2012 05 31 TSW NCSU
Organizers: |
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Local Point of Contact: |
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Trainers: |
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Date: |
9:30 AM - 5 PM on March 21 and 22, 2012 |
Location: |
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Catering Contact: |
Jill at Cateringworks, (919) 625-3693 |
Designated Lodging for Trainers: |
Page Contents
Pre-Workshop Homework
Computers will be available for use at the ITTC Labs. If you choose to bring your own laptop, you must email 411@iplantcollaborative.org with both your wired and wireless MAC addresses by Friday, 5/25. If you don't know how to do this, here is a link that may help: http://www.wikihow.com/Find-the-MAC-Address-of-Your-Computer
- 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
- 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/
- 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
- 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
- Please check your email, and this wiki prior to the workshop, as this is the way we will communicate any important changes.
- 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
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 Handouts
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 31
Time |
Presentation |
Slides |
Links |
Instructor |
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08:30 AM - 09:00 AM |
Arrive/Sign-in/ Verify iPlant accounts |
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09:00 AM - 09:30 AM |
Welcome - Presenter/Participant Introductions |
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Sheldon McKay |
09:30 AM - 09:50 AM |
An Overview of the iPlant Collaborative |
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Sheldon McKay |
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09:50 AM - 10:15 AM |
Overview of the iPlant Discovery Environment (DE) |
Martha Narro |
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10:15 AM - 10:30 AM |
Coffee Break |
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10:30 AM - 11:15 AM |
iPlant Data Store - Managing "Big Data" |
Naim Matasci |
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11:15 AM - 12:00 PM |
Atmosphere - Custom Cloud Computing |
Sheldon McKay |
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12:00 PM - 01:00 PM |
Lunch (Delivered) |
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01:00 PM - 01:30 PM |
Building and Using Workflows Within the DE; Phylogenetics |
Sheldon McKay |
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01:30 PM - 02:45 PM |
Using the DE to Examine Differential Expression with RNA-Seq |
Sheldon McKay |
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02:45 PM - 03:00 PM |
Coffee Break |
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03:00 PM - 04:30 PM |
Extending the DE: Tool Integration and Customization |
Martha Narro |
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04:30 PM - 05:00 PM |
Collaborating with iPlant: Future Projects and Workshop Summary |
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Martha Narro |
Friday June 1
Time |
Presentation |
Sides |
Links |
Instructor |
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08:45 AM - 09:00 AM |
Sign-in/Welcome |
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09:00 AM - 10:30 AM |
Advanced CHiP-seq in the iPlant Cyberinfrastructure |
Sheldon McKay |
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10:30 AM - 10:45 AM |
Coffee Break |
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10:45 AM - 11:30 AM |
Advanced CHiP-seq in the iPlant Cyberinfrastructure (cont'd) |
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Sheldon McKay |
11:30 AM - Noon |
Comparative Phylogenetic Methods in the iPlant Cyberinfrastructure |
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Noon - 01:00PM |
Lunch (On your own) |
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01:00 PM - 02:00 PM |
Powered by iPlant - Consuming iPlant Services in Your Portals |
Naim Matasci |
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02:00 PM - 03:00 PM |
Using XSEDE for Bioinformatics |
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03:00 PM - 04:30 PM |
Additional RNA-seq analysis applications/ hands-on |
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Sheldon McKay |
Attendee List
Name |
Research Area |
Dept. |
User Acct? |
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Felicia Anike |
felicia.anike@gmail.com |
Molecular Biosciences |
Natural Resources and Environmental Design |
Needs All |
Ashley Brooks |
ambrook3@ncsu.edu |
Genetics and Nucleic Acids |
Biochemistry |
Needs Atmo |
Lorenzo Concia |
lconcia@ncsu.edu |
Plant Biology |
Biochemistry |
Ready |
Xin Davis |
xydavis@ncsu.edu |
Algorithm Development |
Forestry and Env. Resources |
Needs Atmo |
Mia Dvora |
mdvora@ncsu.edu |
Plant Biology |
Plant Biology |
Needs Atmo |
Linda Hanley-Bowdoin |
linda_hanley-bowdoin@ncsu.edu |
Plant Biology |
Biochemistry |
Needs Atmo |
Luyan He |
lhe3@ncsu.edu |
Plant Biology |
Plant Biology |
Needs Atmo |
Brian Howard |
itsbehoward@hotmail.com |
Plant Biology |
Plant Biology |
Needs Atmo |
Omoanghe Isikhuemhen |
omon@ncat.edu |
Molecular Biosciences |
Natural Resources & Environmental Design |
Needs Atmo |
Anjali Iyer-Pascuzzi |
asi2@duke.edu |
Plant Biology |
Biology |
Needs Atmo |
Jyoti Kajla |
fjyoti@ncsu.edu |
Plant Biology |
Crop Science |
Needs Atmo |
Tae-Jin Lee |
tjlee3012000@gmail.com |
Cell Biology |
Plant Biology |
Needs Atmo |
Harry Lopez |
horosado@ncsu.edu |
Engineering Systems |
Crop Science |
Needs Acct |
Emily Markham |
eamarkha@ncsu.edu |
Plant Biology |
Plant Biology |
Ready |
Jorge Marques |
jm368@duke.edu |
Plant Biology |
Biology |
Needs Atmo |
Greg O'Brian |
grobrian@ncsu.edu |
Molecular Biosciences |
Plant Pathology |
Needs Atmo |
Niki Robertson |
niki@ncsu.edu |
Plant Biology |
Plant Biology |
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Marie-Laure Sauer |
masauer@ncsu.edu |
Plant Biology |
Plant Biology |
Needs Atmo |
Wei Shen |
wshen@ncsu.edu |
Plant Biology |
Biochemistry |
Needs Atmo |
Soundarya Srirangan |
ssriran@ncsu.edu |
Plant Biology |
Plant biology |
Needs Atmo |
Sermsawat Tunlaya-anukit |
stunlay@ncsu.edu |
Forest Biotechnology |
Forest and Environmental Resource |
Needs Atmo |
Naresh Vasani |
nbvasani@ncsu.edu |
Plant Biology |
Crop Science |
Needs Atmo |
Emily Wear |
emily_wear@ncsu.edu |
Plant Biology |
Plant Biology |
Ready |
Ross Whetten |
ross_whetten@ncsu.edu |
Plant Biology |
Forestry & Environmental Resources |
Needs Atmo |
Qian Wu |
qwu2@ncsu.edu |
Plant Biology |
Plant Biology |
Needs Atmo |
Roopa Yalamanchili |
ryroopa@gmail.com |
Plant Biology |
Plant Biology |
Needs Atmo |
Getting to the Workshop
D. H. Hill Library, 2 W Broughton Dr, Raleigh, NC
Directions to D.H. Hill Library
Parking Information
Library Map
Directions to ITTC Labs:
Enter D. H. Hill Library from the brickyard. Go through the turnstile and turn right. On your left are stairs and elevators; take one to the 2nd floor. Once on the 2nd floor, turn to your left and follow the aisle to the left, keeping the book shelving on your right. At the end of the aisle, continue to the left into the East Wing. Turn right at the second carpeted hallway. The ITTC labs are located on your right and left.
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.