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Organizers:

A. Hlousek-Radojcic, J. Williams

Local Point of Contact:

Alenka Hlousek-Radojcic

Trainers:

Joslynn Lee, Jason WIlliams

Date:

Feb. 3-4, 2015

Location:

University of Delaware

Newark, DE

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

221 Academy St. University of Delaware

Parking Information/Permits

https://udel.t2hosted.com/cmn/index.aspx.

Required Workshop Prep

1. CyVerse Account

  • Get your free account at http://user.iplantcollaborative.org/ . (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 http://user.iplantcollaborative.org/ 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)

Time

Description

Toolkit

Slides

Links

Presenter

08:30 AM

Arrive / Sign-in / Setup Troubleshooting

 

 

Pre-Survey

 

09:00 AM

Welcome - Presenter/Participant Self-Introductions

 slides

PLOS Bioinformatics Competency Paper

 

09:30 AM

Overview of the CyVerse

 

 slides

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)
slides 

11:15 AM

Analyses in the DE; Phylogenetics Example

  • Self-guided (p. 16-18)
 

DE Manual on Workflows

 

12:00 PM

Lunch

 

 

 

 

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)
slides 

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)

slides

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
slides 

04:15 PM

Workshop summary and Conclusion

 

 

Post Survey

 

Draft Workshop Program (DAY 2)

Time

Description

Slides

Links

Presenter

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

slides

 

12:00 PM

Lunch (On your own)

 

 

 

01:00 PM

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

slides

 

 

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: www.udel.edu/transportation/parking/categories_vendor.html/

Travel/Lodging

See the university website: http://www.udel.edu/visitus/

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