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 Congratulations to the participants of the hackathon!

Congratulations to all the participants of the hackathon! This year, the partipants had to use machine learning technique to predict the gestational age based on a dataset of blood transcriptomics from pregnant mothers. This challenge was taken from a worldwide competition organized by the Dream Challenges. 
https://www.synapse.org/#!Synapse:syn18380862/wiki/590485

Jules Lambert and Matthew Salaciak came up with the best solutions, being able to predict within an error margin of 6 weeks the gestational age. This puts them among the top 10 competitors for the world wide challenge, an impressive result in just 24 hours.

Thank to everyone who participated, who helped organize, and the to StartpFest for inviting us to their HackerFest!






 Summer hackathon

Registration is now open for our annual summer hackathon!
To register, click on the link below.
https://www.eventbrite.ca/e/monbug-summer-hackathon-hackerfest-tickets-46443561944

The StartupFest has once again generously agreed to host our hackathon this year, in the context of their HackerFest, that follows the StartupFest.
The registration cost is 12.76$, taxes included, which is a symbolic contribution to the cost of setting up the event, and includes food (I believe).
The organizers have given us a few free tickets.
Just ask us for one, and we’ll send you the link to register for free, until the free tickets are exhausted.
Exceptionally this year, we also have free tickets for the StartupFest itself, provided by both the organizers of the StartupFest and our sponsor, the local bioinformatics startup, Streamline Genomics (http://www.streamlinegenomics.com/)
They’re sold for about 500$ each, I think.
We’ll give them to the first person, registered in the hackathon, to claim them.
The only condition to claiming a free ticket is that you must use it, or you’re depriving someone else of a free ticket.

This year, the hackathon will take place in a park, on a peninsula in front of the Old Port.
It should be a spectacular location.
The problem we will tackle will be a machine learning problem involving a current molecular biology dataset.
You’ll have 24 hours to program a solution.
The winner(s) will get the glory of winning the MonBUG summer hackathon, an opportunity to advance science and a MonBUG t-shirt.

The last 2 years were tremendous fun, and the organization was stellar.
We had huge outdoor tents, so I’m hoping the 2018 edition will be as successful.

Don’t hesitate to ask any questions you have, in the comments section or directly to one of the organizers.
We’ll open a Slack channel the day before the hackathon.

To stay posted on all of MonBUG’s events, register on http://www.meetup.com/monbug.






 Summer hackathon at the Old-Port!

Join us again this year for our summer hackathon at the Old-Port of Montreal.
Register here: http://www.startupfestival.com/hackerfest/
Among the list of hackathons, pick the MonBUG hackathon,

We had a lot of fun last year organizing a hackathon at the HackerFest taking place at the end of the Montreal Startupfest, so we decided to repeat the event this year.

It’s a 24 hour marathon. You can bring your sleeping bag, and sleep on site if you want to. In fact, you are encouraged to spend the night on site.

During the hackathon, you will be given one dataset on which to apply machine learning techniques.
No prior knowledge of machine learning or molecular biology is required.
The winners get bragging rights, a MonBUG t-shirt, and an opportunity to advance scientific knowledge.

The registration fee is 18.98$ (including all taxes and fees), and includes snacks and breakfasts. The fee is mostly symbolic, and does not come anywhere close to covering the costs of the event. If you really don’t want to pay the registration fee, the site will be open to the general public Saturday at 10:00, so you can join us just for the Saturday, but you are encouraged to register officially.

The event is very well-organized. The location is spectacular (tents on the docks of the Old Port), and everything is provided. There will be security provided throughout the event, and there will be food trucks on site (besides the food provided by the event organizers).

There will be other hackathons taking place at the same time, with some of the best programmers in Montreal. We’ll also be collaborating with Bricobio, who will be organizing a hackathon focused on wet-lab biology (https://www.meetup.com/DIYBio-Montreal/).






 February meeting

Auditorium Jacques-Genest, IRCM
Wednesday, January 29th, 17:00 – 18:30
You can register for the meetings on Meetup, http://www.meetup.com/monbug, or by sending an email to register@monbug.ca.

