2012 09 24 TSW U Missouri

Organizers	Uwe Hilgert, 411
Local Point of Contact	Chris Pires, Vicki Bryan
Trainers	Sheldon McKay, Jason Williams, Zhenyuan Lu, Christos Noutsos
Date	September 24-25, 2012 Sept 24 - IPG Seminar Series Presentation, 3:30 PM, Monsanto Auditorium at Life Sciences Ctr
Location	Life Science Center, Rm 171 (available starting 8 AM on 9/24) - max seating 24
Catering Contact	Catalyst snack bar is located in LSC; Ali or Benjamin at Peachtree Catering
Designated Lodging for Trainers	Hampton Inn
Flyer/Listings	flyer, Science Events at Mizzou

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.

4. If you are attending any sessions on day 2 please bring your own laptop!

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 September 24

Time	Presentation	Slides	Links	Trainer
08:00 AM - 08:30 AM	Arrive/Sign-in
08:30 AM - 09:00 AM	Welcome - Presenter/Participant Introductions
09:00 AM - 09:20 AM	An Overview of the iPlant Collaborative	Introduction	iPlant Overview Video	Sheldon McKay
09:20 AM - 09:45 AM	Overview of the iPlant Discovery Environment (DE)	DE Overview.pptx	DE Manual	Jason Williams
09:45 AM - 10:15 AM	iPlant Data Store - Managing "Big Data"	Data Store Overview.pptx	Demo Links Data Store Guide	Jason Williams
10:15 AM - 10:30 AM	Coffee Break (delivered)		Tutorial
10:30 AM - 11:00 AM	Building and Using Workflows Within the DE; Phylogenetics	Introduction	Tutorial	Sheldon McKay
11:00 AM - 12:00 PM	Extending the DE for Your Research: Tool Integration and Customization		TI Quick Start	Jason Williams
12:00 PM - 12:30 PM	Lunch (delivered)
12:30 PM - 01:30 PM	Atmosphere - Custom Cloud Computing	Atmosphere Overview.pptx	Atmosphere Manual	Jason Williams
01:30 PM - 02:30 PM	Using the DE to Examine Differential Expression Within an RNA-seq Dataset	Introduction	/wiki/spaces/eot/pages/241585220	Sheldon McKay
02:30 PM - 03:30 PM	Collaborating with iPlant: Future Projects and Workshop Summary	Workshop Conclusion.pptx		Jason Williams

POST-WORKSHOP Survey Link:

http://www.surveymonkey.com/s/ToolsServices_post

Tuesday September 25

Time	Presentation	Sides	Links	Trainer
09:00 AM - 09:30 AM	Set up resources for advanced RNA-Seq and API tutorials		Tutorial	Sheldon McKay
09:30 AM - 11:00 AM	Powered by iPlant - Consuming iPlant Services in Your Portals	The iPlant Foundation API	Tutorial	Sheldon McKay
11:00 AM - 12:00 PM	Advanced RNA-Seq: Visual Analytics in Atmosphere			Sheldon McKay
12:00 PM - 01:00 PM	Lunch (delivered)
01:00 PM - 01:30 PM	Advanced RNA-Seq (Cont'd)		Tutorial	Sheldon McKay
1:30 PM - 1:40 PM	iplant collaboration with Soybean Genomics Center	slides		Christos Noutsos
01:40 PM - 02:30 PM	Using XCEDE for bioinformaics	XCEDE Infomercial		Sheldon McKay
02:30 PM - end	Open discussion			All

Attendee List

Name	Email	Research Area	Institution	User Acct
Jacob Washburn	washjakepf@yahoo.com	Plant Biology	UMo	needs Atmo
Tatiana Arias	tatiana.tatianaarias@gmail.com	Plant Biology	UMo	needs Atmo
Jinrong Wan CANCELLED	wanj@missouri.edu	Plant Biology	UMo	needs all
Christopher Bottoms	bottomsc@missouri.edu	Bioinformatics	UMo	X
Bill Spollen	spollenw@missouri.edu	Bioinformatics	UMo	needs Atmo
Christopher Childers	genetics.guy@gmail.com	Bioinformatics	UMo	X
Clayton Coffman CANCELLED	cmcz7b@mizzou.edu	Chemical Ecology	UMo	needs Atmo
Jingfen Zhang	zhangjingf@missouri.edu	Bioinformatics	UMo	needs acct
Trupti Joshi	joshitr@missouri.edu	Bioinformatics	UMo	needs Atmo
Saad Khan	smk5g5@mail.missouri.edu	Bioinformatics	UMo	needs all
Brent Buckner	bbuckner@truman.edu	Genetics and Nucleic Acids	Truman State University	X
Yongqin Wang	wangyq@missouri.edu	Plant Biology	UMo	needs Atmo
Chenglin Chai	chenglin.ch@gmail.com	Plant Biology	UMo	needs Atmo
Li Lin	linl@missouri.edu	Biochem and Molecular Structure-Function	UMo	X
Chao Zhang	chaozhang@mizzou.edu	Computer and Computation Research	UMo	needs Atmo
Michael McMullen	mcmullenm@missouri.edu	Genetic and Nucleic Acids	UMo	X
Alejandro Tovar-Mendez	tovarmendeza@missouri.edu	Biochem and Molecular Struc-Function	UMo	needs all
Kate Guill	guillk@missouri.edu	Plant Biology	USDA/UMo	X
Colin Smith-Hammond		Biochemistry	UMo	X
Doug Bryant	dbryant@danforthcenter.org	Adv Scientific Computing	Danforth Ctr	X
Noah Fahlgren	nfahlgren@danforthcenter.org	Molecular Biosciences	Danforth Ctr	X
Samuel McInturf	smcinturf@gmail.com	Plant Biology	UMo	needs Atmo
Theresa Musket	muskett@missouri.edu	Molecular Biosciences	UMo	needs Atmo
Naeem Syed CANCELLED	syedna@missouri.edu	Plant Genetics	UMo	oo
Zhengbin Liu	liuzhen@missouri.edu	Plant Biology	UMo	X
Arun Prabhu Dhanapal	arunprabhu.dhanapal@yahoo.com	Genetics and Nucleic Acids	UMo	X
Songqing Ye	yeso@missouri.edu	Plant Biology	UMo	needs Atmo
Scott Givan	givans@missouri.edu	Bioinformatics	UMo
Waitlist
Hien Nguyen	htnzq8@mail.missouri.edu	Plant Biology	UMo

Getting to the Workshop & Parking

Campus Map showing Bond Life Sciences Center

Parking: Metered parking is available in a surface lot on Virginia Ave., just one block south of the Bond Center. For more information on campus parking, visit the Parking and Transportation Services office.

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.