Course at EMBL-EBI

Introduction to multiomics data integration

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With the increase in the volume of data across the whole spectrum of biology, more researchers are looking to integrate omics 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 and inform experimental design. This introductory course will highlight the challenges that researchers face in integrating multiomics data sets using biological examples. 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. Please note this course does not cover statistical approaches for data integration.

Who is this course for?

This introductory course is aimed at biologists who are embarking on multiomics projects 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. Please note this course does not cover statistical approaches for data integration.

For advanced-level training in using large-scale multiomics data and machine learning to infer biological models you may wish to consider our course on Systems Biology: From large datasets to biological insight.

What will I learn?

Learning outcomes

After this 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 bringing different data types together
  • Use a range of bioinformatics tools to organise and visualise biological data
Course content

During this course you will learn about:

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

Trainers

Ricard Argelaguet
EMBL-EBI, UK
Danila Bredhkin
EMBL Heidelberg, Germany
Nils Eling
EMBL-EBI, UK
Girolamo Giudice
EMBL-EBI, UK
David Fazekas
University of Budapest, Hungary
Asier Gonzalez
EMBL-EBI, UK
Francesco Iorio
Wellcome Sanger Institute, UK
Andrew Jarnuczak
EMBL-EBI, UK
Tamas Korcsmáros
Earlham Insititute, UK
Lee Larcombe
Amphimatic, UK
Rachel Lyne
University of Cambridge, UK
Hanna Najgebauer
EMBL-EBI, UK
Sandra Orchard
EMBL-EBI, UK
Pablo Porras Millan
EMBL-EBI, UK
Claire O’Donovan
EMBL-EBI, UK
Yasset Perez Riverol
EMBL-EBI, UK
Masa Roller
EMBL-EBI, UK
Michaela Spitzer
EMBL-EBI, UK

Programme

Day 1 – Tuesday 12 February 2019
09:45-10:15 Arrival and tea/coffee  
10:15-10:30 Welcome and introductions Melissa Burke
10:30-12:00 Multiple ways to integrate multi-omics data - case studies from studying human diseases Tamás Korcsmáros
12:00-13:00 Lunch  
13:00-14:30 Group Activity All
14:30-15:30 ID Mapping Pablo Porras
15:30-16:00 Tea/coffee break
16:00-17:30 Quality issues – data standards, curation, ontologies and metadata Sandra Orchard
17:30-18:30 Room check-in  
18:30 Dinner at the Wellcome Trust  
Day 2 – Wednesday 13 February 2019
08:45 Arrival  
09:00-10:00 Open Targets introduction and hands on

Michaela Spitzer

Asier Gonzales

10:00-10:30 Tea/Coffee Break
10:30-11:30 Omics Discovery Index Yasset Perez-Riverol
11:30-12:30 Integrated characterization of human cancer using public omics (proteomics, transcriptomics, drug sensitivity) data Andrew Jarnuczak
12:30-13:30 Lunch
13:30-15:00 Open tools for data integration – hands on example with InterMine Rachel Lyne and InterMine team members
15:00-15:30 Tea/Coffee Break  
15:30-17:00 Open tools for data integration – hands on example with InterMine - continued Rachel Lyne and InterMine team members
17:00-18:00 Keynote lecture Francesco Iorio
18:00 End of day  
18:30 Dinner at the Wellcome Trust  
Day 3 – Thursday 14 February 2019
08:45 Arrival  
09:00-10:00 Thoughts on the interpretation of integrated data Lee Larcombe
10:00-10:30 Tea/Coffee Break
10:30-11:00 CELLector Hanna Najgebauer
11:00-12:00 Research-based case studies

Masa Roller

Nils Eling

Girolamo Giudice
12:00-12:45 Lunch
12:45-13:30 Poster session All
13:30-15:30 Multiomics factor analysis - a general framework for unsupervised integration of multiomic data sets

Ricard Argelaguet

Danila Bredhkin

15:30-16:00 Tea/Coffee Break  
16:00-17:00 Introduction to Networks and Pathways Pablo Porras
17:00-18:00 Keynote lecture Claire O'Donovan
18:00 End of day  
18:30 Dinner at the Wellcome Trust  
Day 4 – Friday 15 February 2019
08:45 Arrival  
09:00-10:30 Hands-on data integration with Cytoscape Pablo Porras & Dávid Fazekas
10:30-11:00 Tea/Coffee Break
11:00-12:30 Hands-on data integration with Cytoscape Pablo Porras & Dávid Fazekas
12:30-13:30 Lunch
13:30-15:00 Hands-on data integration with Cytoscape Pablo Porras & Dávid Fazekas
15:00-15:30 Course wrap-up and feedback Melissa Burke
15:30-16:00 Tea/Coffee Break  
16:00 Bus to Cambridge Station  

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

  1. Complete the online application form
  2. Submit a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
  3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course

Please submit all documents to Frank O'Donnell (frank@ebi.ac.uk) by 12:00 GMT on Friday 23 November, 2018.

Incomplete applications will not be considered.

PLEASE NOTE: All participants will be expected to produce an A2 poster for the Poster Session - Posters are to include current research interests relevant to your current work.

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Course materials

12 - 15 February 2019
European Bioinformatics Institute United Kingdom
£450
Contact
Frank O’Donnell

Organisers
  • Melissa Burke
    EMBL-EBI, UK
  • Evangelia Petsalaki
    EMBL-EBI, UK
  • Pablo Porras Millan
    EMBL-EBI, UK

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