Agenda

17:00 – 17:05 Introduction and open floor for community announcements
17:05 – 17:40 “Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas”, Simon Papillon-Cavanagh, McGill University and Genome Quebec Innovation Centre
17:40 – 18:00 Break with snacks and refreshments
18:00 – 18:30 “Essentials of Linux systems administration for bioinformatics”, Hector Galvez, McGill University

Our first spring meeting will be a short one, but with two excellent presenters.

Simon Papillon-Cavanagh will be presenting his research, based on the analysis of publically available genomic datasets, published just last month in Nature Genetics.
Hector Galvez will be doing a tutorial on the administration of Linux systems for bioinformaticians.






 NGS data analysis workshop and Dream Challenges hackathon

The NGS data analysis is full. Thanks to everyone who registered. Looking forward to seeing you Friday.
If you’d still like to attend, you can always put yourself on the waiting list on Meetup (http://meetup.com/monbug), and hope someone cancels.

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Join us for a day long workshop at IRCM on Friday, July 8th, on next-generation (NGS) data analysis. This workshop is open to participants of all levels, and all backgrounds, including wet-lab biologists who have no experience in bioinformatics.

A nominal attendance fee (20$) will be charged to raise funds to cover the operating costs of MonBUG. We’ll use the funds raised to cover the daily costs of running MonBUG (t-shirts, snacks and beverages for meetings, website hosting, …)

MonBUG is a registered non-profit. We’ll provide official receipts to those who request them. You can pay cash or by check. Credit card payments are a bit more complicated, but we’ll see if we can make arrangements.

Tentative schedule

9:30 – 10:30 Introduction to Unix, and the queuing system, on a computing cluster
10:30 – 11:00 Overview of the main file types for NGS
11:00 – 12:00 Introduction to the main steps of an RNA-Seq analysis
12:00 – 12:45 Lunch break
12:45 – 13:15 A practice RNA-Seq analysis, using the Unix command line
13:15 – 13:45 Introduction to ChIP-Seq analysis, using the Unix command line
13:45 – 14:15 A practice ChIP-Seq analysis, using the Unix command line
14:15 – 14:45 Introduction to Exome-Seq analysis, using the Unix command line
14:45 – 15:15 A practice Exome-Seq analysis
15:15 – 16:15 A few examples of how use Galaxy, a Web interface for the most commonly used tools in NGS data analysis
16:15 – 17:00 Question period.

Feel free to bring your own dataset, and to prepare questions for the workshop.

The wiki for the workshop is under active construction, and will contain all the information about the event.
MonBUG workshop – June 8th 2016

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The Dream Challenges hackathon will take place within the HackerFest of the Startupfest. You can register right now on the HackerFest website.  Just pick the biohackathon option when you register.
http://www.startupfestival.com/hackerfest

We’re going to have a tent in the Old Port of Montreal for 24 hours, with power, Internet and all other amenities provided to us, where we can hack on some challenging bioinformatics problems involving machine learning.

We’re going to be working on the DREAM challenges. There will be prizes for the winners of the hackathon (The MonBUG t-shirts have finally been ordered). The DREAM challenges organizers also provide their own rewards, ranging from authorship in publications to significant cash rewards for one of the challenges.

The 15$ registration fee for the hackathon includes coffee, snacks, and breakfast. The site will be open only to those who officially registered from 17:00 Friday to 10:00 Saturday. You may be able to drop by Saturday after 10:00 without registering. I would really encourage you to officially register though to support the event.

There will be 5 DREAM Challenges open for hacking.
http://dreamchallenges.org

The Digital Mammography DREAM Challenge 
Disease Module Identification DREAM Challenge 
Respiratory Viral DREAM Challenge*
ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge
ICGC-TCGA DREAM Somatic Mutation Calling RNA Challenge (SMC-RNA)

At the end of the hackathon, you will present your work on the challenges. We’ll decide the winners based on your presentations. The DREAM challenges are open for several months, so you don’t need to share all your code at the end of the hackathon if you don’t want to. You can share with us what you wish to share, if only your position on the leaderboard, and what you were able to accomplish within the time frame of the hackathon. If you want to continue working on the challenges after the hackathon, you’ll also have the opportunity to present all your work at one of MonBUG’s meetings once the challenges have closed.

