Exploring Plant Variation Data
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Date:
Wednesday 1 - Friday 3 July 2015Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication deadline:
Sunday 26 April 2015Participation:
Open application with selectionContact:
Allison BeaumontRegistration fee:
£105Registration closed
Overview
This workshop will focus on current developments in plant data resources at transPLANT partner sites (www.transplantdb.eu), with a special reference to plant genomic variation data, re-sequencing projects GWAS analyses. The workshop will provide a basic tutorial on SNP calling and analysis as well as hands-on introductions into partner resources and tools and explain how to obtain, search and use this data.
Audience
The workshop is targeted at (experimental) biologists and breeders who have the need to use these resources and concepts in everyday work to interpret own observations and plan new research objectives. No prior (informatics) knowledge or skills are required. Familiarity with using browser-based tools and/or Linux operating systems would be helpful however.
Syllabus, tools and resources
During this course you will learn about:
- Syllabus: SNP calling; variation data; GWAS
- Tools: Introgression Browser, polymarker, VCF viewer
- Resources: Ensembl Plants, GMI GWAS resources
Outcomes
After this course you should be able to:
- Access plant variation data from public resources
- Use appropriate tools to analyse variation
- Explore A. thaliana GWAS data
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Wednesday 1st July | ||
| 12:00 -13:00 | Lunch | |
| 13:00 - 13:30 | Welcome and introduction | Paul Kersey and Manuel Spannagl |
| 13:30 - 14:00 | Plant variation data - what's available, what new projects are expected | Martin Mascher (IPK) |
| 14:00 - 15:30 | Hands-on tutorial on SNP calling and data interpretation | Georg Haberer and Manuel Spannagl (HMGU) |
| 15:30 - 16:00 | Tea/coffee break | |
| 16:00 - 17:15 | Hands-on tutorial on SNP calling and data interpretation (Cotd.) | Georg Haberer and Manuel Spannagl (HMGU) |
| 17:15 - 17:45 | The European Variation Archive: a home for plant variation data | Gary Saunders (EMBL-EBI) |
| Check in | ||
| 19:00 | Dinner Hinxton Hall | |
| Day 2 - Thursday 2nd July | ||
| 09:00 - 10:00 | Tutorial on the Introgression Browser (iBrowser) | Jan - Peter Nap (WUR) |
| 10:00 - 11:00 | 'Hands-on' workshop on variation data in Ensembl Plants | Dan Bolser, Denise Carvalho-Silva, and Brandon Walts (EMBL-EBI) |
| 11:00 - 11:30 | Tea/coffee break | |
| 11:30 - 12:30 | 'Hands-on' workshop on variation data in Ensembl Plants | Dan Bolser, Denise Carvalho-Silva, and Brandon Walts (EMBL-EBI) |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:30 | Presentation and hands-on tutorial of the VCF viewer | Antoine Janssen (KeyGene) |
| 15:30 - 16:00 | Tea/coffee break | |
| 16:00 - 16:30 | Talk: TILLING at TGAC | Sarah Ayling (TGAC) |
| 16:30 - 17:00 | Tutorial: PolyMarker | Ricardo Ramirez (TGAC) |
| 17:00 - 17:30 | Talk: resequencing approaches (WGS vs exome vs Gbs/RAD) | Sarah Ayling (TGAC) |
| 17:30 - 18:00 | Open discussion | All |
| 19:00 | Coach pick up from Hinxton Hall | |
| 19:30 | Dinner | |
| Day 3 - Friday 3rd July | ||
| 09:30 - 11:00 | A hands-on introduction and tutorial to Genome Wide Association Studies (GWAS) | Ümit Seren (GMI) |
| 11:00 - 11:30 | Tea/coffee break | |
| 11:30 - 12:30 | A hands-on introduction and tutorial to Genome Wide Association Studies (GWAS) (Cotd.) | Ümit Seren (GMI) |
| 12:30 - 13:00 | Course wrap up and feedback | |
| 13:00 - 14:00 | Lunch | |
| 14:00 | Participants leave (Shuttle to Cambridge Station departs) | |
In association with
How to apply
Application deadline
26 April 2015
Number of places
30 places
Organisers
Paul Kersey
Manuel Spannagl - Mips - Helmholtz Zentrum München, Germany
Trainers
Paul Kersey - EMBL-EBI, UK
Manuel Spannagl - Mips - Helmholtz Zentrum München, Germany
Martin Mascher - IPK, Germany
Georg Haberer - HMGU, Germany
Gary Saunders - EMBL-EBI, UK
Jan Peter Nap - WUR, The Netherlands
Dan Bolser - EMBL-EBI, UK
Denise Carvalho-Silva - EMBL-EBI, UK
Brandon Walts - EMBL-EBI, UK
Antoine Janssen - KeyGene, The Netherlands
Sarah Ayling - TGAC, UK
Ümit Seren - Gregor Mendel Institute of Molecular Plant Biology, Austria