a number of options; in case you don’t know where to start: href=”http://www.marriott.com/hotels/travel/yulmd-renaissance-montreal-downtown-hotel”>Hotel Renaissance is located next to McGill University among others.

Going out?

Although downtown Montreal is less active after 6pm, you may still find restaurants and pubs are open all night long (although this may not be the best option for high complexity metagenomics workshop). We recommend you chose the extent to which any going out experience will be. Now that you have been warned, Montreal has plenty of places to enjoy and a quick google should help you find your way. What we suggest here are just places that we like

Coffee shops
Café Humble Lion
Café Nocturne
Café Parvis
Food and more
Jatoba
Furco
Balsam Inn
Biiru
Brasserie T!
Kampai Garden

Saint Laurent street and Montreal old port have plenty to offer if you want to explore further. If you have more specific tastes, the easiest way to find what you need is to ask us.

Upcoming events

C3G will be announcing soon a metagenomic workshop. If you are interested, visit our workshop page or just let us know and we will add you to our mailing list.

Mattia Prosperi will be part of the next Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME) in Lisbon, Portugal.

Thanks

The workshop is free and is entirely funded by the Canadian Food Inspection Agency/Agence canadienne d’inspection des aliments. It was made possible through Mattia Prosperi‘s collaborative efforts to make part of his VEME workshop fit into 2 days (VEME 2017) and thanks to the University of Florida. The workshop is organized by the Canadian Center for Computational Genomics (C3G) and Génome Québec.
More thanks: Ron Simpson (McGill computer science), Michel Barrette (Calcul Québec), David Anderson (C3G), David Morais (Calcul Québec), Sharen Roland (Génome Québec), Jean Monlong (McGill University) and Sylvie LaBoissière (Génome Québec)

Pictures

CFIA-WS-group_large

Instructors: Levent Albayrak, Jae Min, Mattia Prosperi, Alberto Riva. Participants: Levent Albayrak, Trisha Barnard, Jasmin Chahal, Frederick Kibenge, Molly Kibenge, Myriam Labbé, Virginie Lachapelle, Christian Lalonde, Émilie Larocque, Genevieve Marchand, Hamza Mbareche, Vani Mohit, Alex Montgomery, Susan Nadin-Davis, Nicolas Nantel-Fortier, Adrian Pelin, Chantale Provost, Philippe Raymond, Selena Sagan, Christian Savard, Jiahu Wang. Organization: Emmanuel GonzaLez, Francois Lefebvre, Sharen Roland.

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