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Organizers:

D. Rhodes, J. Williams

Local Point of Contact:

Douglas Rhoads

Trainers:

John Fonner, Jason WIlliams

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

Morning

Description

Slides

Guide

Links

Arrive / Sign-in / Setup Troubleshooting

 

 

Pre-Survey

Welcome - Presenter/Participant Self-Introductions

slides 

PLOS Bioinformatics Competency Paper

Overview of the CyVerse

 slides

 

Getting Started with CyVerse

Managing "Big Data" using the CyVerse Data Store

slides guideData Store Overview
Navigate the CyVerse Discovery Environment (DE)slidesguide

Atmosphere Cloud Computing

slidesguide

Atmosphere Manual

Afternoon Guided Tutorials

Description

Slides

Links

RNA-Seq in CyVerseslides

Overview and demo of CyVerse GWAS / Transcriptome assembly

slides (TA)

slides (GW)

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

slides (MP)

Visualization of RNA-Seq results in Atmosphere

slides

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

slides

 

Survey 
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