Plant and Pathogen Bioinformatics

Date:

 Tuesday 8 - Friday 11 July 2014

Venue: 

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

Application deadline: 

Friday 02 May 2014

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£100

Registration closed

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 or no 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
  • Sequence searching: Blast, FASTA
  • Alignment: Clustal Omega
  • Interactions and pathways: IntAct, Reactome, Cytoscape
  • Small molecule resources: ChEMBL

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

Additional information

AllBio sponsored travel bursaries are available for applicants currently working in EU based institutions on research that is non-human / non-medical in nature. Please fill the relevant boxes within the application if you wish to be considered for a travel bursary.

Programme

Time Topic Trainer
Day 1 - Tuesday 8 July 2014
12:30 Registration and lunch  
13:00 An introduction to the EBI Laura Emery 
13:30 Plant genome data Paul Kersey 
14:30 Tea/coffee break  
15:00 Pathogen genome data Leighton Pritchard
16:00 Participants’ Presentation Participants 
17:00 Using comparative genomics to understand parasite adaptation to different host environments Steve Kelly
18:00 Networking activity Laura Emery 
18:45 Coach pickup from main campus bus stop (by campus entrance)
  
19:30 Offsite Course Dinner at Sidney Sussex College, Cambridge
  
22:00 Return transport to conference centre  
Day 2 - Wednesday 9 July 2014
09:00 Browsing plant genomes with Ensembl Emily Pritchard
11:00 Tea/coffee break  
11:30 Browsing plant and pathogen genomes with Ensembl genomes Emily Pritchard
12:30 Additional genomics data resources Paul Kersey team
13:00 Lunch and poster session  
14:30 An introduction to alignment Andrew Cowley
16:00 Tea/coffee break  
16:30 An introduction to alignment Andrew Cowley
18:30 Close  
Day 3 - Thursday 10 July 2014
09:00  An introduction to high-throughput sequencing technology Thomas Smith
09:45 ArrayExpress, a public database for functional genomics data
  
10:30 Tea/Coffee break  
11:00 Gene Expression Atlas, a public database for functional genomics data Amy Tang
12:30  Lunch  
13:30  Functional analysis with InterPro  Alex Mitchell 
15:00  Tea/coffee break   
15:30  Data resources for exploring interactions and pathways Sandra Orchard 
17:30  Close  
Day 4 - Friday 11 July 2014
09:00 Exploring interactions with Cytoscape  Pablo Porras 
10:30  Tea/coffee break   
11:00  Exploring interactions with Cytoscape  Pablo Porras 
12:30  Lunch   
13:30  Exploring ChEMBL for plants and pathogens Louisa Bellis 
15:30  Course wrap-up and feedback  Laura Emery 
16:00  Close   
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

At EMBL-EBI, we manage the world’s public biological data and make it freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. Set on the beautiful Wellcome Genome Campus near Cambridge in the UK, we support scientists throughout the world in seeking solutions to challenges in healthcare, agriculture and the environment.

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In association with

How to apply

Registration for this course has now closed.

Application deadline

02 May 2014

Number of places

30 places

Registration closed

Organisers

Paul Kersey

Laura Emery

Trainers

Leighton Pritchard - The James Hutton Institute, United Kingdom

Thomas Smith - EMBL-EBI, UK

Laura Emery - EMBL-EBI, UK

Paul Kersey - EMBL-EBI, UK

Alex Mitchell - EMBL-EBI, UK

Sandra Orchard - EMBL-EBI, UK

Amy Tang - EMBL-EBI, UK

Steven Kelly - The University of Oxford, Department of Plant Sciences, UK

Pablo Porras Millan - EMBL-EBI, UK

Louisa Bellis - EMBL-EBI, UK