EMBL-EBI resources and tools for genomics and proteomics

Date:

 Monday 4 Friday 8 December 2017

Venue: 

National Veterinary Research Institute - Państwowy Instytut Weterynaryjny, Państwowy Instytut Badawczy, Aleja Partyzantów 57, 24-100,  Puławy, Poland

Participation: 

By invitation

Contact: 

Malgorzata Olejnik

Registration closed

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Course Overview

In this course participants, will explore EMBL-EBI data and resources for genomes, functional genomics, sequences, protein structure and function, and protein-ligand interactions. The course is divided into two parts:

Part I Genomics: The sessions focus on accessing, retrieving genomic data for a variety of organisms from Ensembl/Ensembl genome browser, functional genomics data in ArrayExpress, gene expression in Expression Atlas, and Metagenomics data available at EMBL-EBI.

Part II Proteomics: The sessions take the participants through EMBL-EBI protein resources focusing on the study of protein sequences in UniProt database, accessing functional protein classification data in InterPro, and finding and analysing macromolecular structures in PDBe.

The course will be delivered by experienced and dedicated EMBL-EBI trainers, and will involve presentations, demonstrations and practical exercises to give participants hands on experiences. Participants will have the opportunity to address some of their research question and use examples from their work.

Audience

The course is aimed at wet-lab researchers at the NVRI who have minimum or no prior experience in bioinformatics, interested in exploring and using 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:

  • Cross domain: Sequence search and alignment
  • Genomics: Ensembl,  ArrayExpress and Expression Atlas, Metagenomics
  • Proteomics: UniProt,  InterPro and PDBe

Learning outcomes

After this course, you should be able to:

  • Perform sequence search and alignment using specific tools
  • View and explore data in the Ensembl/Ensembl genome browser
  • Explore gene expression analysis results across species and biological conditions
  • Use PDBe to find macromolecular structures and analyse structures using PDBe tools, including PDBeFOLD to search for structure similarity.

Programme

Time

Subject

Trainer

Day 1 – 4th Dec 2017

9:00

Welcome and Introduction

 

Part I: Genomics and Sequences

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

Ensembl/Ensembl genome browser

Ben Moore

12:30-13:30

Lunch

 

13:30-15:00

Ensembl/Ensembl genome browser

Ben Moore

15:00 – 15:30

Tea and coffee

 

15:30-17:00

Ensembl/Ensembl genome browser

Ben Moore

17:00

End of Day 1

 

Day 2 – 5th Dec 2017

9:00 - 10:30

Sequence Searching and Alignments

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 – 6th Dec 2017

9:00 - 10:30

ArrayExpress: public archive for functional genomics data

Laura Huerta

10:30 -  11:00

Tea and coffee

 

11:00 -12:30

ArrayExpress: Data submission using Annotare

Laura Huerta

12:30 -13:30

Lunch

 

13:30 -15:00

Expression Atlas: gene expression data across species and biological conditions

Laura Huerta

15:00 - 15:30

Tea and coffee

 

15:30 -17:00

Expression Atlas: Practical session

Laura Huerta

17:00

End of day 3

 

Day 4 – 7th Dec 2017

Part II: Proteomics

9:00 - 10:30

UniProt

Sangya Pundir

10:30 -11:00

Tea and Coffee break

 

11:00 - 12:30

UniProt

Sangya Pundir

12:30 - 13:30

Lunch

 

13:30 -15:00

PDBe

David Armstrong

15:00 - 15:30

Tea and coffee break

 

15:30 – 17:00

PDBe

David Armstrong

17:00

End of day

 

Day 5 – 8th Dec 2017

9:00 - 10:30

InterPro

Lorna Richardson

10:30 -11:00

Lunch

 

11:00 - 12:30

InterPro

Lorna Richardson

12:30 - 13:30

Lunch

 

13:30 -15:00

Metagenomics

Alex Mitchell

15:00 - 15:30

Tea/Coffee

 

15:30 – 17:00

Metagenomics

Alex Mitchell

17:00

Wrap up & feedback

Lorna Richardson and Alex Mitchell