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A. Hlousek-Radojcic, J. Williams

Local Point of Contact:

Alenka Hlousek-Radojcic


Joslynn Lee, Jason WIlliams


Feb. 3-4, 2015


University of Delaware

Newark, DE

Room: Interdisciplinary Science and Engineering Laboratory (ISE) - 410

221 Academy St. University of Delaware

Parking Information/Permits

Required Workshop Prep

1. CyVerse Account

  • Get your free account at . (Make sure to REMEMBER your username and password.) Please register with an institutional email account as only this will give you access to the CyVerse cloud service Atmosphere (see next bullet). Please avoid gmail, yahoo, hotmail and the like for your CyVerse registration as you would not be able to register for Atmosphere with those.

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 and DNA Subway. 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

Instructional Materials

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

  Download Workshop Packet

Draft Workshop Program (DAY 1)







08:30 AM

Arrive / Sign-in / Setup Troubleshooting





09:00 AM

Welcome - Presenter/Participant Self-Introductions


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

  • Download/use iDrop (p.10)
  • Quick iCommands demo (follow)
  • Importing files via URL (p. 29)
  • Creating Public links (p.11)
  • Sharing Folders (p.12-13)
slides Data Store Overview 

10:30 AM

Coffee Break




10:45 AMNavigate the CyVerse Discovery Environment (DE) cont'd
  • MUSCLE analysis (p. 16-17)
  • Simple upload/download (follow)
  • Moving, renaming, creating (follow)
  • Adding metadata (p. 32)
  • Searching (follow)

11:15 AM

Analyses in the DE; Phylogenetics Example

  • Self-guided (p. 16-18)

DE Manual on Workflows


12:00 PM






01:00 PM

DNA Subway

(Workflows for Bioinformatics Education)

  DNA Subway Website 

01:15 PM

Using the DE for RNA-Seq

  • Launching TopHat (p. 33)
  • Examining outputs (follow along)
  • Visualizing alignments (follow along)

02:15 PM

Atmosphere Cloud Computing

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


Atmosphere Manual


03:00 PM

Coffee Break





03:15 PM

Tool Integration in the DE

  • Building Phyml App(P. 36-40)


03:45 PMSRA Demo
  • Sequence submission to SRA

04:15 PM

Workshop summary and Conclusion



Post Survey


Draft Workshop Program (DAY 2)






09:30 AM

Overview and demo of CyVerse GWAS / Transcriptome assembly

slides (TA)

slides (GW)


10:30 AM

Coffee Break




10:45 AM

Getting started with Annotation: MAKER
Getting started with Assembly: ALLPATHS

slides (MP)


11:15 AM

Visualization of RNA-Seq results in Atmosphere



12:00 PM

Lunch (On your own)




01:00 PM

iCommands and other Data Store applications:
Get started with your own data




01:30 PM

“What Graduate Students should Know about Cyberinfrastructure
- How to be a Successful Data Driven Biologist”




02:30 PM

Individual Consultations


Please posts your requests for 10-15 min

consultations to the Etherpad (from 2:30-3 or so)


Important Pre-Workshop Travel Info 

Neither CyVerse/iPlant Collaborative nor the local host can reimburse lodging or other expenses associated with attending the workshop.

Maps and parking information can be found here:


See the university website:

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