Data Mining with iPlant
Organizers |
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Date/Time |
Sep 17-20, 2013 |
Location |
TBA |
Web site |
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
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 consume and customize iPlant tools and services for your investigations.
Workshop Handouts
Agenda
Tuesday – Introduction to the iPlant Collaborative
10:00 |
Registration / Verify iPlant Accounts |
Wiki |
All |
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10:30 |
iPlant Introduction and Overview |
Slides |
Dan Stanzione |
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11:00 |
Overview of the Discovery Environment (DE) |
Jason Williams |
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11:30 |
iPlant Data Store - Managing "Big Data" |
Data Store Guide , Data Store Overview Video |
Naim Matasci |
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12:15 |
Atmosphere – Custom Cloud Computing |
Matt Vaughn |
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13:00 |
Lunch |
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13:45 |
Building and Using Workflows Within the DE |
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Naim Matasci |
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14:30 |
Powered by iPlant - Consuming iPlant Services |
Slides |
Dan Stanzione |
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15:30 |
Presentation by the Hartree Centre |
Slides |
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16:00 |
Break |
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16:30 |
Extending the DE for Your Research |
Matt Vaughn |
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17:00 |
Collaborating with iPlant |
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Dan Stanzione |
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17:30 |
End |
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Wednesday
09:00 |
Examining Differential Expression Within an RNA-Seq Dataset |
Matt Vaughn |
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11:00 |
Break |
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11:30 |
RNA-Seq Tutorial 1 (continued) |
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Matt Vaughn |
13:30 |
Lunch |
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14:30 |
Getting started with GBS, GWAS, and Genomic Selection |
Tutorial GWAS - MLM, GBS |
Naim Matasci |
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16:30 |
Break |
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17:00 |
Getting started with GBS, GWAS, and Genomic Selection |
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Naim Matasci |
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18:00 |
End |
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Thursday
09:00 |
ChIPseq and genomic interval analysis |
Matt Vaughn |
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11:00 |
Break |
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11:30 |
ChIPseq and genomic interval analysis (con'd) |
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13:30 |
Lunch |
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14:30 |
Presentation by The Genome Analysis Centre |
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15:00 |
Advanced Topics in Extending the iPlant Cyberinfrastructure |
/wiki/spaces/eot/pages/241585174 (in progress) |
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16:15 |
Break |
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16:30 |
Scheduled Meetings with iPlant Consultants |
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17:45 |
End |
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Friday
09:00 |
Scheduled Meetings with iPlant Consultants |
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11:00 |
Break |
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11:30 |
Scheduled Meetings with iPlant Consultants |
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13:30 |
Lunch |
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14:00 |
Bus Depart |
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Consulting Meetings
Name |
iPlant Staff |
Time |
Topic |
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Katie Mayes, Nottingham |
Jason WIlliams |
Thursday, 16:30 |
RNASeq |
Ian Moore, |
Matt Vaughn/Dan Stanzione |
Thursday, 16:30 |
SNP Calling Pipeline/Variant Detection |
Sophie Piquerrez, Warwick |
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CHiPSeq |
Andrea Massiah/Tizianna Sgamma |
Matt |
Friday. 09:30 |
FastQ Data |
Mike Allwright, Southampton |
Naim Matasci |
Thursday, 16:30 |
GWAS, populations sructure and kinship matrices |
Tom Vincent, John Inns Center |
Naim/Jason |
Thursday, 17:00 |
RNASeq |
Kate Lecocq, Exeter |
Matt/Dan |
Thursday, 17:00 |
RNASeq |
Maurice Bosh, Aberdeen |
Naim |
Friday, 9:00 |
RNASeq |
Viktoriya Coneva, University of Guelph |
Jason |
Friday, 9:00 |
RNASeq |
Katherine Denby, Warwick |
Matt |
Friday, 10:00 |
RNASeq |
Jack Davies, Liverpool |
Naim |
Friday,10:00 |
RNASeq |
Lennie Foster, Warwick |
Jason |
Friday, 10:00 |
RNASeq |
Christine Hicks, Warwick |
Naim |
Friday, 10:30 |
RNASeq |
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David Hughes, Rothamsted Research |
Matt |
Friday, 10:30 |
RNASeq |
David Lloyd, Rothamsted Research |
Jason |
Friday, 10:30 |
RNASeq |
Samart Wachana, International Rice Research Institute |
Naim |
Friday, 11:30 |
RNASeq |
Marco Reitz, Warwick |
Jason |
Friday, 11:30 |
QC for RNA-Seq |
Stuart Meier, KAUST |
Matt |
Friday, 11:30 |
Phylogenetic comparisons, differential expression complications |
Jade Waller, Liverpool |
Naim/Jason/Matt |
Friday, 12:30 |
SOLiD vs. 454 Transcriptomes. |