The hackathon is being held in collaboration with Kevin Chen’s Bricobio group. Thanks to Kevin for inviting us!

Most of us come from academia, but the organizers are enthusiastic about having bioinformaticians participate. There will be many excellent programmers at the event, and opportunities for collaborations.

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We’ll be back to our regular meetings in September.
If you’d like to share your research at one of our meetings for our 2016-2017 season, or if you’d like to suggest a speaker, please don’t hesitate to contact one of the organizers.






 December meeting

Dr. Major and his team will present their work on RNA engineering.
Dr. Major, principal investigator at IRIC, is a pioneer in bioinformatics in Montreal.
He has trained a few generations of bioinformaticians.
He is also one of the rare bioinformaticians to open his own wet-lab.

Here is a summary of his research.
We “want to understand and characterize human gene regulatory networks; link cell content to phenotypes; and, design and create artificial molecular components to peek and poke cell information and programmes. […] We are developing a suite of programs to analyze, model, predict, and determine RNA 2D and 3D structure.”
http://www.major.iric.ca/MajorLabEn/Home.html

As this is also the last meeting of 2015, and that the next meeting will not be before February, we are also going to go to Benelux after to celebrate the end of the year.

Agenda
16:00 – 16:05 Introduction and community announcements
16:05 – 16:45 “MiRBooking simulates the stoichiometric mode of action of microRNAs”, Dr. Major (IRIC)
16:45 – 17:05 Snacks and refreshments
17:05 – 17:35 “Structural Dynamics Control the MicroRNA Maturation Pathway”, Paul Dallaire, PhD (IRIC)
17:35 – 18:00 “Identification of dynamic motifs in RNA”, Mathieu Dupont (IRIC)

The meeting will take place Wednesday December the 2nd, from 16:00 to 18:00 in the Jacques-Genest auditorium at IRCM.
You can register at http://www.meetup.com/monbug. If you don’t want to use Meetup, you can register for the next meeting by sending an email to register@monbug.ca.






 November meeting

We hope to see you at our November meeting.

Our keynote speaker will be Dr. Barreiro, principal investigator at CHU Sainte-Justine, who will be presenting his research on the genomics of the immune system. For more information about his exciting research, have a look at his web site.

Ali Emami, who works in Dr. Rabasa-Lhoret at IRCM, will be presenting his research on an artificial pancreas, a project which could “have a great impact on the treatment of type 1 diabetes”.

After all our talks on genomics, we’re happy to have a talk on proteomics.
Bagci Halil, phD student in Dr. Côté’s laboratory, with be presenting his research on the the exploration of the signaling networks of Rho GTPases by BioID.

Agenda
16:00 – 16:05 Introduction and open floor to participants for community announcements (Alain Bateman)
16:05 – 16:45 “Genomics of the Immune System”, Luis Barreiro, phD (CHU Sainte-Justine)
16:45 – 17:05 Snacks and refreshments
17:05 – 17:35 “Glucagon Action Model in Type 1 Diabetes”, Ali Emami (IRCM)
17:35 – 18:00 “Exploring the signaling networks of Rho GTPases by BioID”, Bagci Halil (IRCM)

The meeting will take place Wednesday November the 4th, from 16:00 to 18:00 in the Jacques-Genest auditorium at IRCM.
You can register at http://www.meetup.com/monbug. If you don’t want to use Meetup, you can register for the next meeting by sending an email to register@monbug.ca.

 






 April meeting

We’d like to thank everyone for another great meeting on April 1st: the speakers, our sponsors (especially our new sponsor, the McGill Department of Human Genetics), the attendees, and all the people working behind the scenes to ensure MonBUG’s success.
We’re working on our next meeting in May. 🙂
We’re also going to have some exciting announcements about new sponsors shortly!

