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Organizers:

C.J. Geisler-Lee

Local Point of Contact:

Cheng-Li Jane Heisler-Lee

Trainers:

Joslynn Lee, Kapeel Chougule, Pan Teng

Date:

March 31 - April 1, 2016

Location:

Life Sciences Building II
Room 404
Southern Illinois University Carbondale
Carbondale, IL 62901
Parking Information/Permits

Visitor Parking

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

Joslynn

09:30 AM

Overview of CyVerse

 

slides

Getting Started with CyVerse

Joslynn

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

ftp://ftp.ensembl.org/pub/release-67/fasta/bos_taurus/dna/

10:30 AM

Coffee Break: Room LSII 460

 

 

 

 
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)
slidesKapeel

11:15 AM

Analyses in the DE; Phylogenetics Example

  • Self-guided (p.18-19)
 

DE Manual on Workflows

Kapeel

12:00 PM

Lunch: LSII 453

 

 

 

 

01:00 PM

DNA Subway

(Workflows for Bioinformatics Education)

 slidesDNA Subway WebsiteJoslynn

01:15 PM

Using the DE for RNA-Seq

  • Launching TopHat (p.31)
  • Examining outputs (follow)
  • Visualizing alignments (follow)
slidesKapeel

02:15 PM

Atmosphere Cloud Computing

  • Launching an instance (follow)
  • Connecting via VNC (p.24)
  • Desktop sharing via VNC (follow)
  • Connect via SSH (p.25)

slides

Atmosphere Manual

Joslynn

03:00 PM

Coffee Break: Room LSII 460

 

 

 

 

03:15 PM

Tool Integration in the DE

  • Building Phyml App (follow)
 

 

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

04:15 PM

Workshop summary and conclusion

 

 

Post Survey

 

Draft Workshop Program (DAY 2)

slides

slides

Time

Description

Slides

Links

Presenter

09:30 AM

Transcriptome assembly (TA) with Trinity and

quantification with Kallisto tools

slides (TA)

slides (kallisto)

Kapeel

10:30 AM

Coffee Break: Room LSII 460

 

 

 

10:45 AM

Getting started with Annotation: MAKER (MP)

slides (MP)

 

Kapeel

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

Joslynn

01:30 PM

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

Pan

02:30 PM

Individual consultations

 

Please posts your requests for 10-15 min

Post Survey

 

Links to paper/tools/resources

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim et al.
Nature Protocols Mar 1, 2012

Sleuth http://pachterlab.github.io/sleuth/about.html

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: http://parking.siu.edu/on-campus/index.html

Visitor Information: http://admissions.siu.edu/visit/visitor-information.php 

Travel/Lodging

See the city of Carbondale, IL website: http://www.carbondaletourism.org/categories/stay

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