Bioinformatics for Plant Biology

Date:

 Tuesday 6 Friday 9 November 2018

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Friday May 11 2018

Application deadline: 

Friday August 03 2018

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£560 (Including Accommodation)

Overview

Recent developments in sequencing technologies have led to a dramatic increase in the generation of plant genomic data. In order to facilitate accessibility and analysis of this data, a range of bioinformatics resources have been developed. This course will provide an introduction to these resources and tools to help manage, discover and analyse genomics data, with a particular focus on cereal genomics. It will be delivered through a combination of hands-on training sessions and lectures on how to make the most of the tools offered by each plant resource.

Audience

This course is aimed at plant biologists who have an interest in accessing and exploring the huge amount of data being generated by high-throughput technologies. No prior experience of bioinformatics is required, but familiarity with biological use cases of high throughput sequencing would be of benefit.

Syllabus, tools and resources

The course will be structured in two parts covering:

1) Tools and resources for comparative genomics

2) Plant variation data.

Outcomes

After this course you should be able to:

  • Browse genes and genomes using leading public repositories
  • Use comparative analysis of plant species to explore plant genomes
  • Access plant variation data from public resources and use appropriate tools to analyse variation
  • Find transcriptomics data across different plant species and biological conditions
  • Explore GWAS data
  • Effectively navigate within different resources, integrating them and answering biological research questions

Programme

Day 1 – Tuesday 06 November 2018

12:00 Arrival, registration and lunch  
13:00 Introduction to EMBL- EBI Alexandra Holinski, EMBL-EBI
13:30 Introduction to comparative genomics Guy Naamati + Ensembl team, EMBL-EBI
14:00 Ensembl Plants Guy Naamati + Ensembl team, EMBL-EBI
15:30 Tea & Coffee  
16:00 Expression Atlas Laura Huerta Martinez, EMBL-EBI
18:00 Networking and Poster  
19:30 Dinner  

Day 2 – Wednesday 07 November 2018

09:00 Composition and structure of large plant genomes (barley, tetra- and hexaploid wheat) (PlantsDB and other resources) Heidrun Gundlach, Manuel Spannagl, Helmholtz Institute Muenchen
11:00 Tea & Coffee  
11:30 Barlex and IPK resources Sebastian Beier, IPK Gatersleben
12:30 Lunch
13:30 Barlex and IPK resources continued Sebastian Beier, IPK Gatersleben
14:30 Keynote lecture: Assembling complex crop genomes for comparative analyses Bernardo Clavijo, Earlham Institute
15:30 Tea & Coffee  
16:00 COPO data management tools Anthony Etuk, Earlham Institute
17:00 End of the day  
18:00 Dinner  

Day 3 – Thursday 08 November 2018

09:00 Introduction to plant variation data TBC
09:30 Cereals DB Paul Wilkinson, University of Bristol
11:00 Tea & Coffee
11:30 Ensembl variation tools (VEP) Guy Naamati + Ensembl team, EMBL-EBI
12:30 Lunch
13:30 Ensembl variation tools (VEP) Guy Naamati + Ensembl team, EMBL-EBI
14:30 Keynote lecture Cristobal Uauy, John Innes Centre
15:30 Tea & Coffee  
16:00 KnetMiner Keywan Hassani-Pak, Rothamstead
17:30 End of day  
18:00 Dinner  

Day 4 – Friday 09 November 2018

09:00 GWAS Uemit Seren, Gregor Mendel Institute
10:30 Tea & Coffee  
11:00 GWAS Uemit Seren, Gregor Mendel Institute
12:00 Lunch
13:00 Quantitative RNA seq + eQTL analysis TBC
14:30 Wrap-up and feedback Alexandra Holinski, EMBL-EBI
14:45 End of course - Coach to Cambridge Train Station