April 6, 2017

PoreCamp USA 2017

        PORECAMP USA


NanoPore Workshop

Description

PoreCamp is part of the PoreCamp series,  This series was founded by Nick Loman, Matt Loose and Mick Watson in 2015 and has been run as a 1-week hands-on course led by Nick, Matt, Josh Quick, Justin O’Grady and John Tyson. It is a training bootcamp based around Oxford Nanopore Technology (ONT) MinION sequencing system. The workshop will be a unique opportunity to learn about this exciting sequencing platform (Oxford Nanopore Technolgie sequencing technology) from some of the leading experts in the field – Drs. Nick Loman, Josh Quick, Matt Loose, John Tyson, and Mick Watson are all coming to Aggieland! All are featured speakers at ONT’s annual user group meeting, London Call 2017 conference

  • Workshop dates: 5 – 9 June 2017
  • Limited number of students can attend (36)
  • 5 day hands-on training in the use of the Oxford Nanopore MinION
  • Including both laboratory and bioinformatics training
  • Workshop shall be held at CBGSE

Camp Objectives

  • To develop best wet-lab practices to produce high-quality MinION libraries
  • To provide hands-on experience running MinION on your own computer.
  • To discover data-handling methods for MinION output.
  • To discuss the latest bioinformatic methods for analysis of real-time nanopore data.

Application

  • Particupants will need to apply to attend PoreCamp USA.
  • Please download and complete the application form and return to Charles Johnson
  • Applicant reviews will begin May 4, but applications accepted until May 8th at 8am CST.
  • Space is very limited and will fill up quickly
  • Students will be informed if they are accepted or wait listed by May 8th
  • Ideally we would like a mix of students with laboratory and bioinformatics experience
  • Priority will be giving to graduate students in CVM and AgriLife

Requirements

  • Basic understanding of nanopore sequencing
    • Read the papers listed on this site
  • Students must agree to attend ALL porecamp actives during the week of June 5-9th, with the exception of the optional social activities Friday afternoon. For those students with a course scholarship, failure to attend required activities will result lose of your scholarship and you will be charged the full cost of the course
  • Join the ONT community
  • Join Twitter and follow instructors
  • Run at least one minION flow cell in your own lab before the workshop
    • TxGen will help students order minION starter kits for those that don’t already have one.

Cost

  • The cost of the course is $1,489
    • All Texas A&M applicants automatically qualify for one of three scholarships. See below
    • The price includes 4.5 days of combined hands and classroom training.
    • On the last day we will have an optional field trip to Jester King Brewery in Austin. Where we will be sequencing samples from Jester King’s wild farmhouse yeast/bacteria collection and local BBQ.
    • There will be a kickoff dinner sponsored by the College of Veterinary Medicine.
    • Participants are responsible for their own food (with the exceptions listed above) and lodging.  College Station have many hotels and restaurants around the university. We will provide suggestions for lodging.

Scholarships

Each Texas A&M student will get one of three scholarships if they are accepted into Porecamp USA

  • $100 scholarship
  • AgriLife and CVM have provided funds for their students to participate in porecamp. Both scholarships have approximately the same value
    • MinION starter kit scholarship. Your MinION starter kit purchase will be subsidized, and your porecamp tuition. Reducing your cost for both porecamp and starter kit to $597*. (15 scholarships) *details to follow
    • Your lab must have a MinION or be willing to buy a MinION starter kit ($1000 plus shipping from ONT) before the class.  Then you quality for this scholarship, reducing your tuition to $97 for porecamp. (15 scholarships)

Instructors

Nick Loman
Birmingham University
@pathogenomenick 
Josh Quick
Birmingham University
@Scalene 
Matt Loose
University of Nottingham
@mattloose
Mick Watson
University of Edinburgh
@BioMickWatson 
John Tyson
University of British Columbia
@DrT1973

Some PoreCamp History

 

Location

  • TxGen : 101 Gateway Blvd., Suite A, College Station, Texas

 

Sponsors

This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562 [1].

[1] John Towns, Timothy Cockerill, Maytal Dahan, Ian Foster, Kelly Gaither, Andrew Grimshaw, Victor Hazlewood, Scott Lathrop, Dave Lifka, Gregory D. Peterson, Ralph Roskies, J. Ray Scott, Nancy Wilkins-Diehr, “XSEDE: Accelerating Scientific Discovery“, Computing in Science & Engineering, vol.16, no. 5, pp. 62-74, Sept.-Oct. 2014, doi:10.1109/MCSE.2014.80