2012 06 29 TSW NDSU
Organizers: | |
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Local Point of Contact: | |
Trainers: | Sheldon McKay, Christos Noutsos, Shannon Oliver, Jason Williams |
Date: | 12:00PM - 6:00PM on June 29, 9:30AM - 4:00PM on June 30, 2012 |
Location: | Barry Hall, Rm 260 |
Goal
To provide an interactive, hands-on training of iPlant Tools and Services so that participants can begin to use iPlant cyberinfrastructure in their research.
Pre-Workshop Homework
1. Please test 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 check your email and this wiki prior to the workshop, as this is the way we will communicate any important changes.
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 are Your Data"
Agenda
Friday June 29th
Time | Presentation | Audience/Prerequisites* | Presenter | Slides, Links |
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12:00 PM - 12:30 PM | Arrive / Sign-in / Verify iPlant Accounts | N/A |
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12:30 PM - 01:00 PM | Welcome - Presenter/Participant Introductions | N/A |
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01:00 PM - 01:20 PM | An Overview of the iPlant Collaborative | All researchers |
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01:20 PM - 01:45 PM | Overview of the iPlant Discovery Environment (DE) | All researchers | ||
01:45 PM - 02:15 PM | iPlant Data Store - Managing "Big Data" | All researchers | ||
02:15 PM - 02:30 PM | Break |
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02:30 PM - 03:00 PM | Building and Using Workflows Within the DE; Phylogenetics | All researchers |
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03:00 PM - 04:15 PM | Using the DE to Examine Differential Expression Within an RNA-seq Dataset | All researchers - Background in | ||
04:15 PM - 4:30 PM | Break |
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04:30 PM - 05:00 PM | Atmosphere - Custom Cloud Computing | All researchers - Background in | ||
05:00 PM - 06:00 PM | Extending the DE for Your Research: Tool Integration and Customization | Intermediate - Background in |
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06:00 PM - 06:15 PM | Collaborating with iPlant: Future Projects and Workshop Summary | All researchers |
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Saturday June 30th
Time | Presentation | Audience/Prerequisites* | Presenter | Slides/Links |
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09:30 AM - 09:40 AM | Installing Java | All of you |
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09:40 AM - 11:00 AM | Advanced CHiP-seq in the iPlant Cyberinfrastructure | Intermediate - knowledge of | ||
11:00 AM - 11:15 AM | Break |
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11:15 AM - 12:00 PM | Topics and Questions in RNA-Seq | All researchers | ||
12:00 PM - 01:00 PM | Lunch |
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01:00 PM - 01:15 | Upcoming Features in the DE | All |
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01:15 PM - 01:30 PM | Using XSEDE for Bioinformatics | Advanced- Background | ||
01:30 PM - 02:00 PM | Powered by iPlant - Using the iPlant API | Intermediate/Advanced - Background | ||
02:00 PM - 02:45 PM | iCommands for data transfer | Intermediate/Advanced Background in command line |
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02:45 PM - 03:45 PM | Using Atmosphere to visualize RNA-Seq data | Intermediate/Advanced- Background in RNA-Seq | ||
03:45 PM | Conclusion and Free Form Work | All audiences as needed. |
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* Audience/Prerequisites - These prerequisites are meant as helpful suggestions to get the most out of each module. Everyone can attend
any/all modules and are free to follow along (or not) as their own interests and abilities dictate.
Attendee List
First | Last | User Acct | |
|---|---|---|---|
Omar | Al-Azzam | omar.al-azzam@ndsu.edu | X |
Aman | Anand | aman.anand@my.ndsu.edu | no acct |
Deepika | Arora | deepika.arora@my.ndsu.edu | X |
Filippo | Bassi | filippo.bassi@ndsu.edu | X |
Ryan | Burciaga | ryan.burciaga@my.ndsu.edu | X |
Anne | Denton | anne.denton@ndsu.edu | X |
Sandra | Dunckel | sdunckel@ksu.edu | needs Atmo |
Morgan | Echeverry-Solarte | morgan.echeverry-solarte@my.ndsu.edu | X |
Ahmed | Eldoliefy | ahmed.el-doleify@my.ndsu.edu | needs Atmo |
Farhad | Ghavami | farhad.ghavami@ndsu.edu | needs Atmo |
David | Horvath | david.horvath@ars.usda.gov | X |
Shalu | Jain | shalu.jain@ndsu.edu | needs Atmo |
Renata | Jung | renata.jung@ndsu.edu | needs Atmo |
Vedbar | Khadka | vskhadka@jacks.sdstate.edu | needs Atmo |
Shahryar | Kianian | s.kianian@ndsu.edu | needs Atmo |
Ajay | Kumar | ajayguptajammu@gmail.com | needs Atmo |
Cindy |