EMBL-EBI Bioinformatics Resources and Biological Networks Workshop

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Date:

 Thursday 1 Saturday 3 June 2017

Venue: 

National University of Kyiv-Mohyla Academy - Hryhoriya Skovorody St 2, Kiev,  04070, Ukraine

Application opens: 

Thursday April 13 2017

Application deadline: 

Sunday April 30 2017

Participation: 

By invitation

Contact: 

Derrin Crawte

Registration fee: 

£0

Registration closed

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Course Overview

This course has been designed specifically for researchers  in the biological sciences working at research institutions and universities in Kyiv, Ukraine to enable them to learn more about the bioinformatics resources and tools available at EMBL-EBI. 

In the first part of the course, participants will be introduced to the resources EMBL-EBI provides, focusing on the resources for genome browsing, protein data and sequence search. The second part will introduce the concept of reproducible research and explore approaches to study genetic variation and relevant resources.  Next, the focus will shift to the functional annotation of gene products (Gene Ontology), protein-protein interactions and the use of Cytoscape to visualise networks.

Activities will include presentations by the trainers and webinars presented by EBI staff in Hinxton, UK, demonstrations and practical exercises for trainees aimed to illustrate the use of the tools.

Audience

This workshop is aimed at postgraduate students and researchers worlking in the biological sciences who would like to explore and use open bioinformatics resources provided by EMBL-EBI to enhance their research, and who have a minimum or no prior experience in bioinformatics. 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:

  • Ensembl
  • UniProt
  • Sequence similarity searching
  • Variation resources: GWAS Catalog, ExAC, gnomAD
  • Gene Ontollogy and enrichment analysis
  • Protein interactions and cytoscape

Learning outcomes

After this course you should be able to:

  • Search EMBL-EBI resources to find appropriate data and tools for your research
  • Access and explore data within Ensembl, UniProt and the GWAS Catalog
  • Use sequence similarity tools and select appropriate tools for different applications
  • Perform enrichment analysis on a set of proteins using the Gene Ontology
  • Import, visualise and perform basic analysis on a protein interaction network using Cytoscape.

Programme

 

Time Topic Trainer
Day 1 - 31 May 2017
TBA

Introduction to EMBL-EBI resources - (Lecture)

Vitalii Kleshchevnikov

Veronika Kedlian

Day 2 - 01 June 2017
11:00 Welcome and Introduction
 
11:15-12:10 Exploring EMBL-EBI resources using search tool
Vitalii Kleshchevnikov

Veronika Kedlian

12:10-12:30 Tea and coffee
 
12:30-14:00 Ensembl: introduction, genes and transcripts
Emily Perry (webinar)

Vitalii Kleshchevnikov

Veronika Kedlian

14:00-15:00 Lunch  
15:00-16:30

Ensembl: variation data and Variant Effect Predictor

or

Comparative genomics and variation data
Emily Perry (webinar)

Vitalii Kleshchevnikov

Veronika Kedlian

16:30-17:00 Tea and coffee
 
17:00-19:00 UniProt

Sangya Pundir (webinar)

Vitalii Kleshchevnikov

Veronika Kedlian

19:00 End of Day 2
 
Day 3 - 02 June 2017
11:00-12:30 An introduction to sequence searching
 
 

Andrew Cowley (webinar)

Vitalii Kleshchevnikov

Veronika Kedlian
12:30-13:00 Tea and coffee  
13:00-14:30 An introduction to sequence searching
 

Andrew Cowley (webinar)

Vitalii Kleshchevnikov

Veronika Kedlian
14:30-15:30 Lunch  
15:30-16:10 What is the purpose of research? reproducible research and statistics
Vitalii Kleshchevnikov
16:10-17:30 Genetic variation and approaches to study it
Veronika Kedlian
17:30-18:00 Tea and coffee  
18:00-19:30 Use of GWAS Catalog, ExAC, gnomAD
 
Veronika Kedlian
19:30 End of day 3  
Day 4 - 03 June 2017
11:00-12:00 Introduction to Gene Ontology
Vitalii Kleshchevnikov
12:00-12:30 Tea/coffee break  
12:30-13:15 Gene Ontology enrichment
Vitalii Kleshchevnikov
13:15-14:15 Lunch -  
14:15-15:45 Introduction to protein interaction networks
Vitalii Kleshchevnikov
15:45-16:05 Tea/coffee break  
16:05:17:30 Exploring protein interaction network in Cytoscape
Vitalii Kleshchevnikov
17:30-17:45 Tea and coffee  
17:45-19:00 Exploring protein interaction network in Cytoscape
Vitalii Kleshchevnikov
19:00-19:30 Wrap up and feedback

Vitalii Kleshchevnikov

Veronika Kedlian

19:30 End of workshop