2012 05 21 TSW Purdue University

Organizers:	Uwe Hilgert, Special Assts, Jason Williams
Local Point of Contact:	Peter Baker, Jyothi Thimmapuram Connie Moore, Administrative Assistant, Cyber Center, YONG 928, ph. 765-494-7918; Fax: 765-496-2275; ckmoore@purdue.edu Catering: Casey Dexter, ph. 765-494-8908
Trainers:	Jason Williams, Sheldon McKay, Naim Matasci and Andy Lenards
Date:	May 21-22, 2012
Location:	Purdue University, NLSN 1195 Nelson (Phillip E.) Hall of Food Science (NLSN) Seats 37
Online Registration:	http://www.iplantcollaborative.org/purdue2012
Important Dates:	Registration Opens: April 6th Registration Closes: May 4th

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. The use of Atmosphere will require a VNC viewer which can be downloaded here.

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 are 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 use and customize iPlant tools and services for your investigations.

Agenda

Please check here for the latest updates to this workshop agenda

Monday May 21st

Time	Presentation	Slides	Links
08:30 AM - 09:00 AM	Arrive/Sign-in/ Verify iPlant accounts
09:00 AM - 09:30 AM	Welcome - Presenter/Participant Introductions
09:30 AM - 09:50 AM	An Overview of the iPlant Collaborative	iPlant intro.pptx
09:50 AM - 10:15 AM	Overview of the iPlant Discovery Environment (DE)	DE Overview.pptx	www.iplantcollaborative.org/de1
10:15 AM - 10:30 AM	Coffee Break
10:30 AM - 11:15 AM	iPlant Data Store - Managing "Big Data"	Data Store Overview.pptx
11:15 AM - 12:00 PM	Atmosphere - Custom Cloud Computing	Atmosphere Overview.pptx	Atmosphere lab www.iplantcollaborative.org/atm1
12:00 PM - 01:00 PM	Lunch (Delivered)
01:00 PM - 01:30 PM	Building and Using Workflows Within the DE; Phylogenetics	intro_phylo_workflow.pptx	www.iplantcollaborative.org/pw1
01:30 PM - 02:45 PM	Using the DE to Examine Differential Expression Within an RNA-seq Dataset	Indroductory_RNA-seq.ppt	Helpful Article www.iplantcollaborative.org/rs1
02:45 PM - 03:00 PM	Coffee Break
03:00 PM - 04:30 PM	Extending the DE for Your Research: Tool Integration and Customization	Tool_Integration-1.pptx	Integrating a New Tool Interface into the Discovery Environment
04:30 PM - 05:00 PM	Collaborating with iPlant: Future Projects and Workshop Summary	Workshop Conclusion.pptx

Tuesday May 22nd

Time	Presentation	Sides	Links
08:45 AM - 09:00 AM	Sign-in/Welcome
09:00 AM - 10:30 AM	Advanced CHiP-seq in the iPlant Cyberinfrastructure	AdvancedChIPSeq.ppt	/wiki/spaces/eot/pages/241585258
10:30 AM - 10:45 AM	Coffee Break
10:45 AM - 11:30 AM	Advanced CHiP-seq in the iPlant Cyberinfrastructure (cont'd)
11:30 AM - 12:00 PM	Comparative Phylogenetic Methods in the iPlant Cyberinfrastructure
12:00 PM - 01:00 PM	Lunch (On your own)
	Data Clinic Appointments
01:00 PM - 02:00 PM	Powered by iPlant - Consuming iPlant Services in Your Portals	poweredby.pptx	https://pods.iplantcollaborative.org/wiki/x/EAm
02:00 PM - 03:00 PM	Using XSEDE for Bioinformatics
03:00 PM - 04:30 PM	Additional RNA-seq analysis applications/ hands-on		/wiki/spaces/eot/pages/241585166

Attendee List (those waitlisted in blue) (Actual Attendee List)

