Introduction to Omics data integration

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Date:

 Tuesday 7 Friday 10 March 2017

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Wednesday October 05 2016

Application deadline: 

Friday January 13 2017

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

£500 (fee includes 3 nights accommodation)

Registration closed

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Overview

With the increase in the volume of data across the whole spectrum of biology, more researchers are looking to integrate data of different types to inform hypotheses and biological questions. This may also include public domain data, which can provide added value to data derived through researcher’s own work. This course will provide participants with biological examples of data integration, and the challenges that researchers face. The course will focus on the use of public data resources and open access tools for enabling integrated working, with an emphasis on data visualisation.

Audience

This course is aimed at biologists who have some experience of working with at least one type of omics data, and computational biologists / bioinformaticians who wish to gain a better understanding of the biological challenges when working with integrated datasets.   No programming or command line experience is required to attend this course, but please note this course does not cover statistical approaches for data integration.

Syllabus, tools and resources

During this course you will learn about:

  • Data standards, curation and ID mapping
  • Quality control for data integration
  • Analysis and visualistion: Cytoscape, Genestack/KnetMiner, InterMine, Open Targets, Omics DI
  • Challenges and best practice for working in an integrated manner with genomic, transcriptomic, and proteomic data

Outcomes

At the end of the course you should be able to:

  • Discuss motivations for working in an integrated manner
  • Comprehend the importance of data standards and the collection of metadata
  • Identify challenges for bring different data types together
  • Use a range of bioinformatics tools to integrate and visualise biological data

Programme

Time Topic Trainer
Day 1 - 
08:45 - 9:15 Registration  
09:15 - 09:30 Welcome and introduction Melissa Burke
09:30 - 10:30 Introduction to data integration – Why, how, promise and pitfalls Lee Larcombe
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 Group activity: designing a data integration study Brandon Invergo
12:30 - 13:30 Lunch  
13:30 - 15:00 Quality issues – data standards, curation, ontologies and metadata  Sandra Orchard
15:00 - 15:30 Tea/coffee break  
15:30 - 17:00 A brief introduction to the nature of different data types  Tamás Korcsmáros
17:00 - 18:00 Keynote – Integration in public resources: Expression Atlas Amy Tang
19:00 Evening meal   
Day 2 - 
09:00 - 10:00 Open Targets  Denise Carvalho-Sliva
10:00 - 10:30 Tea/coffee break  
10:30 - 11:30 Open Targets – hands on example Denise Carvalho-Sliva
11:30 - 12:30 Omics discovery index Yasset Perez-Riverol
12:30 - 13:30 Lunch  
13:30 - 15:00 Open tools for data integration – hands on example with InterMine  Rachel Lyne
15:00 - 15:30 Tea/coffee break  
15:30 - 16:30 Open tools for data integration – hands on example with InterMine  Rachel Lyne
16:30 - 17:30 Case study lecture  Evangelia Petsalakis
18:30 Evening meal  
Day 3 - 
09:00 - 10:30

ID mapping

Pablo Porras

10:30 - 11:00 Tea/coffee break  
11:00 - 12:30

GENESTACK platform for omics data analysis and integration

Keywan Hassani-Pak, Ajit Singh, Misha Kapushesky, Kevin Dialdestoro
12:30 - 13:30 Lunch   
13:30 - 15:00 KnetMiner App for network mining and candidate gene discovery Keywan Hassani-Pak, Ajit Singh, Misha Kapushesky, Kevin Dialdestoro
15:00 - 15:30 Tea/coffee break  
15:30 - 17:00 Metabolomics and data integration Thomas Lawson
17:00 - 18:00 The IMPC: Large-Scale Phenotyping Analysis to Provide insight into Human Disease Terry Meehan
19:00  Evening meal  
Day 4 - 
09:00 - 10:30 Hands-on data integration with Cytoscape Pablo Porras, David Fazekas
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 Hands-on data integration with Cytoscape Pablo Porras, David Fazekas
12:30 - 13:30 Lunch  
13:30 - 15:00 Hands-on data integration with Cytoscape Pablo Porras, David Fazekas
15:00 - 15:30 Tea/coffee break  
15:30 - 16:00 Course wrap-up and feedback Melissa Burke
16:00 Bus to Cambridge train station