2012 08 20 TSW UWisconsin-Madison
Organizers |
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|---|---|
Local Point of Contact |
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Trainers |
Jason Williams, Andy Lenards, Roger Barthelson, Edgar Spalding, Nathan Miller |
Date |
August 20-21, 2012 |
Location |
30 seats classroom style |
Catering Contact |
Lisa Loup, Steenbocks/Foodfight |
Designated Lodging |
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Flyer/Advertising |
TSW |
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. The use of Atmosphere will require a VNC viewer which can be downloaded here.
5. If you are attending any sessions on day 2 (Genome Center Conference Room 4202) 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
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
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 August 20th
Time |
Presentation |
Presenter |
Slides |
Links |
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08:00 AM - 08:30 AM |
Arrive/Sign-in |
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08:30 AM - 09:00 AM |
Welcome - Presenter/Participant Introductions |
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09:00 AM - 09:20 AM |
An Overview of the iPlant Collaborative |
Jason |
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09:20 AM - 09:45 AM |
Overview of the iPlant Discovery Environment (DE) |
Jason |
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09:45 AM - 10:15 AM |
iPlant Data Store - Managing "Big Data" |
Jason |
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10:15 AM - 10:45 AM |
Building and Using Workflows Within the DE; Phylogenetics |
Andy |
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10:45 AM - 11:00 AM |
Coffee Break |
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11:00 AM - 12:00 PM |
Using the DE to Examine Differential Expression Within an RNA-seq Dataset |
Roger |
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12:00 PM - 1:00 PM |
Lunch |
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1:00 PM - 2:00 PM |
Atmosphere - Custom Cloud Computing |
Andy |
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2:00 PM - 2:45PM |
Extending the DE for Your Research: Tool Integration and Customization |
Andy |
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2:45 PM - 3:00 PM |
Collaborating with iPlant: Future Projects and Workshop Summary |
Jason/Andy |
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Tuesday August 21st
Time |
Presentation |
Presenter |
Slides |
Links |
|---|---|---|---|---|
09:30 AM - 10:30 PM |
Powered by iPlant - Using the iPlant API |
Jason |
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10:30 AM - 12:00 PM |
Advanced RNA-Seq - Visualizations with R |
Roger |
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12:00 PM - 1:00 PM |
Lunch (On your own) |
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1:00 PM - 2:30 PM |
Phytobisque |
Nate/Edgar et.al. |
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2:30 PM - 3:00 PM |
Using XSEDE for Bioinformatics |
Jason |
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3:00 PM - 3:30 PM |
Data Store Applications |
Andy |
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3:30 PM - 4:00 PM |
Open topics |
Andy/Jason |
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Attendee List
Name |
Affiliation |
User Acct |
|
|---|---|---|---|
Danielle Nevarez-McBride |
nevarezmcbri@wisc.edu |
UW Madison |
X |
Douglas Senalik |
dsenalik@wisc.edu |
USDA |
X |
Marisa Otegui CANCELLED |
otegui@wisc.edu |
UW Madison |
needs Atmo |
Massimo Iorizzo |
iorizzo@wisc.edu |
UW Madison |
needs acct |
Stephanie Lyon |
slyon@wisc.edu |
UW Madison |
needs Atmo |
Amy Jancewicz |
amy.jancewicz@gmail.com |
UW Madison |
needs acct |
Shih-heng Su |
ssu1@wisc.edu |
UW Madison |
needs acct |
Bryan Drew |
bdrewfb@yahoo.com |
UFL |
needs Atmo |
Bruce Veit |
bruce.veit@agresearch.co.nz |
AgResearch (NZ gov inst) |
needs Atmo |
Joohyun Lee |
jlee332@wisc.edu |
UW Madison |
needs Atmo, DE |
Steve Deslauriers |
sdeslauriers@wisc.edu |
UWisconsin |
needs Atmo |
Brandon Fonnemann |
bfonne2@uic.edu |
U Illinois Chicago |
needs Atmo |
David Zaya CANCELLED |
dzaya1@uic.edu |
U Illinois Chicago |
X |
Nicholas Gladman |
gladman@wisc.edu |
UW Madison |
needs Atmo |
Claudia Calderon |
cicalderon@wisc.edu |
UW Madison |
X |
David Baum |
dbaum@wisc.edu |
UW Madison |
X |
Annett Milling CANCELLED |
amilling@wisc.edu |
UW Madison |
NA |
Jennifer Knack |
jjknack@wisc.edu |
UW Madison |
X |
Aaron Lomax |
lomax@wisc.edu |
UW Madison |
needs acct |
Robert Augustine |
raugustine@wisc.edu |
UW Madison |
needs Atmo |
Zhihua Hua |
hua3@wisc.edu |
UW Madison |
needs Atmo, DE |
Dhileepkumar Jayaraman |
djayaraman@wisc.edu |
UW Madison |
needs Atmo |
Muthusubramanian Venkateshwaran |
venkateshwar@wisc.edu |
UW Madison |
needs Atmo, DE |
Ranjinder Dhall |
rkdhall@wisc.edu |
UW Madison |
needs Atmo |
Shelby Repinski |
slrepinski@wisc.edu |
UW Madison |
needs Atmo |
Richard Barker |
dr.richard.barker@gmail.com |
UW Madison |
X |
Joel Stafstrom |
stafstrom@niu.edu |
Northern Illinois U |
needs Atmo |
Amy Runck |
arunck@winona.edu |
Winona State U |
needs Atmo |
Keir Wefferling CANCELLED |
wefferl2@uwm.edu |
UW Milwaukee |
needs Atmo |
Dana Martinez |
danaethelmy@yahoo.com |
Conicet |
needs Atmo, DE |
Yury Bukhman |
ybukhman@glbrc.wisc.edu |
UW Madison |
X |
Periannan Senapathy (TUES only) |
psenapathy@genome.com |
Genome International Corp |
needs Atmo |
Getting to the Workshop
Campus Map: http://discovery.wisc.edu/home/discovery/plan-your-visit/location/
Parking: http://discovery.wisc.edu/home/discovery/plan-your-visit/parking/
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 (material, services, tools, training techniques, etc.). We'd also like to know if there are computational bottlenecks in your research that iPlant could target to assist in developing community-scale solutions.
https://www.surveymonkey.com/s/ToolsServices_post