Introduction to Integrative Omics

Date:

 Tuesday 3 Friday 6 March 2015

Venue: 

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

Application opens: 

Friday 21 November 2014

Application deadline: 

Friday 30 January 2015

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

£300

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 be public domain data which researchers themselves have not generated, but can provide added value to datasets derived through their own work. This course will provide participants with an overview of working with a number of ‘omics’ data types in a more integrated manner; considering both its potential and caveats. 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 researchers who either have multiple omic datasets which they wish to interpret in an integrated manner, or those who wish to explore public datasets to “add-value” to those which they have generated themselves. The course assumes you will have a minimum of one year’s experience working with at least one type of omics data.

Syllabus, tools and resources

During this course you will learn about:

  • Data standards, curation and ID mapping
  • Quality control for data integration
  • Public resources for data access
  • Analysis and visualistion: Cytoscape, Ondex/QTLNetMiner, InterMine
  • Challenges and best practice for working in an integrated manner with genomic, transcriptomic, proteomic and metabolomic 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 - Introduction to integration - Tuesday 3 March 2015
09:00 - 09:30 Welcome and introduction  Laura Emery
09:30 - 10:30 Introduction to data integration – Why, how, promise and pitfalls  Lee Larcombe, University of Oxford
10:30 - 11:00 Tea/coffee break  
11:00 - 12:00 Group Activity  BPA Trainers
12:00 - 13:00 Lunch  
13:00 - 14:15 Quality issues – data standards, curation, ontologies and metadata  Sandra Orchard
14:15 - 15:00 Identifier mapping  Pablo Porras
15:00 - 15:30 Tea/coffee break  
15:30 - 16:30 Accessing public resources  BPA Trainers
16:30 - 17:30 Keynote I – Integration in public resources: Expression Atlas  Amy Tang
18:30 Evening Meal @ Wellcome Trust Conference Centre  
Day 2 - Genomics and Transcriptomics - Wednesday 4 March 2015
09:00 - 10:30 The nature of genomic data – caveats for integration Leo Goodstadt,  University of Oxford
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 The nature of transcriptomic data – caveats for integration Jelena Aleksic, GeneAdviser 
12:30 - 14:30 Lunch and poster session  
14:30 - 16:00 Open tools for data integration – hands on example with InterMine  Rachel Lyne, University of Cambridge
16:00 - 16:30 Tea/coffee break  
16:30 - 17:30 Open tools for data integration – hands on example with InterMine cont…  Rachel Lyne, University of Cambridge
17:30 - 18:00 Keynote Lecture II  Laurent Gatto, University of Cambridge
19:00 Evening meal  
Day 3 - Thursday 5 March 2015
09:00 - 10:30 The nature of proteomics data – caveats for integration  Kathryn Lilley / Laurent Gatto, University of Cambridge
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 The nature of metabolomics data – caveats for integration  Reza Salek
12:30 - 13:30 Lunch  
13:30 - 15:00 Open tools for data integration – hands on example with Ondex/QTLNetMiner  Keywan Hassani-Pak, Rothamsted
15:00 - 15:30 Tea/coffee break  
15:30 - 17:30 Open tools for data integration – hands on example with Ondex/QTLNetMiner cont…  Keywan Hassani-Pak, Rothamsted
17:30 Keynote III - Industry  Richard Stark, SEAC, Unilever
19:00 Evening meal  
Day 4 - Friday 6 March 2015
09:00 - 10:30 Hands-on data integration with Cytoscape  Pablo Porras / Tamás Korcsmaros
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 Hands-on data integration with Cytoscape cont…  Pablo Porras / Tamás Korcsmaros
12:30 - 13:30 Lunch  
13:30 - 15:30 Hands-on data integration with Cytoscape cont…  Pablo Porras / Tamás Korcsmaros
15:30 - 16:00 End of course wrap up and feedback  
16:30 Free coach to Cambridge train Station