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 11 May 2018

Application deadline: 

Friday 17 August 2018

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£560 (Including Accommodation)

Registration closed

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

Day 3 – Thursday 08 November 2018
09:00 Introduction to plant variation data Paul Wilkinson, University of Bristol
09:30 Cereals DB Paul Wilkinson, University of Bristol
11:00 Tea & Coffee
11:30 Ensembl variation tools (VEP) Guy Naamati/Erin Haskell, EMBL-EBI
12:30 Lunch
13:30 Ensembl variation tools (VEP) Guy Naamati/Erin Haskell, 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 Wheat Training Jemima Brinton, John Innes Centre
14:30 Wrap-up and feedback Alexandra Holinski, EMBL-EBI
15:00 End of course - Coach to Cambridge Train Station  
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

How to apply

In order to be considered for a place on this course, the application process is as follows:

  1. Complete the online application form
  2. Submit a WORD document to johanna@ebi.ac.uk containing a short biography (Text only, no CV's), including your work history and a description of your current research interests (by 03 August 2018). Each section should be no longer than 100 words (300 words total)
  3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course

Further details will be provided on your confirmation email after completing the online form.

Incomplete applications will NOT be considered. Please read through the following guidance document for further information regarding how to complete your application.

The registration fee includes:

  • 3 nights accommodation at the Wellcome Trust Conference Centre (Onsite) - (Arriving Tuesday 06 November 2018 - Departure Friday 09 November 2018)
  • Breakfast, tea/coffee, lunches and evening meals will be provided for the duration of the course
  • Shuttle bus to Cambridge Train Station at the end of the course
  • Use of the course training room
  • Course materials provided

Application deadline

17 August 2018

Number of places

30 places

Registration closed

Organisers

Laura Huerta Martinez - EMBL-EBI, UK

Alexandra Holinski - EMBL-EBI, UK

Guy Naamati - EMBL-EBI, UK

Trainers

Alexandra Holinski - EMBL-EBI, UK

Materials & attachments

Course materials