Bioinformatics of Plants and Plant Pathogens 2016


 Monday 23 Wednesday 25 May 2016


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

Application opens: 

Thursday 07 January 2016

Application deadline: 

Friday 25 March 2016


Open application with selection


Johanna Langrish

Registration fee: 


Registration closed

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This course will provide an introduction to data resources, tools and essential bioinformatic techniques for biologists studying plants and their pathogens.  It will be delivered using a mixture of lectures, practical computer sessions and include discussions based on relevant case studies and public domain data.



During this course you will learn about:

  • Genome browsing: Ensembl Plants, PhytoPath, WormBase
  • NGS analyses: QC, SNP calling, RNA Assembly
  • Analyses for Genome-wide association studies

Learning Objectives

  • Browse and access a range of data types from leading public repositories
  • Use bioinformatics tools to explore plant and pathogen-related biological data


Time Topic Trainer
Day 1 – Monday 23 May 2016
09:45 Registration and tea/coffee  
10:00 An introduction to the EBI Annalisa Mupo
10:30 Ensembl Plants Denise Carvalho-Silva
12:30 Lunch  
13:30 PhytoPath Helder Pedro
14:15 PHI-base Kim Hammond-Kosack and Martin Urban
15:00 Tea/Coffee Break  
15:30 WormBase ParaSite Bruce Bolt
16:30 Pathogen genome data Leighton Pritchard
17:30 Poster session  
19:00 Dinner at Hinxton Hall  
Day 2 - Tuesday 24 May 2016
09:00 Introduction to high-throughput sequencing technologies Thomas Smith
10:00 The European Variation Archive Cristina Yenyxe Gonzalez
10:30 Tea/Coffee Break  
11:00 QC and Variant calling Dan Bolser
12:30 Lunch  
13:30 QC and Variant calling cont… Dan Bolser
14:30 A hands-on introduction and tutorial to Genome Wide Association Studies (GWAS) Ümit Seren (GMI)
15:30 Tea/Coffee Break  
16:00 A hands-on introduction and tutorial to Genome Wide Association Studies (GWAS) cont… Ümit Seren (GMI)
17:30 Free time  
19:00 Dinner at the Red Lion Hinxton  
Day 3 - Wednesday 25 May 2016
09:00 Exploring transcriptomics data with ArrayExpress and Gene Expression Atlas  Laura Huerta Martinez and Melissa Burke
10:30 Tea/Coffee Break  
11:00 RNA Assembly  Steve Kelly
12:00 Course feedback and wrap up Annalisa Mupo

Lunch and departure - Coach leaves for Cambridge Train Station at 12:45