SACNAS 2018 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 2018 SACNAS that will introduce participants to best practices, tools, and platforms for doing data-intensive research.
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.
Travel Scholarships
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
](https://software-carpentry.org/)[
](https://data-carpentry.org/)Wednesday, October 10, 9am- 6pm
Room 303 B
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
- efficiently work in the unix shell for file manipulation and
- 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 - 12:15p | Overview of more capabilities in the Command Line User Interface |
| 12:15p - 1:45p | Lunch on your own |
Session 2 : Python
| Time | Topic |
|---|---|
| 1:45p - 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
](https://www.cyverse.org/)[
](/)Wednesday, October 10, 9am- 6pm
Room 303 C
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
- Blake Joyce, CyVerse and the University of Arizona
- Dave Clements, Galaxy Project and Johns Hopkins University, clements@galaxyproject.org
- Joslynn Lee, Howard Hughes Medical Institute and University of Maryland Baltimore County, joslynnlee@gmail.com
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 - 12:15p | Analyzing data with Discovery Environment, continued |
| 12:15p - 1:45p | Lunch on your own |
| 1:45p - 2:15p | Discuss your data! |
Session 2 : Galaxy
| Time | Topic |
|---|---|
| 2:15p - 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 |
Help Get the Word Out!
We need your help advertising this workshop. Please distribute the workshop flier to your colleagues.