The bar has been set high for the level of the talks during our first two meetings in 2015.
We think we’ll be able to follow up with some equally great speakers in May.
We’ll be confirming the data and the list of speakers in the next week or two.
Stay tuned!

The bigger auditorium got positive reviews, so that will now be our default room.
We have space for 150, so don’t be shy about inviting all your colleagues and friends to come.
We deliberately keep our meetings short, but everyone is welcome to stay after the meeting to continue the discussion around some drinks and food.

Again, thank you to all our speakers, and our new sponsor, the McGill Department of Human Genetics.

We’ve left the agenda for the April meeting below, but we’ll be posting the agenda for the May meeting shortly.

Agenda for April 1st meeting (May meeting agenda to be posted shortly)

4:00 PM
Introduction and open floor for announcements/questions/comments – Alexis Blanchet-Cohen, IRCM

4:15 PM 
“Personalized Targeted Therapy for Refractory Childhood Cancers” – Mathieu Lajoie, PhD, CHU Ste-Justine

5:00 PM  
Break (Snacks and beverages)

5:15 PM 
“PyGeno: A Python package for Personalized Medicine and Proteogenomics” – Tariq Daouda, IRIC

5:45 PM 
“Everything you’ve ever wanted to know about Git” – Nicolas De Jay, Lady Davis Institute

You can let us know you’re coming by RSVP, sending us an email at info[@]monbug.ca, or by any other means, as long as we know that you will be attending the meeting.

We’re always looking for new speakers, of all levels: keynote speakers, short presentations about your favourite programming library or tool, …
Please contact us if you would like to present.

Abstract for the keynote presentation

“In Canada, about 1500 pediatric cancers are diagnosed each year. Despite improvements in risk-based treatment protocols, ~20% of childhood cancer patients do not respond to current therapies and ultimately succumb to their disease, urging the need for new and more effective therapeutic approaches. Since individual tumours of the same clinical type harbour diverse sets of genomic alterations that drive oncogenesis and modulate drug response, personalized targeted therapy based on next generation sequencing may be a key to increase curerates and decrease treatment-related morbidity and mortality.

In this project, we implemented an automated pipeline to identify single nucleotide variants, indels, gene fusions, and copy number variations from DNA and RNA sequencing data. We use Perl wrappers to encapsulate well-established softwares (e.g. Bowtie2, STAR, PicardTools) and connect them using a common interface. Our goal is to detect prognostic markers and drug-actionable targets in a rapid and standardized way, going from biopsy to detailed tumour analysis within a clinically-relevant timeframe. Actionable variations are validated by re-sequencing or qPCR, detailed in a report with supportive information and communicated to the physician. Preliminary results on 10 cases indicate the feasibility and great potential of our approach; indeed, the final report can be in the treating oncologist’s hands in less than 8 weeks. This represents a first step towards the implementation of a targeted therapy program for children with relapse or refractory cancer.”






 MonBUG is back!

Please RSVP for the first MonBUG meeting in 2015, on Wednesday March the 4th at 16:00.

We are establishing lists of potential speakers for future meetups. Please do not hesitate to contact us if you want to present on the project on which you are working, a bioinformatics tool you like, mathematics, … Given the diversity of fields covered by bioinformatics, we will try and organize each meeting around a common theme.

Stay tuned.






 Marie-Pierre Dubé

Talk Title :
Pharmacogenomics of warfarin: beyond dose prediction

Date / Time / Location:
Thursday April 12th, 2012 – 4:00 pm
Room S1-151 at IRIC

Affiliation :
StatGen

URL :
Marie-Pierre Dubé

Abstract :
Warfarin is the most widely used medication to treat blood clots and to prevent new clots from forming. Unfortunately, it is also associated with serious bleeding that can lead to hospitalization and death. Despite recent advances in our ability to use genetics to predict a patient’s optimal warfarin therapeutic dose, a significant portion of patients still experience wide fluctuations in their monitoring results during long term therapy with warfarin. The present talk will present the strategies used by our group to find predictive genetic signatures of unstable warfarin test results associated with higher risk of bleeding.