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V. Schneider, J. Williams

Local Point of Contact:

Christina Hall


Jason Williams


April 11, 2016


Lab-14 Seminar Space, VLSCI –

The University of Melbourne 700 Swanston St (cnr Grattan St),

Carlton, VIC 3053, Australia


Required Workshop Prep

1. CyVerse Account

  • Get your free account at . Please register with an institutional email account as only this will give you access to the CyVerse cloud service Atmosphere (see next bullet).

2. Atmosphere Access

  • Once you have your account, go to and log in. Under "Apps and Services," scroll down to  "Available Services" and request access to Atmosphere. Indicate that you are attending a workshop when you are asked for justification. (This will only be granted if you registered for CyVerse using an institutional account; see above.)

3. Laptop

Please bring your own WiFi enabled laptop to the workshop. Make sure your laptop has the following:

4. Pre-Workshop Guide and Homework

  • Download and complete the exercises in the PRE-WORKSHOP PACKET to get the most out of the workshop.
  • Complete this Pre-Workshop Survey
  • Note (4/9): The wiki instructions for iCommands are not rendering properly. If you are setting up iCommands, you will need the following info when prompted.
irodsUserNameyour cyverse username
Current iRODS passwordyour cyverse password

Instructional Materials

You can download a copy of the workshop packet (CyVerse Toolkit) to follow along:

 Download Workshop Packet

Workshop Program (DAY 1)







09:00 AM

Arrive / Sign-in / Setup Troubleshooting




09:15 AM

Welcome - Presenter/Participant Self-Introductions

 slides PLOS Bioinformatics Competency Paper

09:30 AM

Overview of the CyVerse



 Getting Started with CyVerse

09:45 AM

Managing "Big Data" using the CyVerse Data Store

  • Using Cyberduck (p.10)
  • Quick iCommands demo (follow)
  • Importing files via URL (follow)
  • Creating Public links (p.11)
  • Sharing Folders (p.12)
slidestutorialData Store Overview

10:30 AM

Coffee Break



10:45 AM

Navigate the CyVerse Discovery Environment (DE)


  • MUSCLE analysis (p.16-17)
  • Simple upload/download
  • Moving, renaming, creating
  • Adding metadata (follow)
  • Searching (follow)

11:15 AM

Workflows and HT-Jobs in the DE.

  • Self-guided (p.18-19)
 (p.17-18)DE Manual on Workflows

12:00 PM

Lunch Provided



01:00 PM

DNA Subway

(Workflows for Bioinformatics Education)

   DNA Subway Website

01:15 PM

Using the DE for RNA-Seq

  • Launching TopHat (p.31-33)
  • Examining outputs (follow)
  • Visualizing alignments (follow)
  • Pseudoalignment methods
01:45Stretch Break    

02:15 PM

Atmosphere Cloud Computing

  • Launching an instance (p.23)
  • Connecting via VNC (p.24)
  • Desktop sharing via VNC (follow)
  • Connect via SSH (follow)


Atmosphere Manual

03:00 PM

Advanced CyVerse Applications

  • Tool integration
  • Bringing your tools with Docker
  • Data Commons: SRA Submission



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