2013 01 11 TSW San Diego
Organizers |
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Trainers |
Damian Gessler, Sheldon McKay, Nirav Merchant, Joshua Stein, Matthew Vaughn, Jason Williams |
Date |
Jan 11, 2013 |
Location |
Sheraton Hotel and Marina, San Diego, CA |
Please Remember to Bring
- Wi-Fi enabled laptop and power supply:
- Please have JAVA installed and enabled (help)
- Please have an up-to-date web browser (Recommended Firefox or Safari )
Workshop Notes
Here are a few important links that you may wish to refer to during and after the workshop:
Account/Password Problems
iPlant Help and Discussion Forums
General iPlant Support Issues
iPlant Privacy (And other) policies - "Your Data is Your Data"
- www.iplantcollaborative.org/privacy
- www.iplantcollaborative.org/about/data-set-hosting
- www.iplantcollaborative.org/about/general-usage-policy
Workshop Handout
Workshop Program
Friday, January 11, 2013
Time |
Description |
Slides |
Links |
Presenter |
12:45 PM - 01:00 PM |
Arrive / Sign-in / Verify iPlant Accounts/ Grab Lunch |
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01:00 PM - 01:20 PM |
Welcome - Presenter/Participant Self-Introductions |
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All |
01:20 PM - 01:30 PM |
A (short!) Overview of the iPlant Collaborative |
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01:30 PM - 02:15 PM |
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02:15 PM - 02:45 PM |
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02:45 PM - 03:00 PM |
Coffee Break |
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03:00 PM - 04:00 PM |
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04:00 PM - 05:00 PM |
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05:00 PM - 05:15 PM |
Stretch Break |
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05:15 PM - 05:45 PM |
GBS/GWAS Pipeline Demo |
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05:45 PM - 06:10 PM |
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06:10 PM - 06:30 PM |
Utilizing the iPlant API |
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06:20 PM - 06:50 PM |
iPlant Semantic Web Demo |
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06:50 PM - 07:00 PM |
Workshop summary and conclusion |
Attendee List
Name |
Research Area |
Acct Status |
|
|---|---|---|---|
Eric Haas-Stapleton |
Molecular Biosciences |
Eric.Haas-Stapleton@csulb.edu |
needs Atmo |
Hashini Batugedara |
Molecular Biosciences |
hashinib@msn.com |
needs Atmo |
Aniska Chikhalya |
Molecular Biosciences |
achikhalya@gmail.com |
needs Atmo |
Ingrid Lindquist |
Genetics and Nucleic Acids |
iel@ncgr.org |
needs Atmo |
Frank You |
Bioinformatics |
frank.you@agr.gc.ca |
needs Atmo |
Christopher Bidwell |
Genetics and Nucleic Acids |
cbidwell@purdue.edu |
needs Atmo |
Loretta Johnson |
Ecological Studies |
johnson@ksu.edu |
needs Atmo |
Yvonne Badke |
Genomics |
badkeyvo@msu.edu |
needs Atmo |
Imad Eujayl |
Genetics and Nucleic Acids |
imad.eujayl@yahoo.com |
X |
Christopher Ashwell |
Genetics and Nucleic Acids |
cmashwel@ncsu.edu |
needs Atmo |
Sam Fox |
Plant Biology |
foxsa@onid.orst.edu |
needs Atmo |
Prabin Tamang |
Genetics and Nucleic Acids |
prabin.tamang@ndsu.edu |
needs Atmo |
Anjan Neupane |
Plant Biology |
anjan.neupane@ndsu.edu |
needs Atmo |
Jillian Foerster |
Genetics and Nucleic Acids |
jfoerster@wisc.edu |
X |
Laurel Cooper |
Plant Biology |
cooperl@science.oregonstate.edu |
needs Atmo |
Chris Town |
Plant Biology |
cdtown@jcvi.org |
needs all |
Sean Rogers |
Plant Biology |
srogers@msu.edu |
X |
Srikar Chamala |
Biological and Critical Systems |
srikarchamala@gmail.com |
needs Atmo |
Yogendra Kalenahalli CANCELLED flight delay |
Plant Biology |
yogendra.kalenahalli@mcgill.ca |
needs Atmo |
Mohammed Al Abri |
Genetics and Nucleic Acids |
