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Organizers:

R.R. Álvarez, J. Williams

Local Point of Contact:

Rubén Rellán Álvarez

Trainers:

John Fonner (TACC), Jason Williams (CSHL)

Date:

May 30-31

Location:

Langebio - Cinvestav: Auditorium
Parking Information/Permits

A parking permit is NOT needed

Associated WorkshopData Carpentry: http://jasonjwilliamsny.github.io/2016-06-01-langebio/

 

Required Workshop Prep


See detailed instructions in sections 1-5 of the workshop packet (pg. 5-10)

Download: Genomics Workflows in CyVerse

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

Etherpad

Connect to the etherpad at : TBA

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

 

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

Jason

09:30 AM

Overview of the CyVerse

 

slides

Getting Started with CyVerse

Jason

09:45 AM

Managing "Big Data" using the CyVerse Data Store

  • Use Cyberduck (p.16)
  • Quick iCommands demo (follow)
  • Importing files via URL (p.35)
  • Creating Public links (p.17)
  • Sharing Folders (p.18)
slidesData Store OverviewJohn

10:30 AM

Coffee Break

 

 

 

 
10:45 AM

Navigate the CyVerse Discovery Environment (DE)

 

  • MUSCLE analysis (p.22-23)
  • Simple upload/download (follow)
  • Moving, renaming, creating (follow)
  • Adding metadata (p.36)
  • Searching (follow)
slidesJason

11:15 AM

Analyses in the DE; Phylogenetics Example

  • Self-guided (p.23-24)
 

DE Manual on Workflows

John

12:00 PM

Lunch

Food available for purchase on-site

 

 

 

01:00 PM

DNA Subway

(Workflows for Bioinformatics Education)

  DNA Subway WebsiteJason

01:15 PM

Using the DE for RNA-Seq

  • Launching TopHat (p.37)
  • Examining outputs (follow)
  • Visualizing alignments (follow)
slidesJason

02:15 PM

Atmosphere Cloud Computing

  • Launching an instance (p.29)
  • Connecting via VNC (p.30)
  • Desktop sharing via VNC (follow)
  • Connect via SSH (follow)

slides

Atmosphere Manual

John

03:00 PM

Coffee Break

 

 

 

 

03:15 PMSequence Read Archive Demo
  • Sequence submission to SRA
slidesJason

04:00 PM

Workshop summary and conclusion

 

 

 

Draft Workshop Program (DAY 2)

slides

Time

Description

Slides

Links

Presenter

09:30 AM

Demo: CyVerse Transcriptome assembly;

microbiome tools

slides


Jason

10:00 AM

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

slides (MP)

Jason

10:30 AMCoffee Break   
11:15 AMVisualization of RNA-Seq results in AtmosphereslidesJason

12:30 PM

Lunch

 

 

 

01:30 PM

Brining your tools to CyVerse with Docker

slides

Docker @ Cyverse Tutorial

John

02:15 PMAdding new Apps/Systems using the Agave API  

02:30 PM

Individual consultations

 

 

 

Important Pre-Workshop Travel Info 

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

 

Travel/Lodging

 

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