EMBL-EBI: Exploring genomic, protein and chemical data, Oviedo

Date:

 Monday 15 Friday 19 May 2017

Venue: 

University of Oviedo - Calle San Francisco 1, 33003,  Oviedo,  Asturias, Spain

Participation: 

By invitation

Contact: 

Frank O’Donnell

Registration closed

Course Overview

This workshop has been organised for PhD students, Postgraduates and Faculty members within the Departments of Biochemistry, Cell Biology, Ecology, Food Biotechnology, Genetics, Medicine, and Microbiology, at University of Oviedo, Spain.
Participants will explore EMBL-EBI resources for genome browsing, gene expression, protein structure and protein-ligand interactions, diseases, targets and small molecules to illustrate how to navigate from one tool to the other. Activities will include presentations by the trainers, demonstrations and practical exercises by trainees to illustrate the use of the tools. Case studies will be used to demonstrate how to access relevant data and help answer research questions.

Audience

The sessions are aimed at wet-lab researchers within the Departments of Biochemistry, Cell Biology, Ecology, Food Biotechnology, Genetics, Medicine, and Microbiology who have minimum or no prior experience in bioinformatics, who want to explore, and use EMBL-EBI resources for their research. No knowledge of programming is required, but an undergraduate level knowledge of biology and/or biochemistry would be beneficial.

Modules and resources

During this course you will learn about:

  • Sequence searching and alignments
  • Ensembl/Ensembl genome
  • Gene expression: Expression Atlas
  • Macromolecular Structure: PDBe and EMDB
  • ChEMBL, Open Targets, ChEBI, Enzyme Portal

Learning outcomes

After this course you should be able to:

  • Use the EMBL-EBI search tool to access genome, protein and chemical data
  • Perform and assess sequence searching against EMBL-EBI databases using a variety of tools such as BLAST and PSI-SEARCH and sequence alignments using tools such as Clustal Omega and MUSCLE.
  • Access different data types available in the Ensembl/Ensembl Genomes genome browsers
  • View and explore data in the Ensembl browser
  • Use Expression Atlas to search for gene expression analysis results across species and biological conditions
  • Use PDBe and EMDB to find macromolecular structures, assess their quality and relate the structure to function
  • Analyse structures with PDBe tools, including PDBeFOLD to search for structure similarity.
  • Search, and extract chemical and bioactivity data including protein targets, from the small molecule databases.

 

Programme

Time

Subject

Trainer

Day 1 – 15th May 2017

9:00

Welcome and Introduction

 

9:10 - 10:30

Introduction to EBI resources, EMBL-EBI search tool

Ben Moore

10:30 - 11:00

Tea and Coffee

 

11:00 - 12:30

Introduction to the Ensembl/Ensembl Genomes genome browsers

Ben Moore

12:30 - 13:30

Lunch

 

13:30 - 15:00

Ensembl Gene and Transcript Annotation

Ben Moore

15:00 - 15:30

Tea and coffee

 

15:30 - 17:00

Ensembl tools: BioMart and the VEP

Ben Moore

17:00

End of Day 1

 

Day 2 – 16th  May 2017

9:00 - 10:30

Introduction to Sequence searching

Andrew Cowley

10:30 - 11:00

Tea and coffee

 

11:00 - 12:30

Sequence searching and alignments

Andrew Cowley

12:30 - 13:30

Lunch

 

13:30 - 15:00

Sequence searching and alignments

Andrew Cowley

15:00 - 15:30

Tea and Coffee

 

15:30 - 17:00

Sequence searching and alignments

Andrew Cowley

17:00

End of Day 2

 

Day 3 – 17th May 2017

9:00 - 10:30

Introduction to Expression Atlas

Laura Huerta

10:30 - 11:00

Tea and coffee

 

11:00 - 12:30

Exploring gene expression data using Expression Atlas

Laura Huerta

12:30 - 13:30

Lunch

 

13:30 -15:00

Introduction to ChEMBL, SureChEMBL and Open Targets

Anna Gaulton

15:00 - 15:30

Tea and coffee

 

15:30 -17:00

Selecting the best drug targets: exploring disease, drug and target information

Anna Gaulton

17:00

End of day 3

 

Day 4 – 18th May 2017

9:00 - 12:30

Finding and assessing quality of macromolecular structures at the PDBe

David Armstrong

10:30 - 11:00

Tea and Coffee

 

11:-00 - 12:30

Using PDBe tools to relate structure to function

David Armstrong

12:30 - 13:30

Lunch

 

13:30 -15:00

PDBeFOLD: search for structural similarity between proteins

David Armstrong

15:00 -15:30

Tea and coffee

 

15:30 -17:00

Finding and viewing EM data at the PDBe and EMDB

David Armstrong

17:00

End of day

 

Day 5 – 19th May 2017

9:00 - 10:30  

Introduction to ChEBI and the ChEBI Ontology

Gareth Owen

10:30 - 11:00

Tea and coffee

 

11:00 - 12:30

Introduction to Enzyme resources and the Enzyme Portal

Gareth Owen

12:30 - 13:30

Lunch

 

13:30 -14:00

The Enzyme Portal and Brenda

Gareth Owen

14:00 - 15:30

Introduction to MetaboLights

 

Keeva Cochrane

 

15:30 - 16:00

Wrap up and feedback

Keeva Cochrane and

Gareth Owen

16:00

End of Workshop