2012 12 10 TSW University of Hawaii, Manoa

Organizers	Jason Williams, Gernot Presting
Local Point of Contact	Gernot Presting
Trainers	Jason Williams, Sheldon McKay
Date	December 10th - 11th, 2012
Location	Agriculture Building Rm. 215
Catering Contact	TBD
Flyer

Page Contents

Pre-Workshop Homework

1. Please try out your iPlant credentials to ensure you have access. You can Log-in from user.iplantcollaborative.org, click the button "iPlant Login"

Once authenticated click the "My Services" link
Under "My Services" please ensure you have access to: Atmosphere, Discovery Environment, iPlant Data Store. You can also request access to other services here
If you have account problems, please email support@iplantcollaborative.org

2. Please be sure that your name is listed in the Attendee List (below) for the workshop section(s) you were accepted to. If there is a discrepancy, please email 411@iplantcollaborative.org

3. Please check your email, and this wiki prior to the workshop, as this is the way we will communicate any important changes.

Workshop Notes

Here are a few important links that you may wish to refer to during and after the workshop:

Account/Password Problems http://user.iplantcollaborative.org

user.iplantcollaborative.org

iPlant Help and Discussion Forums

forums.iplantcollaborative.org/

General iPlant Support Issues

support@iplantcollaborative.org

iPlant Privacy (And other) policies - "Your Data is Your Data"

Goal

The goal of this workshop is to demonstrate some of the ways that iPlant Cyberinfrastructure can advance your scientific objectives.
As you navigate the through demonstrations and hands-on activities presented at the workshop, you will gain a sense of how to consume
and customize iPlant tools and services for your investigations.

Agenda

Please check here for the latest updates to this workshop agenda

Monday December 10th

Time	Presentation	Slides
08:30 AM	Arrive/Sign-in
09:00 AM - 09:30 AM	Welcome - Presenter/Participant Introductions
09:30 AM - 09:50 AM	An Overview of the iPlant Collaborative	iPlant Introduction	Getting Started w/iPlant Guide, iPlant Overview Video,
09:50 AM - 10:15 AM	Overview of the iPlant Discovery Environment (DE)	Introduction	DE Overview Video,
10:15 AM - 10:30 AM	Break
10:30 AM - 11:15 AM	iPlant Data Store - Managing "Big Data"	Introduction	Data Store Guide, Data Store Overview Video Workshop URLs
11:15 AM - 12:00 PM	Building and Using Workflows Within the DE; Phylogenetics	Introduction	/wiki/spaces/eot/pages/241585221
12:00 PM - 01:00 PM	Lunch
01:00 PM - 02:00 PM	Atmosphere - Custom Cloud Computing	Introduction	Atmosphere Manual, Atmosphere Video
02:00 PM - 02:30 PM	Using the DE to Examine Differential Expression Within an RNA-Seq Dataset	Introduction	/wiki/spaces/eot/pages/241585220, C.Trapnell RNA-seq protocol paper, Nature Prtcls.
02:30 PM - 02:45 PM	Break/ RNA-Seq continued
02:45 PM - 03:15 PM	Extending the DE for Your Research: Tool Integration and Customization		Quick Start -- Using Tool Integration
04:00 PM - 04:30 PM	Collaborating with iPlant: Future Projects and Workshop Summary	Workshop Conclusion.pptx

Tuesday December 11th

Time	Presentation	Links
09:30 AM - 10:00 AM	Powered by iPlant - Consuming iPlant Services in Your Portals
10:00 AM - 10:30 AM	Tool intergration
10:30 AM- 12:00 PM	Advanced RNA-Seq (break included)	/wiki/spaces/eot/pages/241585220
01:00 PM - 01:30 PM	More on transferring data with icommands (BYO data)
01:30 PM - 02:00 PM	Using the iPlant Data Store as a Reliable Repository for Your Lab
02:00 PM - 03:00 PM	Starting data transfers/ open topics

Reading on Chip-Seq

Introductory slides Advanced_ChIP-Seq.ppt
on-line training module /wiki/spaces/eot/pages/241585258

Attendee List (32 max)

Name	Email	Affiliation	User Acct
Zidian Xie	zidianx@hawaii.edu	UH Manoa	needs Atmo
Kevin Schneider	kevinls@hawaii.edu	UH Manoa	X
Robert Paull	paull@hawaii.edu	UH Manoa	needs acct
Donovan Bailey	dbailey@nmsu.edu	New Mexico State University	X
Alison Sherwood	asherwoo@hawaii.edu	UH Manoa	X
Sterling Keeley	sterling@hawaii.edu	UH Manoa	needs Atmo
Jeff Boutain	boutain@hawaii.edu	UH Manoa	needs acct
Matthew Campbell	matthew.a.campbell89@gmail.com	UH Manoa	X
Mitsuko Yorkston	mitsuko@hawaii.rr.com	UH Manoa	needs Atmo
Michael Thomas	mbthomas@hawaii.edu	UH Manoa	needs all
Timothy Gallaher	tjgallaher@gmail.com	UH Manoa	X
Shelley James	sajames@bishopmuseum.org	Bishop Museum	needs Atmo
Guangxiang Zhang	gzhang8@hawaii.edu	UH Manoa	needs Atmo
Glorimar Marrero	glorimar@hawaii.edu	UH Manoa	X
Thomas Wolfgruber	tomwolf@hawaii.edu	UH Manoa	X
Michael Melzer	melzer@hawaii.edu	UH Manoa	needs Atmo
Richard Manshardt	manshard@hawaii.edu	UH Manoa	needs Atmo
Jason Cantley	caecan@gmail.com	UH Manoa	needs Atmo
Anne Alvarez	alvarez@hawaii.edu	UH Manoa	needs Atmo
Changying Zeng	changyingzeng@gmail.com	Inst Trop Biotech and Biosciences	X
Liguang Shi	shiliguan123@gmail.com	Chinese Acad Trop Ag Sciences	needs Atmo
Laying Yang	layingyang@sohu.com	Chinese Acad Trop Ag Sciences	needs Atmo
Pei-Luen Lu	peiluen@hawaii.edu	UH Manoa	X
John Hu	johnhu@hawaii.edu	UH Manoa
Dung Pham	phamdung@hawaii.edu	UH Manoa
Reason Spare	reasonspare@gmail.com	Hawaii Ag Research Center
Judy Zhu	jzhu@harc-hspa.com	Hawaii Ag Research Center
Kazue Ishihara	kazuei@hawaii.edu	UH Manoa

Getting to the Workshop

Campus Map:

Survey

iPlant is by, for, and of the community. It is important for us to hear from you about what works and what doesn't. We'd also like to know about computational bottlenecks in your investigations that iPlant should target for developing community-scale solutions. We want to know how you found out about the workshop, and what you would like to see iPlant do to further assist you in using iPlant CI in your research. Therefore, we ask you to please answer the survey you will receive by email post-workshop.

Schedule of Events