2015 05 07 Tools and Services Workshop - University of Georgia, Athens

2015 05 07 Tools and Services Workshop - University of Georgia, Athens

Organizers

C.J. Tsai, W. Lorenz, A. Zaid, J. Williams

iPlant Trainers

Jeremy DeBarry, Jason Williams

UGA
Local TAs

Johnathan Gent
Hongye Zhou
Sara Byers

Date

May 7-8, 2015

Location

Forestry Complex Building 1, Rm. 304

Workshop Checklist

1. iPlant Account

2. Atmosphere Access

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

Download and complete the exercises in this guide to get the most out of the workshop: PRE-WORKSHOP PACKET

Office Hour

We will be online live for any special assistance you need prior to the workshop (e.g. if you ran into trouble setting up your computer or uploading data). The live help for this workshop will be:

Friday May 1st from 12:00-12:30PM - session is finished if no one requests joins/requests help by 12:15 EDT)

URL: http://cshl.adobeconnect.com/iplant_livehelp

Etherpad/Chatroom

We will use the following etherpad for workshop live chat/help:

https://etherpad.mozilla.org/cTKp2HLnc6

Livestream

You can watch the Livestream of this event.

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. Launch the following Image (at default tiny1 size)tat least one day before the workshop: TSW Workshop Williams 1.0
  2. Please use the etherpad chat (https://etherpad.mozilla.org/cTKp2HLnc6) to ask questions. Livestream chat will not be monitored. if any question is not followed up on, please post to ask.iplantcollaborative.org
  3. Download the Workshop Packet to follow along
  4. Please complete the post-survey

Livestream URLS:

Day 1: https://new.livestream.com/cshl-dnalc/uga-day-I

Day 2: https://new.livestream.com/cshl-dnalc/uga-day-II

Instructional Materials

You can download a copy of the workshop packet to follow along:

WORKSHOP PACKET

Draft Workshop Program (DAY 1)

Time

Description

Slides

Links

Presenter

09:00 AM

Arrive / Sign-in / Verify iPlant Accounts 

 

Pre-Survey

 

09:30 AM

Welcome - Presenter/Participant Self-Introductions

slides

PLOS Bioinformatics Competency Paper

 

09:45 AM

Overview of the iPlant Collaborative

slides

Getting Started with iPlant

Jason

10:00 AM

Overview of the iPlant Discovery Environment (DE)

slides

DE Manual

Jeremy

10:45 AM

Coffee Break

 

 

 

11:00 AM

iPlant Data Store - Managing "Big Data"

slides

Data Store Overview

Jeremy

11:30 AM

Workflows in the DE; Phylogenetics Example

slides

DE Manual on Workflows

Jeremy

12:10 PM

Lunch

 

 

 

01:00 PM

Using the DE for RNA-Seq

slides

Jason

02:00 PM

Atmosphere Cloud Computing

slides

Atmosphere Manual

Jason

03:00 PM

Coffee Break

 

 

 

03:15 PM

Tools Integration in the DE

slides

 

Jeremy

03:45 PM

Educational Bioinformatics - DNA Subway

 

DNA Subway Website

Jason

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 iPlant GWAS / Transcriptome assembly

slides (TA)

slides (GW)

Jason

10:30 AM

Coffee Break

 

 

 

10:45 AM

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

slides (MP)

Jason

11:15 AM

Visualization of RNA-Seq results in Atmosphere

slides

Jason

12:00 PM

Lunch (On your own)

 

 

 

01:00 PM

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

slides

 

Jeremy

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)

 

Travel and Campus Map and Parking

Information on the UGA Campus can be found here: http://www.architects.uga.edu/maps/current