2015 01 29 Tools and Services Workshop - Clemson University

2015 01 29 Tools and Services Workshop - Clemson University

Organizers

Stephen Kresovich, Victoria Artigliere, Jason Williams

iPlant Trainers

Christos Noutsos, Jason Williams

Clemson University
Local TAs

Date

Jan 29-30, 2015

Location

Academic Success Center Room 118,
Celmson University

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: Jan 2015 Guide

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 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

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

http://etherpad.iplantcollaborative.org/p/uga2015

Livestream

You can watch the Livestream of this event. Please register first at: http://www.iplantcollaborative.org/content/livestream-registration-clemson-workshop-jan-29th-30th-2015

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:

  • Use the instructions in the homework packet to request access to Atmosphere. Launch the following Image at least one day before the workshop: TSW Workshop Williams 1.0
  • Please use the etherpad chat rather than the Livestream chat; if any question is not followed up on, please post to ask.iplantcollaborative.org

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: Jan_2015_ClemsonPacket.pdf

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

All

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

Jason

10:45 AM

Coffee Break

 

 

 

11:00 AM

iPlant Data Store - Managing "Big Data"

Slides

Data Store Overview

Christos

11:30 AM

Workflows in the DE; Phylogenetics Example

 

DE Manual on Workflows

Christos

12:10 PM

Lunch

 

 

 

01:00 PM

Using the DE for RNA-Seq

Slides

Jason

02:00 PM

Atmosphere Cloud Computing

Slides

Atmosphere Manual

Christos

03:00 PM

Coffee Break

 

 

 

03:15 PM

Tools Integration in the DE

 

 

Jason

03:45 PM

Educational Bioinformatics - DNA Subway

 

 

Jason

04:15 PM

Workshop summary and conclusion

 

Post Survey

Jason

Draft Workshop Program (Day 2)

Time

Description

Slides

Links

Presenter

09:30 AM

Overview and demo of iPlant GWAS / Transcriptome assembly

GWAS Slides
Transcriptome Slides

  • Tutorials (including GWAS)

Jason

10:30 AM

Coffee Break

 

 

 

10:45 AM

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

Slides

Christos

11:15 AM

Visualization of RNA-Seq results in Atmosphere

Slides

Jason

12:00 PM

Lunch (On your own)

 

 

 

01:00 PM

Integrated Browser Demo

Handout

Bioviz Website

Nowlan

01:45 PM

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

 

https://pods.iplantcollaborative.org/wiki/display/start/Using+icommandsicommands tutorial

Christos

02:30 PM

Individual Consultations

 

Get Started Cheat Sheet

 

03:30 PM

“The opportunities and challenges of using
cyberinfrastructure to elucidate the relationship
between hybrid vigor and the molecular
mechanisms underlying aging”.

 

Location: Biosystems Research Complex G100

Steve Goff

Travel and Campus Map and Parking

Information on the Clemson Campus can be found here: http://www.clemson.edu/visit/

Metered parking closest to the Life Sciences Building would be Strom Thurmond Institute, Brooks Center and Hendrix Center.  See details, rules, and maps below.

http://www.clemson.edu/campus-life/campus-services/parking/visitors.html