EMBL-EBI: Exploring bioinformatics resources, sequence and genomic data

Date:

 Monday 18 Tuesday 19 September 2017

Venue: 

The Francis Crick Institute - 1 Midland Road, London,  NW1 1AT, United Kingdom

Application opens: 

Tuesday May 23 2017

Application deadline: 

Tuesday May 23 2017

Participation: 

By invitation

Contact: 

Derrin Crawte

Registration closed

Course Overview

This course is divided into three sessions that introduce researchers to EMBL-EBI, major databases and tools for sequence searching.

Session one focuses on a general overview of the major bioinformatics resources and tools and EMBL-EBI and on helping researchers to identify resources to use in areas of interests. This will involve presentations and practical activities to give participants experiences on searching and retrieving data. Session two introduces sequence similarity searching and focuses on how to use tools like BLAST and PSI-Search to find homologous sequences in EMBL-EBI databases, including tips on which tool and database to use. Session three offers hands-on experiences in using the Ensembl/Ensembl Genomes browsers including viewing, manipulating genomic data and handling bulk data using BioMart.

Audience

The course has been designed for bench - based (wet-lab) researchers with minimum or no prior experience in bioinformatics and would like to explore, and use EMBL-EBI resources to handle and interpret the genomic and sequence data.

There are no specific prerequisites for the course, however an undergraduate level knowledge in life sciences would be beneficial.

Modules and resources

During this course you will learn about:

  • EMBL-EBI bioinformatic resources
  • Sequence searching and alignments
  • Ensembl/Ensembl Genome

Learning outcomes

After this course you should be able to:

  • Use a variety of EMBL-EBI tools and resources to search and link genomic and small molecule data from different databases.
  • Perform and assess sequence searching against EMBL-EBI databases using a variety of tools such as BLAST and PSI-SEARCH.
  • Access different data types available in the Ensembl/Ensembl Genomes, view and explore data in the Ensembl browser

Programme

Time Topic Trainer
Day 1 - 18th September 2017
13:15 Welcome and Introduction  Sarah Morgan
13:30 - 15:00 Introduction to EMBL-EBI resources  Sarah Morgan
15:00 - 15:30 Tea/coffee break  
15:30 - 17:00 EMBL-EBI search tool  Sarah Morgan
17:00  End of Day 1  
Day 2 - 19th September 2017
09:00 - 10:30 Introduction to Sequence searching  Andrew Cowley
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 Sequence searching  Andrew Cowley
12:30 - 13:30 Lunch  
13:30 - 15:00

Introduction to the Ensembl/Ensembl Genomes

Ensembl Gene and Transcript Annotation

 Benjamin Moore
15:00 - 15:30 Tea/coffee break  
15:30 - 17:00 Ensembl Gene and Transcript Annotation Benjamin Moore
17:00

Wrap-up and feedback

End of course

 Benjamin Moore