2019-04-11-gwu
Data Carpentry Genomics Workshop - George Washington University
WHEN: April 11-12, 2019 (9:30 AM - 5:30 PM)
WHERE: Gelman Library, 2130 H St NW, Room 301/302, Washington, DC 20052 . Get directions with OpenStreetMap or Google Maps.
HOW TO APPLY: Click on this link to register for the workshop.
TARGET AUDIENCE: Students, Researchers & Faculty
Little to no prior computational experience required.
The instructors will prioritize creating a friendly environment that will empower researchers and enable data-driven discovery. Even those with some experience will benefit, as the goal is to teach not only how to do analyses, but how to manage the process to make it as automated and reproducible as possible.
Learning objectives for this workshop:
- Accessing Cloud Computing Resources
- UNIX command line
- Environment management using Conda & Bioconda
- Building Reproducible Workflows
REQUIREMENTS:
- Laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) and administrative privileges.
No prior-software installation required. Windows users can install mobaxterm for a UNIX terminal.
-
Register for a free account on CyVerse Here
- Complete Pre-Workshop survey. We use this to calibrate the pace of the workshop and, together with a post-workshop survey, to assess how it went.
CODE OF CONDUCT:
- The workshop follows a code of conduct, which can be found here. (tl;dr: Be Nice and Respect each other.)
ACCESSIBILITY: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:
- The room is wheelchair / scooter accessible.
- Accessible & Gender-Neutral restrooms are available.
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
CONTACT: Please email Megan Potterbusch at (mpotterbusch@email.gwu.edu) for more information.
INSTRUCTORS
- Niel Infante
- Twitter - (https://twitter.com/Niel_Infante)
- Email: (aminfante@hsc.wvu.edu)
- Sateesh Peri
- Twitter - (https://twitter.com/perisateesh)
- Email: (perisateesh@nevada.unr.edu)
HELPERS
- Adam Wong - (aklwong@gwu.edu)
- Keylie Gibson - (kmgibson@gwmail.gwu.edu)
- Rebecca Clement - (rebeccaclement@gwmail.gwu.edu)
- William Bonnett - (synchronous@email.gwu.edu)
SCHEDULE
Day-1
09:30-10:15am : Introduction and Genomics Workshop Overview
10:15-11:00am : Introduction to CyVerse Atmosphere Cloud
11:00-11:15am : Coffee/Tea break
11:15-12:30pm : BASH - Command Line for Genomics
12:30-1:30pm : Lunch Break
01:30-3:00pm : BASH - Continued & Bioconda
03:00-3:30pm : Coffee/Tea Break
03:30-4:30pm : Overview of Genomics Analysis Workflow
04:30-5:30pm : Assessing Read Quality
Day-2
09:30-10:15am : Trimming and Filtering
10:15-11:00am : Variant Calling Workflow
11:00-11:15am : Coffee/Tea break
11:15-12:30pm : Automating the workflow using shell scripts
12:30-01:30pm : Lunch Break
01:30-04:30pm : Building Reproducible Workflows with Snakemake
02:30-03:00pm : Coffee/Tea Break
04:30-05:30pm : Discussion & End of workshop
Notepad for the workshop : Click here
SURVEYS
Please click on the links below to complete the surveys before and after the workshop.
Data Carpentry (part of The Carpentries) develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners’ existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. For more information on what we teach and why, please see our paper “Good Enough Practices for Scientific Computing”.