Name	Research Area	Email	Dept	Position	Lab PI	User Acct
Gladys Andino	Genetics and Nucleic Acids	gandino@purdue.edu	Entomology	Graduate Student	Greg Hunt	X,
Tatiana Arias-Garzon	Plant Biology	tatiana.tatianaarias@gmail.com	Biological Sciences	Graduate Student	Chris Pires	X, no atmo
Nadia Atallah	Molecular Biosciences	natallah@purdue.edu	Botany Y	Graduate Student	Jody Banks
Peter Baker	Software Engineering	pnbaker@purdue.edu	Cyber Center, Discovery Park	University/College Staff	Cyber Center	X , no atmo
Ketaki Bhide	Other	bhide@purdue.edu	Bioinformatics Core,Cyber Center	University/College Staff	Dr.Jyothi Thimmapuram	X, no atmo
David Bos	Genetics and Nucleic Acids	dbos@purdue.edu	Biological Sciences	University/College Faculty	David Bos	X, no atmo
Naila Cannes	Molecular Biosciences	ncannes@purdue.edu	Comparative pathobiology	Postdoctorate	Joanne Messick	X , no atmo
Basudev Chowdhury	Molecular Biosciences	bchowdhu@purdue.edu	Biology	Graduate Student	Joseph Irudayaraj
Hyonho Chun	Statistics and Probability	chunh@purdue.edu	Statistics	University/College Faculty		X, no atmo
Emily Dierking	Plant Biology	dierking@indianacrop.org	Agronomy	Other	Emily Dierking	X, no atmo
Navin Elango	Biological and Critical Systems	nelango@dow.com	Information Technology and Data Analysis	Industrial User	Jacob Koehler	X, no atmo
Alan Galbreth	Plant Biology	dierking@indianacrop.org	Genetics Program	Other	Emily Dierking
Ana Guimaraes	Other	anamsg@purdue.edu	Comparative Pathobiology	Graduate Student	Joanne Messick	X , no atmo
Greg Hunt	Behavioral and Neural Sciences	ghunt@purdue.edu	Entomology	University/College Faculty	Greg Hunt
Steve Kimble	Genetics and Nucleic Acids	skimble@purdue.edu	FNR	Graduate Student	Williams	X, no atmo
Shaneka Lawson	Plant Biology	shaneka.lawson@gmail.com	Forestry	Government User	Shaneka Lawson	X, no atmo
Yupeng Li	Plant Biology	yupengli@uga.edu	Plant Breeding, Genetics, & Genomics	Grad Student	Scott Jackson	X
Minming Li	Bioinformatics	li362@purdue.edu	Biological Sciences	Graduate Student	Gribskov	X, no atmo
Yanyan Liu	Genetics and Nucleic Acids	liu342@purdue.edu	Agronomy	Postdoc	Ohm	X, no atmo
Joanne Messick	Other	jmessic@purdue.edu	Comparative Pathobiology	University/College Faculty	Joanne Messick	X, no atmo
Mike Mickelbart	Plant Biology	mickelbart@purdue.edu	Horticulture	University/College Faculty	Micklebart	X, no atmo
Lucio Navarro	Other	navarroe@purdue.edu	Entomology	Grad student	Stuart
Krista Nichols	Genetics and Nucleic Acids	kristamnichols@gmail.com	Biological Sciences	Other	Krista Nichols	X
John Patton	Patton Environmental Biology	jcpatton@purdue.edu	Forestry and Natural Resources	University/College Faculty	John Patton/John Bickham	X, no atmo
Bryan Penning	Other	bpenning@purdue.edu	Biology	University/College Staff	Maureen McCann	X, no atmo
Marc Ridilla	Biochem and Mol Structure and Function	ridilla@purdue.edu	Biological Sciences	Grad student	Yernool	X, no atmo
Andrea Santos	Molecular Biosciences	santos1@purdue.edu	Comparative pathobiology	Postdoctorate	Joanne Messick	X, no atmo
Arun Seetharam	Molecular Biosciences	ASEETHARAM@SYCAMORES.INDSTATE.EDI	Biology	Graduate Student	Dr. Gary Stuart	X
Arvind Kumar Thirumalaiswamy Sekhar	Other	asekhar@dow.com	Genomics	Industrial User	None	X, no atmo
Jacob Shreve	Other	jtshreve@purdue.edu	ENTM / Bioinformatics Core	Graduate Student	Rich Shukle, Christie Williams	X, no atmo
Whitney Soltau	Biochem, Molec Stucture and Function	wsoltau@purdue.edu	Biochemistry	Grad student	Chapple	X
John Springer	Adv Scientific Computing	jaspring@purdue.edu	Computer and IT	University/College Faculty	Virt Tissue Bank project	X , no atmo
Rebecca Stevenson	Plant Biology	stevenra@purdue.edu	Horticulture and Landscape Architecture	University/College Staff	Jian-Kang	X, no atmo
Kai Tang	Genetics and Nucleic Acids	tang58@purdue.edu	HORT	Graduate Student	Jian-Kang Zhu	X, no atmo
Jyothi Thimmapuram	Other	jyothit@purdue.edu	Bioinformatics Core	University/College Staff	Jyothi Thimmapuram	X, no atmo
Jennifer Tsuruda - May 21 ONLY	Molecular Biosciences	jtsuruda@purdue.edu	Entomology	Postdoctorate	Greg Hunt	X
Gregory Weber	Environmental Biology	gjweber@purdue.edu	School of Health Sciences	Graduate Student	Jennifer Freeman	X
Rick Westerman	Genetics and Nucleic Acids	westerman@purdue.edu	Horticulture/Genomics	University/College Staff	Phillip San Miguel	X
Xiangye Xiao	Plant Breeding	xiaoxiangye111@hotmail.com	Agronomy	Grad Student	Ohm	X, no atmo
Doug Yatcilla	IT and Orgs	yatcilla@purdue.edu	Horticulture	University/College Staff	N/A	X, no atmo
Meixia Zhao	Genetics and Nucleic Acids	zhao185@purdue.edu	Agronomy	Graduate Student	Jianxin Ma

Post-Workshop Survey

iPlant is by, for and of the community. It is extremely important for us to hear from you about what works and what doesn't in our training workshops. We'd also like to know about computational bottlenecks you've encountered in your research for which iPlant could develop community-scale solutions. We want to know how you found out about the workshop, and what you would like to see iPlant do, so please respond to the survey you will receive by email after the workshop has been completed.