Plant and Pathogen Bioinformatics

Date:

 Monday 13 Wednesday 15 November 2017

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday June 12 2017

Application deadline: 

Friday August 25 2017

Participation: 

Open application with selection

Contact: 

Emily Rees

Registration fee: 

£430

Overview

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.

Audience

This course is aimed at biologists studying plants and/or plant pathogens, with little previous experience in bioinformatics, and who are seeking to incorporate some bioinformatics in their work.

Syllabus, tools and resources

During this course you will learn about:

  • Genome browsing: Ensembl, Ensembl genomes
  • Basic NGS analyses: QC, variant calling
  • Analyses for Genome-wide association studies
  • Exploring plant-pathogen interactions

Outcomes

After this course you should be able to:

  • Browse and access a range of   data types from leading public repositories
  • Use bioinformatic tools to explore plant and pathogen-related biological data
  • Discuss the benefits and limitations of various bioinformatic techniques
  • Assess the purpose of specific  analyses in a wider context

Programme

Time Topic Trainer
Day 1 - Monday 13 November 2017
09:00 - 10:00 Registration and tea/coffee  
10:00 - 10:30 An Introduction to EBI Laura Emery
10:30 - 12:30 Ensembl Plants  Team Ensembl
12:30 - 13:30 Lunch  
13:30 - 15:00 Exploring Plant Pathogen Interactions Leighton Pritchard 
15:00 - 15:30 Tea/coffee break  
15:30 - 16:30 Introduction to high-throughput sequencing technologies  Thomas Smith 
16:30 - 17:30 Genome assembly in wheat  Matthew Clark 
17:30 - 19:00 Poster session  
19:00 Evening meal @ Hinxton Hall  
Day 2 - Tuesday 14 November 2017
09:00 - 10:30 QC  Dan Bolster
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 Hands-on tutorial on SNP calling and data interpretation Georg Haberer and Manuel Spannagl 
12:30 - 13:30 Lunch  
13:30 - 14:45 Hands-on tutorial on SNP calling and data interpretation Georg Haberer and Manuel Spannagl
14:45 - 15:15 Tea/coffee break  
15:15 - 19:00 A hands-on introduction and tutorial to Genome Wide Association Studies (GWAS) Arthur Korte (GMI)
19:00 Evening meal @ Red Lion, Hinxton  
Day 3 - Wednesday 15 November 2017
09:00 - 10:30 Exploring plant transcriptomics data with Expression Atlas Laura Huerta 
10:30 - 11:00 Tea/coffee break  
11:00 - 13:00 Using KnetMiner to explore biological data in plants Keywan Hassani-Pak 
13:00 Course feedback and wrap up