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 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.