July - NGS data analysis workshop and DREAM Challenges hackathon¶
Event Details
Date/Time:
Friday, July 8th, 2016 09h30 - 17h00
Location:
Location: IRCM (workshop); HackerFest tent, Old Port of Montreal (hackathon)
Schedule:
09h30 - 10h30 — Introduction to Unix, and the queuing system, on a computing cluster
10h30 - 11h00 — Overview of the main file types for NGS
11h00 - 12h00 — Introduction to the main steps of an RNA-Seq analysis
12h00 - 12h45 — Lunch break
12h45 - 13h15 — A practice RNA-Seq analysis, using the Unix command line
13h15 - 13h45 — Introduction to ChIP-Seq analysis, using the Unix command line
13h45 - 14h15 — A practice ChIP-Seq analysis, using the Unix command line
14h15 - 14h45 — Introduction to Exome-Seq analysis, using the Unix command line
14h45 - 15h15 — A practice Exome-Seq analysis
15h15 - 16h15 — A few examples of how to use Galaxy, a Web interface for the most commonly used tools in NGS data analysis
16h15 - 17h00 — Question period
A day long workshop at IRCM on next-generation sequencing (NGS) data analysis, open to participants of all levels and all backgrounds, including wet-lab biologists with no experience in bioinformatics. Participants were invited to bring their own dataset and to prepare questions for the workshop.
The workshop was followed by the MonBUG DREAM Challenges hackathon at the Startupfest HackerFest (see below).
DREAM Challenges hackathon¶
The Dream Challenges hackathon took place within the HackerFest of the Startupfest (HackerFest). We had a tent in the Old Port of Montreal for 24 hours, with power, Internet and all other amenities provided to us, where we could hack on some challenging bioinformatics problems involving machine learning. The site was open to registered participants from 17:00 Friday to 10:00 Saturday.
There were 5 DREAM Challenges open for hacking:
- 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, participants presented their work on the challenges, and the winners were decided based on the presentations. The DREAM challenges organizers also provide their own rewards, ranging from authorship in publications to significant cash rewards for one of the challenges.
The hackathon was held in collaboration with Kevin Chen's Bricobio group. Thanks to Kevin for inviting us! Most of us come from academia, but the organizers were enthusiastic about having bioinformaticians participate.
Winners¶
Congratulations to the winners of the hackathon, Kira McLean, Nadia Tahiri and Vero Rebagliatte!
Kira, Nadia and Vero worked through the night on the Digital Mammography DREAM Challenge, and came up with some impressive results. Their full project was to be presented once the online competition for this Challenge ended in December.
Thanks to everyone who attended!
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