2012 05 31 TSW NCSU
Organizers: | |
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Local Point of Contact: | |
Trainers: | |
Date: | 9:30 AM - 5 PM on March 21 and 22, 2012 |
Location: | |
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
General iPlant Support Issues
iPlant Privacy (And other) policies - "Your Data is Your Data"
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 |
| | Sheldon McKay |
09:50 AM - 10:15 AM | Overview of the iPlant Discovery Environment (DE) |
| Martha Narro | |
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 | |
11:15 AM - 12:00 PM | Atmosphere - Custom Cloud Computing |
| Sheldon McKay | |
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 | |
01:30 PM - 02:45 PM | Using the DE to Examine Differential Expression with RNA-Seq |
| Sheldon McKay | |
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 |
| , Manual | Martha Narro |
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 | |
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 | |
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 |
| Sheldon McKay |
Attendee List
Name | Research Area | Dept. | User Acct? | |
|---|---|---|---|---|
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 |