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T. Meulia

Local Point of Contact:

Tea Meulia
Hosted By: MCIC Computational Biology Lab (MCBL);
College of Food, Agricultural, and Environmental Sciences


Joslynn Lee, Jason Williams


March 17-18, 2016


College of Food, Agricultural, and Environmental Sciences
Shisler Conference Center
1680 Madison Avenue
Wooster, OH 44691
Parking Information/Permits

A parking permit is NOT needed


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


You can watch the Livestream of this event:

Day 1:

Day 2:

Instructions for virtual attendees:

While it is not possible to have the exact in-person experience, you can follow along to a good extent, please observe the following suggestions:

  1. Use the instructions in the  PRE-WORKSHOP PACKET to request access to Atmosphere.
  2. Use etherpad chat to ask question. if we don't get a chance to address your question please post to
  3. Download the Workshop Packet to follow along
  4. Please complete the post-survey.


Connect to the etherpad at

You can use the etherpad at the workshop to ask questions and share information, links, etc.

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

  • Use Cyberduck (p.10)
  • Quick iCommands demo (follow)
  • Importing files via URL (p.29)
  • Creating Public links (p.11)
  • Sharing Folders (p.12)
slidesData Store OverviewJoslynn

10:30 AM

Coffee Break




10:45 AM

Navigate the CyVerse Discovery Environment (DE)


  • MUSCLE analysis (p.17-18)
  • Simple upload/download (follow)
  • Moving, renaming, creating (follow)
  • Adding metadata (p.31)
  • Searching (follow)

11:15 AM

Analyses in the DE; Phylogenetics Example

  • Self-guided (p.18-19)

DE Manual on Workflows


12:00 PM

Lunch Provided (UPDATED)





01:00 PM

DNA Subway

(Workflows for Bioinformatics Education)

  DNA Subway WebsiteJason

01:15 PM

Using the DE for RNA-Seq

  • Launching TopHat (p.32)
  • Examining outputs (follow)
  • Visualizing alignments (follow)

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

Coffee Break





03:15 PM

Tool Integration in the DE

  • Building Phyml App (follow)


03:45 PMSequence Read Archive Demo
  • Sequence submission to SRA

04:15 PM

Workshop summary and conclusion




Draft Workshop Program (DAY 2)







09:30 AM

Overview and demo of CyVerse GWAS /

Transcriptome assembly (TA)

slides (TA)

slides (GWAS)


10:30 AM

Coffee Break




10:45 AM

Getting started with Annotation: MAKER (MP)
Getting started with Assembly: ALLPATHS

slides (MP)


11:15 AM

Visualization of RNA-Seq results in Atmosphere

slides (V2)

12:00 PM

Lunch Provided (UPDATED)




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 in Etherpad


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 city of Wooster, OH website:

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