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Tracy Teal edited this page Mar 27, 2015 · 41 revisions

Welcome to the genomics-hackathon wiki!

Data Carpentry Genomics and Assessment Hackathon Information

Dates: March 23 - 25
Times: 9am - approx 5pm each day
Meet in the hotel lobby at 8:30am to get a ride to go over to the lab
Location: Cold Spring Harbor Laboratory

Communication Channels

Slack channel: https://datacarpentry-ngs.slack.com
Etherpad: https://datacarpentry.etherpad.mozilla.org/43
Twitter hashtag: http://twitter.com/hashtag/datacgen

Goals of the workshop

The goals of the workshop are to:

  • Identify the fundamental data management and analysis skills needed to work with genomic data. We will not be able to address particular bioinformatics pipelines, but aim to teach researchers the skills they need to handle files, get started with using bioinformatics tools and analyzing the output.
  • Determine a set of modules that would address these needs
  • Determine learning objectives for each module
  • Develop assessment to determine if the learning objectives are being met
  • Identify a dataset to be used throughout the workshop, likely a paired set of genomic data and its metadata
  • Develop the teaching materials for that each module with the learning objective and assessment incorporated, using the workshop dataset
  • If all content can't be developed, which is likely, have a clear set of issues for follow-up work on each module
  • Develop an assessment framework for Data Carpentry that the Genomics lessons will also use

Materials

For the Genomics Data Carpentry workshop, we have developed modules in

Before the workshop

All travel should have been booked through SESYNC Travel Services. Please get in touch right away if you have any questions about your travel arrangements.

In order to give people a chance to talk with some of the other participants and get started on conversations about what content should be in a Data Carpentry Genomics workshop, we've set up small groups and ask that before the workshop you talk with your group to discuss what topics should be covered. We've started with some ideas in a Google doc. Each group (listed below) will receive an email and a link to a Google doc for editing. We ask that when you get that email, you introduce yourself to each other and if you can set up a teleconference with your group to discuss your ideas for content.

Introduction groups

Group A (Wendt): https://docs.google.com/document/d/1gqJ0OKvHN3HxwHtiIJcp47yEnw6IHNPd10hPksJEXqs/edit

  • Shari Ellis
  • Chris Fields
  • Randall Hayes
  • Adina Howe
  • Sarah Stevens

Group C (Library: Sibalski ): https://docs.google.com/document/d/1uKS6JE5yGcvE-7htqjeLuxuXtdbMBd4ibGcVAt0tQPk/edit

  • Mary Shelley
  • Chris Hamm
  • Kate Hertweck
  • Blaine Marchant
  • Greg Wilson

Group T (Bush): https://docs.google.com/document/d/1vsNMGZ1KnAeJuLYyuSzAtK2fM8b7qLp9rsJPUlpcdkw/edit?pli=1

  • Mike Smorul
  • Amanda Charbonneau
  • Bob Freeman
  • Josh Herr
  • Susan Miller
  • Deb Paul

Group G (Mclintock): https://docs.google.com/document/d/11V0di6H57qrvDuTrOkujOSpzpUNMQ6DP6YKGAGKc6QA/edit

  • Tracy Teal
  • Jon Badalamenti
  • Sheldon McKay
  • Laura Williams
  • Ryan Williams
  • Michael Linderman

Group U (Library: RareBook) : https://docs.google.com/document/d/1koDAZZfbu3jVi9NiG5Zul7K9zyZRE-DiFSp3FRHaWuc/edit

  • Jason Williams
  • Andréa Matsunaga
  • Sue McClatchy
  • Jeramia Ory
  • Juan Ugalde

Tuesday Afternoon Breakouts

Project Setup/Organization
Wendt

Know your data
DeMattis

Cloud-genomics
McClintock

Wrangling-genomics
Bush Fireplace

R-genomics
Library: Rare book room

Logistical Information

####What Participants should bring to CSHL

  • Please bring Wi-Fi enabled laptop and charger
  • Dress warmly (NY is cool/cold in March), but the CSHL campus is casual
  • On-campus there are some amenities (small gym, laundromat, dining facilities (with vegetarian options)/coffee, bar) but there are not generally stores in walking-distance.
  • You will be staying off campus. Please bring whatever personal items you think you will need.

####Public Transportation from Recommended Airports

JFK: Take a Jamaica-bound Airtrain to Jamaica train station LIRR (Long Island Rail Road). Take the LIRR (Huntington/Port Jefferson line) to Syosset. Taxis are available and there is also a CSHL shuttle during AM/PM commuting times see below.

LGA: Take a taxi to Jamaica Train Station. Take the LIRR (Huntington/Port Jefferson line) to Syosset. Taxis are available and there is also a CSHL shuttle during AM/PM commuting times see below.

AirTrain Info ($5.00 Pay at Jamaica) http://www.panynj.gov/airports/jfk-airtrain.html LIRR Schedules (Jamaica to Syosset $15/$12 peak/off-peak, pay at Jamaica) http://www.mta.info/lirr CSHL Meetings Website (Additional travel info and campus to Syosset shuttle schedules) http://meetings.cshl.edu/travel.html Travel by Private Car Services: This is the most expensive option, but we do have discounted arrangements via Syosset Limo. There is a neuroscience meeting on campus during our event, so maybe you will fortunate enough for them to offer you a rideshare possibility. http://meetings.cshl.edu/syossetlimo/SyossetLimoForm.htm: (516) 364-9681.

####Booking Return Travel: All the information above applies. The hackathon will end Wednesday, March 25th at 2:00PM. Budget at least an hour of travel time back to the JFK/LGA. Since many of your fellow attendees will all be traveling back, you may have a greater chance at rideshare with Syosset limo on the way back.

####Hotel Information (getting to campus each day) Participants will all be staying at the same hotel.

Transportation will be provided each day to and from the hotel to CSHL. Meet in the lobby at 8:30am to go to the workshop.

####Reimbursement

  1. Save all transportation receipts.
  2. Meals will be reimbursed based on the SESYNC per diem described in their travel policies: http://www.sesync.org/sites/default/files/visitorsInfo/sesync-travel-policies.pdf
  3. Please fill out the form at http://www.sesync.org/sites/default/files/visitorsInfo/ExpenseReimbursementForm.pdf and email or fax it to SESYNC and send original receipts to SESYNC.
  4. You will receive an expense statement which you will need print, sign and mail back to SESYNC for final processing.

Please email travel@sesync.org if you have any travel questions, or see Mary or Mike while onsite

Potential workshops

  • Iowa State or Granel - Adina, Ryan and other local instructor
  • Harvard - Bob, maybe Tracy (July)
  • iPlant - ISPB and Jon, Adina, July 30-31, Minnesota
  • iPlant - Stoneybrook or CSHL
  • iDigBio - Deb

##Post hackathon survey https://docs.google.com/forms/d/1rMxRW0GImOqitsOu2UilqGt6nikmSDNlt5t7iTCcqRg/viewform?usp=send_form

##Group Photo ![Group Photo](http://de.iplantcollaborative.org/dl/d/CE5CF954-4D3C-4009-B1AF-B8B11B58235A/Group shot with rainbow cat.png) Without the cat

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