Bioinformatics for Crop Plants


 Monday 18 Thursday 21 November 2019


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

Application opens: 

Tuesday 28 May 2019

Application deadline: 

Friday 16 August 2019


Open application with selection


Meredith Willmott

Registration fee: 

£690 (including accommodation and meals)


This course will introduce plant biologists to methods and approaches for analysing the genomic data. During the course participants will learn about comparative genomics using Ensembl, analyse variation data with Ensembl Variant Effect Predictor and the European Variation Archive, and explore the concepts of genome wide association studies (GWAS). The content will explain how to make use of existing public data, retrieve, submit and share your data with the community. It will be delivered through a combination of hands-on training sessions and lectures.

Please note: The course will use genomic data from crop plant species throughout the week. It will not explore in detail methods for read mapping and assembling genomes.


This course is aimed at plant biologists, in particular those with wet-lab experience needing to learn about methods and approaches for analysing plant genomic data. It will help those wanting to start basic comparative genomics, identification of genetic variation and using public data to interpret new findings.

Participants will require a basic knowledge of the Unix command line and the R statistical packages. We recommend these free tutorials:

Syllabus, tools and resources

During this course you will learn about the following resources and tools:

  • Ensembl for comparative genomics and Ensembl Variant Predictor
  • Methods for retrieving data from Ensembl
  • EVA
  • Expression Atlas
  • Cereals DB


After this course you should be able to:

  • Browse, retrieve, submit and share data
  • Use Ensembl for comparative analysis to explore plant genomes
  • Access plant variation data from public resources and use appropriate tools to analyse variation
  • Explore GWAS data
  • Find transcriptomics data in Expression Atlas across different plant species and biological conditions

Additional information

All participants are expected to present a poster that will be displayed during the course outside the training room. 

All posters should:

•             be A2 in size - 420mm x 594 mm
•             be in a portrait orientation
•             include your photograph and contact information

We expect the posters to act as a talking point between you, other participants and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.


This is a draft programme and changes might still occur.

Day 1 – Monday 18th November
11:30 - 12:30 Arrival, registration and lunch  
12:30 - 13:00 Introduction to EMBL-EBI Alexandra Holinski
13:00 - 14:00 Introduction to Ensembl Ensembl Team
14:00 - 15:30 Using Ensembl for comparative studies Ensembl Team
15:30 - 16:00 Break  
16:00 - 17:30 Challenges in the field Ricardo Ramirez-Gonzalez
18:00 Evening meal Hinxton Hall
Day 2 – Tuesday 19th November
09:00 - 10:00 Introduction to variation data and variant calling Paul Wilkinson
10:00 - 11:00 Practical on variant calling (including an introduction to computational skills) Paul Wilkinson & Guy Naamati
11:00 - 11:30 Break  
11:30 - 13:00 Practical on variant calling continued Paul Wilkinson
13:00 - 14:00 Lunch + Posters  
14:00 - 15:30 Ensembl Variant Predictor Ensembl Team
15:30 - 16:00 Break  
16:00 - 17:00 European Variation Archive (EVA) Baron Koylass
18:00 Evening meal Hinxton Hall
Day 3 – Wednesday 20th November
09:00 - 10:30 Overview of reduced representation sequencing, overview of GWAS Sanjeev Kumar Sharma
10:30 - 11:00 Break  
11:00 - 13:15 GWAS Sanjeev Kumar Sharma
13:15 - 14:00 Lunch + Posters  
14:00 - 15:30 Cereals DB Paul Wilkinson
15:30 - 16:00 Break  
16:00 - 17:00 Keynote lecture To be comfirmed
18:00 Evening meal Red Lion, Hinxton
Day 4 – Thursday 21st November
09:00 - 11:00 Methods for accessing and retrieving data from Ensembl Ensembl Team
11:00 - 11:15 Break  
11:15 - 13:00 Expression Atlas Nancy George & Silvie Fexova
13:00 - 13:15 Wrap-up and feedback Alexandra Holinski
13:15 - 14:00 Lunch  
14:15 Coach to Cambridge train station