Wageningen university workshop
Organizers |
Eric Schranz, Eric Lyons, Jason Williams |
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Trainers |
Eric. L, Jason W. |
Date |
March 3-4, 2014 |
Location |
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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 Program (Monday, March 3rd)
Time |
Description |
Slides |
Links |
Presenter |
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09:00 |
Arrive / Sign-in / Verify iPlant Accounts |
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09:15 |
Welcome - Presenter/Participant Self-Introductions |
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09:30 |
Overview of the iPlant Collaborative |
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09:40 |
Overview of CoGe |
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09:50 |
Overview of the iPlant Discovery Environment (DE) |
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10:15 |
Coffee Break |
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10:30 |
iPlant Data Store - Managing "Big Data" |
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11:15 |
Workflows in the DE; Phylogenetics Example |
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12:00 |
Lunch |
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13:00 |
Using the DE for RNA-Seq |
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14:00 |
Atmosphere Cloud Computing |
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15:00 |
Coffee |
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15:15 |
ALLPATHS genome assembly |
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15:45 |
Intro to comparative genomics with CoGe |
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How to use CoGe (example Brassica and Arabidopsis genome analysis) |
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16:30 |
Day - wrap up |
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Workshop Program (Tuesday, March 4th)
Time |
Description |
Slides |
Links |
Presenter |
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09:30 |
iPlant GWAS FaSTLMM |
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10:15 |
Data management with CoGe |
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EPIC-CoGe: Coge's user-data management system |
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11:45 |
Lunch |
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13:00 |
Genome annotation with MAKER |
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13:30 |
xGDMvm /T3 Toolbox in Atmosphere - Customizing databases |
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14:00 |
Visualizing RNA-Seq data with CummeRbund |
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14:45 |
Advanced analyses with CoGe |
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15:15 |
Coffee |
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15:30 |
Educational: DNA Subway |
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16:00 |
Wrap up and Individual Consultations |
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