maa288@cornell.edu |
X |
Timothy Swaller |
Visualization, Graphics, and Image Processing |
tswaller@ceres.net |
needs Atmo |
shivappa hukkeri CANCELLED flight delay |
Biochemistry and Molecular Structure and Function |
shivappa.hukkeri@gmail.com |
needs Atmo |
Jennifer Shelton |
Plant Biology |
sheltonj@ksu.edu |
has Atmo, needs "community" services |
Michael Thomson |
Genetics and Nucleic Acids |
m.thomson@irri.org |
needs Atmo |
Mohen Ekhtiari CANCELLED |
Genetics and Nucleic Acids |
e_ekhtiari@yahoo.com |
no acct |
MeiYee Law |
Genetics and Nucleic Acids |
mylaw.09@gmail.com |
needs Atmo |
Lukas Mueller |
Plant Biology |
lam87@cornell.edu |
X |
Mohammad Khan |
Plant Biology |
mohammad.khan.1@kaust.edu.sa |
no acct |
Igor Yakovlev |
Molecular Biosciences |
yai@skogoglandskap.no |
needs Atmo |
Richard Buggs |
Genetics and Nucleic Acids |
r.buggs@qmul.ac.uk |
needs Atmo |
Dr. Mansir Yusuf |
Genetics and Nucleic Acids |
mansiryusuf@yahoo.com |
no acct |
Rosangela Resende |
Forage Breeding |
rmsimeao@gmail.com |
needs Atmo |
Wenbin Mei CANCELLED |
Computer and Computation Research |
wmei@ufl.edu |
needs Atmo |
Vijay Tiwari |
Plant Biology |
vijtiwari@gmail.com |
X |
Mahmoud Wahb-Allahpl |
Plant Breeding |
mwahballah@ksu.edu.sa |
no acct |
Abdelhalim Ghazy |
Plant Biotechnology |
ghazyai@yahoo.com |
no acct |
Clay Birkett |
Genetics and Nucleic Acids |
claybirkett@gmail.com |
needs Atmo |
Laura Miller |
Cell Biology |
laura.miller@ars.usda.gov |
needs Atmo |
Stephen White |
|
stephen.white@ars.usda.gov |
needs Atmo |
Judy Brusslan CANCELLED |
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|
needs Atmo |
Original Announcement information
Announcement and Agenda:
This free workshop, adjacent to the 2013 International Plant & Animal Genome meeting, will kick-off a number of events at PAG to further engage you in making use of and collaborating with the iPlant Collaborative. Through several hands-on demos and guided exercises, workshop participants will get a comprehensive look at iPlant's tools and services for large-scale data analysis. We will start with an introduction to iPlant’s tools to manage, analyze, and share data – then apply these resources to structured use cases such as analyzing differential gene expression in an RNA-Seq dataset, analyzing high-throughput phenotyping data, and more. Participants will get hands-on experience with the following iPlant cyberinfrastructure:
- Discovery Environment: A powerful web portal for managing data, conducting analyses, and building workflows. Complex bioinformatics applications can be run without knowing command line programming, and users can customize the platform by integrating their own tools.
- Data Store: Scalable, secure, and reliable storage for gigabytes to terabytes of data; co-localized with iPlant analysis tools.
- Atmosphere: 1-click, on-demand cloud computing, comparable to Amazon Web Services, but simpler (and free).
Who Should Attend?
Any investigator (PIs, post-docs, grad students, industry users) who is or will be working with large datasets and computation-intensive research questions in the life-sciences (plants and animals!). Space is limited; register at:
http://www.iplantcollaborative.org/pag21reg
What Should I Bring?
This workshop is hands-on so please bring a Wi-fi enabled laptop. Lunch and breaks will be provided.
How Do I Get There?
This workshop is located at the Room 3A/3B at the Sheraton San Diego Hotel and Marina, which is adjacent to the airport. There are shuttles to and from the airport. The airport also offers multiple ground transportation options.
How Can I Connect with iPlant at PAG XXI?
iPlant is offering individual consultations/appointments, presentations and workshops. For the latest information see http://www.iplantcollaborative.org/pag21or follow iPlant on Twitter @iPlantCollab