Data Mining with iPlant
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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"
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 |
11:00 | Overview of the Discovery Environment (DE) |
| Jason Williams | |
11:30 | iPlant Data Store - Managing "Big Data" |
| Data Store Guide , Data Store Overview Video | Naim Matasci |
12:15 | Atmosphere – Custom Cloud Computing |
| Matt Vaughn | |
13:00 | Lunch |
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13:45 | Building and Using Workflows Within the DE |
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| Naim Matasci |
14:30 | Powered by iPlant - Consuming iPlant Services | lides | Dan Stanzione | |
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 | |
17:00 | Collaborating with iPlant |
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| Dan Stanzione |
17:30 | End |
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Wednesday
09:00 | Examining Differential Expression Within an RNA-Seq Dataset |
| Matt Vaughn | |
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 | Slides , | Tutorial GWAS - MLM, GBS | Naim Matasci |
16:30 | Break |
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17:00 | Getting started with GBS, GWAS, and Genomic Selection |
| Naim Matasci | |
18:00 | End |
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Thursday
09:00 | ChIPseq and genomic interval analysis |
| Matt Vaughn | |
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 | Tutorial (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 |