SACNAS 2017 Pre-Conference Workshops

Galaxy, CyVerse, Data abd Software Carpentry

Do you have data and don’t know where to start with analysis?

There will be two parallel full day pre-conference workshops at 2017 SACNAS that will introduce participants to best practices, tools, and platforms for doing data-intensive research.

  1. Software and Data Carpentry
  2. Data Platforms for Life Science Researchers

Together, CyVerse, Galaxy, Software Carpentry, and Data Carpentry will introduce participants to best practices, tools, and platforms for data-intensive research in two parallel workshops at the SACNAS pre-conference workshops. Workshops are for any researcher who has data they want to analyze, and no prior computational experience is required.

These hands-on workshops teach basic concepts, skills and tools for working more effectively with data. Attendees will learn the best practices for data organization and analysis using the command line and Python (Software and Data Carpentry workshop) or working with data-analysis platforms to manage, integrate, analyze, and visualize your data (Data Platforms for Life Science Researchers).

Registration

Registration is free but space is limited. You are strongly encouraged to register soon.

Register Now

Travel Scholarships

NOTE: As of September 1, all funds for SACNAS Travel Scholarship Recipients to attend this workshop have been allocated. If you register now, you will need to provide your own lodging costs for the extra night.

The Galaxy Community Fund is augmenting SACNAS Travel Scholarships awards for the first ~ 28 scholarship recipients that register for these workshops. The additional funds will cover an extra night's lodging for scholarship recipients, enabling you to arrive the day before the workshops. Space is limited, and once the funds are allocated, they are gone. Register Now

Workshop 1: Software and Data Carpentry

Software Carpentry

Data Carpentry

Wednesday, October 18, 9am- 5pm

Room 251 A

Ever find yourself manually repeating coding tasks? Do you feel like there should be an easier way to go about doing data analysis and visualization? Join us for a Software and Data Carpentry session to learn how to

  1. efficiently work in the unix shell for file manipulation and
  2. use Python in a sample workflow of data analysis from loading to visualization.

Bring your laptop for a series of hands-on exercises.

Instructors

  • Tracy Teal, Executive Director, Data Carpentry, tkteal@datacarpentry.org
  • Camille Avestruz, Postdoctoral Research Fellow at the University of Chicago, avestruz@uchicago.edu

Required Software

You will need bash and anaconda set up. Please follow the installation instructions outlined here for your operating system (either Windows, Mac OS X, or Linux) to make sure you have the “Bash Shell” and “Python” installed.

Session 1 : Unix Shell

Time Topic
9:00a - 9:30a Software check
9:30a - 10:15a Navigating the shell; file creation & manipulation; basic loops.
10:15a - 10:30a Break
10:30a - 11:15a Editing text files and simple bash scripts
11:15a - 11:30a Break
11:30p - 12:30p Overview of more capabilities in the Command Line User Interface
12:30p - 1:30p Lunch on your own

Session 2 : Python

Time Topic
1:30p - 2:45p Navigating Python in the Jupyter notebook; object orientation; basic loops and function syntax
2:45p - 3:00p Break
3:00p - 4:15p Loading, manipulating, and visualizing sample data
4:15p - 4:30p Break
4:30p - 5:15p Overview of more capabilities with Python libraries and porting code from the notebook to scripts
5:15p - 5:55p Final thoughts and evaluations
5:55p - 6:00p Group Picture

Workshop 2: Data Platforms for Life Science Researchers

CyVerse

Galaxy

Wednesday, October 18, 9am- 6pm

Room 251 B

Want to do data analysis and don’t know where to start? CyVerse and Galaxy are two widely used and freely available data analysis platforms for life science research. This workshop will cover both platforms and by the end of the day you’ll know how to use both to manage, integrate, analyze, and visualize your data. The focus will be on interactive hands-on exercises with life science data. Bring your laptop and your curiosity.

Instructors

  • Amanda Cooksey, CyVerse and the University of Arizona
  • Joslynn Lee, Howard Hughes Medical Institute and University of Maryland Baltimore County, joslynnlee@gmail.com
  • Dave Clements, Galaxy Project and Johns Hopkins University, clements@galaxyproject.org

Session 1 : CyVerse

This website contains instructions for 1) signing up/registering for a CyVerse account and 2) downloading CyberDuck (PC/Mac). If you can do the prior to the workshop, that would be very helpful!

Time Topic
9:00a - 9:30a Workshop & Participant Introductions
9:30a - 10:15a Navigating CyVerse, finding data, and exploring tools
10:15a - 10:30a Break
10:30a - 11:00a Navigating CyVerse, continued
11:00a - 11:15a Analyzing data with Discovery Environment
11:15a - 11:30p Break
11:30a - 12:00p Analyzing data with Discovery Environment, continued
12:30p - 1:30p Lunch on your own
1:30p - 2:00p Discuss your data!

Session 2 : Galaxy

Time Topic
2:00p - 2:45p Galaxy Basics: Loading data and running and connecting tools
2:45p - 3:00p Break
3:00p - 3:30p Galaxy Basics, continued
3:30p - 4:15p Collaboration and repeatable recipes
4:15p - 4:30p Break
4:30p - 5:00p Collaboration and repeatable recipes, continued
5:00p - 5:15p Galaxy Community
5:15p - 5:55p Compare & Contrast: CyVerse, Galaxy, and other options
5:55p - 6:00p Group Picture

Resources and Techniques for Training Students in Computational Skills

Friday, October 20, 8:45-10:15am

Room 250 F

Want to learn more about how to train students in computational methods? The four instructors are also presenting a Resources and Techniques for Training Students in Computational Skills session during the 2017 SACNAS Conference.