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:
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"
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 |
| 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 |
| 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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