Introduction to Integrative Omics

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Date:

 Monday 7 Thursday 10 March 2016

Venue: 

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

Application opens: 

Friday September 18 2015

Application deadline: 

Thursday December 31 2015

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

£500

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 with experience of working with at least one type of omics data. Computational biologists are welcome to attend but please note that the course will not cover computational 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, Ondex/QTLNetMiner, InterMine
  • 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 - Monday 7th March 2016
08:45 - 09:00 Registration  
09:00 - 09:30 Welcome and introduction Annalisa Mupo, EMBL-EBI
09:30 - 10:30  Introduction to data integration – Why, how, promise and pitfalls Lee Larcombe, Elixir-UK
10:30 - 11:00 Break  
11:00 - 12:30 Group activity: designing a data integration study Brandon Invergo, EMBL-EBI
12:30 - 13:30 Lunch  
13:30 - 14:45 Quality issues – data standards, curation, ontologies and metadata Sandra Orchard, EMBL-EBI
14:45 - 16:00 A brief introduction to the nature of different data types Tamás Korcsmáros, TGAC-UK
16:00 - 16:30 Tea/coffee break  
16:30 - 17:30 Keynote I – Integration in public resources: Expression Atlas Amy Tang, EMBL-EBI
17:30 - 19:00 Poster session I  
19:00 Evening meal on campus  
Day 2 - Tuesday 8th March 2016
09:30 - 11:00 Using integrative omics: a case study Bissan Al-Lazikani, Institute of Cancer Research
11:00 - 11:30 Tea/coffee break  
11:30 - 12:30 Open tools for data integration – hands on example with InterMine Rachel Lyne, University of Cambridge
12:30 - 14:00 Lunch and poster session II  
14:00 - 16:00 Open tools for data integration – hands on example with InterMine cont… Rachel Lyne, University of Cambridge
16:00 - 16:30 Tea/coffee break  
16:30 - 17:30 Keynote Lecture II Laurent Gatto, University of Cambridge
18:00 Evening meal on campus  
Day 3 - Wednesday 9th March 2016
09:00 - 10:30 Data integration using Ensembl Benjamin Moore, EMBL-EBI
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 Open tools for data integration – hands on example with Ondex/QTLNetMiner hands on Keywan Hassani-Pak, Rothamsted Research-UK
12:30 - 13:30 Lunch -  
13:30 - 15:00 Open tools for data integration – hands on example with Ondex/QTLNetMiner cont… Keywan Hassani-Pak
15:00 - 15:30 Tea/coffee break  
15:30 - 16:30 Open tools for data integration – hands on example with Ondex/QTLNetMiner cont… Keywan Hassani-Pak
16:30 - 17:00 ID mapping Pablo Porras, EMBL-EBI
17:00 - 18:00 Keynote Lecture III Aleksej Zeleniak, University of Cambridge
18:30 Evening meal on campus  
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 cont… Pablo Porras / David Fazekas
12:30 - 13:30 Lunch  
13:30 - 15:00 Hands-on data integration with Cytoscape cont… Pablo Porras / David Fazekas
15:30 - 16:00 End of course wrap up and feedback  
16:00 Bus to Cambridge train station  
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

At EMBL-EBI, we manage the world’s public biological data and make it freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. Set on the beautiful Wellcome Genome Campus near Cambridge in the UK, we support scientists throughout the world in seeking solutions to challenges in healthcare, agriculture and the environment.

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How to apply

In order to be considered for a place on this course applicants must do the following:

  1. Complete the online application form.
  2. Submit a PDF document to frank@ebi.ac.uk containing a short biography including your work history and a description of your current research interests. Each document should be no longer than 150 words.
  3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course.

Further details will be provided on your confirmation email after completing the online form.

Incomplete applications will NOT be considered. Please read through the following guidance document for more information on how to complete your application.

Application deadline

31 December 2015

Number of places

30 places

Registration closed

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Organisers

Annalisa Mupo

Pablo Porras Millan

Trainers

Lee Larcombe - ELIXIR-UK

Brandon Invergo - EMBL-EBI, UK

Sandra Orchard - EMBL-EBI, UK

Tamas Korcsmáros - TGAC, UK

Rachel Lyne - University of Cambridge

Bissan Al-Lazikani - ICR, London, UK

Laurent Gatto - University of Cambridge

Keywan Hassani-Pak - Rothamsted Research, UK

Pablo Porras Millan - EMBL-EBI, UK

Benjamin Moore - EMBL-EBI, UK

Amy Tang - EMBL-EBI, UK

Annalisa Mupo - EMBL-EBI, UK

Aleksej Zelezniak - University of Cambridge

Fazekas David - University of Budapest

Materials & attachments