2012 05 17 TSW U of Arkansas

Organizers	Jason Williams (mailto: williams@cshl.edu), 411
Local Point of Contact	Emily Devereux, Roger Hall
Trainers	Jason Williams, Sheldon McKay, John Fonner, and Joshua Stein
Date	May 17-18, 2012
Location	University of Arkansas at Little Rock EIT 318 (Seats 40) 2801 S University Little Rock, AR 72205
Catering:	Contact Kindra @ Sodexo 501.569.3360; catering delivered/consumed in EIT 303

Page Contents

Pre-Workshop Homework

Please note. All participants are required to bring a laptop to this workshop. A limited number of laptops may be available. Please email williams@cshl.edu ASAP if you need us to provide you with a laptop.

1.Please ensure you have up-to-date antivirus software installed on your laptop. You can obtain free antivirus software at: http://free.avg.com/us-en/free-antivirus-download

2. Please make sure you have the latest version of your web browser. Firefox is preferred. You may find browsers at the links below:

Firefox (preferred): http://www.mozilla.org/en-US/firefox/new/
Google Chrome:https://www.google.com/chrome
Safari:http://www.apple.com/safari/

3. 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

4. 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

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

6. 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 is Your Data"

Wireless and account info and FTP URLs for Demo

Please use the assigned wireless credentials here (https://pods.iplantcollaborative.org/wiki/display/Events/Wireless+access+and+demo+links)

If your name is not listed here and you need a wireless account please see an instructor.

Workshop handouts

The stept-by-step handouts are available here: Arkansas Workshop Handout

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

Thursday May 17th

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	Jason's iPlant intro.pptx
09:50 AM - 10:15 AM	Overview of the iPlant Discovery Environment (DE)	Jason's 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"	Jason's Data Store Overview.pptx	Links for Tutorial
11:15 AM - 12:00 PM	Atmosphere - Custom Cloud Computing	Atmosphere_Workshop_Arkansas.pptx	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	Jason's_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	Slides, 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.pptx	DE tool integration documentation
04:30 PM - 05:00 PM	Collaborating with iPlant: Future Projects and Workshop Summary	Jason's Workshop Conclusion.pptx

Friday May 18th

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	Slides	/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	iPlant API 5-18-12.pdf	Hand-on Tutorial
02:00 PM - 03:00 PM	Using XSEDE for Bioinformatics	XSEDE_iPlant_5-18-12.pdf
03:00 PM - 04:30 PM	Additional RNA-seq analysis applications/ hands-on		RNA-seq reading room

Attendee List (No Show in blue)

