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Organizers

Charis Cook

Date/Time

Sep 17-20, 2013

Location

TBA

Web site

http://www2.warwick.ac.uk/fac/sci/lifesci/news/iplant

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

Pre-survey link

All

10:30

iPlant Introduction and Overview

Slides

iPlant intro.pptx

Dan Stanzione

11:00

Overview of the Discovery Environment (DE)

Slides

DE User Manual | iPlant Forums

Jason Williams

11:30

iPlant Data Store - Managing "Big Data"

Slides

Data Store Guide , Data Store Overview Video
Workshop URLs , iDrop Download

Naim Matasci

12:15

Atmosphere – Custom Cloud Computing

Slides

Atmosphere Manual | Introductory Video

Matt Vaughn

13:00

Lunch

 

 

 

13:45

Building and Using Workflows Within the DE

Slides

 

Naim Matasci

14:30

Powered by iPlant - Consuming iPlant Services

Slides

API Tutorial

Dan Stanzione

15:30

Presentation by the Hartree Centre

Slides

 

 

16:00

Break

 

 

 

16:30

Extending the DE for Your Research

Slides

Application Creator manual

Matt Vaughn

17:00

Collaborating with iPlant

Slides

 

Dan Stanzione

17:30

End

 

Post-survey link

 

Wednesday

09:00

Examining Differential Expression Within an RNA-Seq Dataset

Slides

Tutorial

Matt Vaughn

11:00

Break

Demo Account Assignments

 

 

11:30

RNA-Seq Tutorial 1 (continued)

 

 

Matt Vaughn

13:30

Lunch

 

 

 

14:30

Getting started with GBS, GWAS, and Genomic Selection 

Slides GBSGWAS

Tutorial GWAS - MLMGBS 

Naim Matasci

16:30

Break

 

 

 

17:00

Getting started with GBS, GWAS, and Genomic Selection

 

Genomic Selection Using GenSel Tutorial

Naim Matasci

18:00

End

 

 

 

Thursday

09:00

ChIPseq and genomic interval analysis

Slides

Tutorial

Matt Vaughn

11:00

Break

 

 

 

11:30

ChIPseq and genomic interval analysis (con'd)

 

 

 

13:30

Lunch

 

 

 

14:30

Presentation by The Genome Analysis Centre

 

 

 

15:00

Advanced Topics in Extending the iPlant Cyberinfrastructure

Tutorial (in progress)

 

 

16:15

Break

 

 

 

16:30

Scheduled Meetings with iPlant Consultants

 

 

 

17:45

End

 

 

 

Friday

09:00

Scheduled Meetings with iPlant Consultants

 

 

 

11:00

Break

 

 

 

11:30

Scheduled Meetings with iPlant Consultants

 

 

 

13:30

Lunch

 

 

 

14:00

Bus Depart

 

 

 

Consulting Meetings 


Name

iPlant Staff

Time

Topic

Katie Mayes, Nottingham

Jason WIlliams

Thursday, 16:30

RNASeq

Ian Moore, 
Hayley McCullough, Sainsbury

Matt Vaughn/Dan Stanzione

Thursday, 16:30

SNP Calling Pipeline/Variant Detection

Sophie Piquerrez, Warwick

 

 

CHiPSeq

Andrea Massiah/Tizianna Sgamma

Matt

Friday. 09:30

FastQ Data

Mike Allwright, Southampton
Guillaume Menard, Rothamsted

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
Daniel Tomei, 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

 

 

 

 

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.

Attendees

Attendee List

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8 Comments

  1. Would appreciate the opportunity to discuss (probably one-to-one) GWAS in more detail especially with regard to the incorporation of population structure and kinship matrices and the programs used to generate them i.e. STRUCTURE, ADMIXTURE, etc.

    Thanks.

    Mike.

  2. Please could I ask about how to analyse RNAseq data without a reference genome? And any tools to look at quality of data and of the replications?

    And if it's possible to put on annotations from elsewhere (e.g. BLAST results and then GO terms from other related species) - because there's no nice sequence viewer from TAIR or ensembl or anything (sorry I'm waffling - I'll have formulated more precise questions by tomorrow).

    Thanks, Katie

  3. It would be great to have a one-to-one session to help me set up a workflow to use in my future RNAseq experiments, and to taylor the apps within it to the needs of my specific project.

    Thanks, Tom.

  4. I would like to have a one on one session about how I could use my RNAseq data to design microarray array probes which are specific to my organism. I can't attend Friday afternoon, but any time before then would be appreciated. 

    Thanks, 

    Christine 

  5. Is there a way to create an App using script or executable uploaded by us users?

    Thanks,

    Minghui

    1. Yes, Minghui. This is covered in detail in here

  6. We would like to know how we can use RNASeq to extract information regarding sequence variation.

  7. Could you please update me on a time for tomorrow one-to-one discussion about ChIP Seq?

    I can do anytime except 3-4pm.