First Name	Last Name	Research Area	Email	Institution	Department	Position	User Acct?
Siddique	Aboobucker	Molecular Biosciences	siddique.aboobucker@smail.astate.edu	Arkansas State University	Arkansas Biosciences Institute	Grad Student	X
Solomon	Adekunle	Genetics and Nucleic Acids	sadekunl@suno.edu	southern university at new orleans	natural sciences	University/College Faculty	X, no atmo
Tony	Arick	Computer and Computation Research	maa146@igbb.msstate.edu	Mississippi State University	IGBB	University/College Staff	X
Carlos	Avila	Plant Biology	cavila@uark.edu	University of Arkansas	Entomology	University/College Faculty	X
Linda	Ballard	Genetics and Nucleic Acids	linda.ballard@ars.usda.gov	USDA-ARS	Genomics and Bioinformatics Research Unit	Government User	X
Caroline	Borges Bevilacqua	OtherSeed science and technology	carolinebevi@gmail.com	University of Arkansas	Crop Soil and Environment Sciences	Graduate Student	X
Teresia	Buza	Molecular Biosciences Bioinformatics	ndelly@gmail.com	Mississippi State University	CVM Basic sciences	Postdoctorate	X
Venu R.	Channarayappa	Plant Biology	venurekha12@gmail.com	USDA- Dale Bumpers National Rice Research Center	Molecular Plant Pathology	Postdoctorate	X
Jose	Condori	BioStrategies LC	jcondori@biostrategies-lc.com	Lectin	Therapeutic protein	Research Scientist	X, no atmo
Richard	Connor	Molecular Biosciences	raconnor1@ualr.edu	University of Arkansas at Little Rock	Applied Science	Graduate Student	X, no atmo
Carole	Cramer	Biochemistry and Molecular Structure and Function	ccramer@astate.edu	Arkansas State University	Arkansas Biosciences Institute	University/College Faculty	X
Randy	Dinkins	Plant Biology	Randy.dinkins@ars.usda.gov	USDA ARS		Government User	X
Robert	Fjellstrom	Genetics and Nucleic Acids	bob.fjellstrom@ars.usda.gov	USDA Agricultural Research Service	Dale Bumpers National Rice Research Center	Government User	X
Fiona	Goggin	Plant Biology	fgoggin@uark.edu	University of Arkansas	Entomology	University/College Faculty	X
Cathy	Gresham	Software Development	gresham@hpc.msstate.edu	Mississippi State University	Institute for Genomics, Biocomputing and Biotechnology	University/College Staff	X
Thomas	Hahn	Other tbt	tfhahn@ualr.edu	UALR	Bioinf	Graduate Student
Elizabeth	Hood	Plant Biology	ehood@astate.edu	Arkansas State University	Agriculture	University/College Faculty	X, no atmo
Aaron	Jackson	Genetics and Nucleic Acids	aaron.jackson@ars.usda.gov	USDA ARS	DBNRRC	Government User	X
Mihir	Jaiswal	Bioinformatics	msjaiswal@ualr.edu	UALR	Bioinformatics	Graduate Student	X, no atmo
Melissa	Jia	Genetics and Nucleic Acids	melissa.jia@ars.usda.gov	USDA ARS		Government User	X
Yulin	Jia	Plant Biology	yulin.jia@ars.usda.gov	USDA- Dale Bumpers National Rice Research Center	Molecular Plant Pathology	University/College Faculty	X
Katherine	Lisko	Molecular Biosciences	katherine.lisko@smail.astate.edu	Arkansas State University	Arkansas Biosciences Institute	Graduate Student	X
Yan	Liu	Crop genetics and breeding	lyan.2009@gmail.com	USDA-ARS Dale Bumpers National Rice Research Center	plant pathology	Postdoctorate	X, no atmo
Argelia	Lorence	Plant Biology	alorence@astate.edu	Arkansas State University	Arkansas Biosciences Institute	University/College Faculty	X
Travis	Marsico	Plant Biology plant-insect interactions; species invasions	tmarsico@astate.edu	Arkansas State University	Biological Sciences	University/College Faculty	X
Fiona	McCarthy	Bioinformatics & Genomics	fmccarthy@cvm.msstate.edu	Mississippi State University	Dept Basic Sciences	University/College Faculty	X
Giuliana	Medrano	Molecular Biosciences	gmedrano@astate.edu	ASU	ABI	University/College Faculty	X, no atmo - CANCELLED
Ravi	Mural	Molecular Biosciences	rxmural@ualr.edu	University Of Arkansas at Little Rock	Biology	Graduate Student
Bindu	Nanduri	Systems biology	bnanduri@cvm.msstate.edu	Mississippi State University	CVM/DBS	University/College Faculty	X
Cesar	Nopo-Olazabal	Molecular Biosciences	Cesar.NopoOlazabal@smail.astate.edu	Arkansas State University	Arkansas Biosciences Institute	Graduate Student	X, no atmo
Sathish Kumar	Ponniah	Plant Biology	ponniahs@uapb.edu	University of Arkansas at Pine Bluff	Agriculture	University/College Staff	X
Joseph	Reddy	Bioinformatics	jsr256@msstate.edu	Mississippi State University	Dept. of Basic Sciences, CVM	Graduate Student	X
Nathan	Reyna	Plant Biology	reynan@obu.edu	Ouachtia Baptist University	Biology	University/College Faculty	X
Rinku	Saha	Computational Mathematics	rxsaha@ualr.edu	UALR	Bioinformatics	Graduate Student	X, no atmo
Reiofeli	Salas	Plant Biology	rasalas@uark.edu	University of Arkansas	Department of Crop, Soil and Environmental Sciences	Graduate Student	X
Vibha	Srivastava	Plant Biology	vibhas@uark.edu	University of Arkansas	Crop, Soil & Environmental Scienecs	University/College Faculty	X, no atmo
Thomas	Teoh	Molecular Biosciences	kteoh@astate.edu	Arkansas State University	College of Agriculture and Technology	University/College Faculty	X
Sreerekha M.	Venkatarau	Plant Biology	sreerekha12@gmail.com	USDA-ARS Dale Bumpers National Rice Research Center	Molecular Genetics	Postdoctorate	X
Deborah	Vicuna Requesens	Plant Biology	deborah.vicuna@gmail.com	Arkansas State University	Arkansas Biosciences Institute	Postdoctorate	X, no atmo
Tianhong	Yang	Plant Biology	tianhong.yang@smail.astate.edu	Arkansas State University	Biological sciences	Graduate Student	X, no atmo
Price	Hardin		matthew.hardin@smail.astate.edu
Xiuzhen	Huang		zhuang@astate.edu
Charan	Sharefa		sscharan@udr.edu
Wengui	Yan		wengui.yan@ars.usda.gov

Getting to the Workshop

Please plan to park in Lot 13.

Campus Map:http://ualr.edu/www/features/map/

There is a parking map at the above link. I took this section from that map.

1. (Red Line) Take Exit 5B (University South) from I-630 and drive south on University (coming in from bottom left towards the right on this image).

2. (Red Line) Turn left at campus entrance on 28th Street.

3. (Red Line) Turn left into Lot 13 West (if you are early, or Lot 13 East if late).

4. (Orange Line) Cross street at light/crosswalk and continue on sidewalk through trees.

5. (Orange Line) EIT is six stories with blue windows and silver accen

Survey

iPlant is by and for the community. It is extremely important for us to hear from our colleagues about what works for them and what doesn't.
We'd also like to what computational bottlenecks in your investigations are possible challenges you think iPlant should target for developing
community-scale solutions.We want to know how you found the workshop, and what you would like to see iPlant do, so please answer the
survey you will receive by email post workshop.