Introduction to Multiomics Data Integration

Date:

 Tuesday 12 Friday 15 February 2019

Venue: 

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

Application opens: 

Friday August 31 2018

Application deadline: 

Friday November 09 2018

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

£450 including onsite accommodation

Overview

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.

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.

Audience

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.

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, InterMine
  • Challenges and best practice for working in an integrated manner with genomic, transcriptomic, and proteomic data

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

Programme

Day 1 – Tuesday 12 February 2019
09:45-10:15 Arrival and tea/coffee  
10:15-10:30 Welcome and introductions Melissa Burke
10:30-11:30 Introduction to data integration – Why, how, promise and pitfalls Lee Larcombe
11:30-12:15 Group Activity TBC
12:15-13:15 Lunch
13:15-14:00 Group Activity continued TBC
14:00-15:30 Multiple ways to integrate multi-omics data - case studies from studying human diseases Tamás Korcsmáros
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 ID Mapping Pablo Porras
10:00-10:30 Tea/Coffee Break
10:30-11:30 Omics Discovery Index Yasset Perez-Riverol
11:30-12:00 Multiomics factor analysis - a general framework for unsupervised integration of multiomic data sets Ricard Argelaguet
12:00-13:00 Lunch
13:00-14:30 Open tools for data integration – hands on example with InterMine Rachel Lyne and InterMine team members
14:30-15:00 Tea/Coffee Break  
15:00-16:30 Open tools for data integration – hands on example with InterMine - continued Rachel Lyne and InterMine team members
16:30-17:30 Keynote lecture Francesco Iorio
17:30 End of day  
18:30 Dinner at the Wellcome Trust  
Day 3 – Thursday 14 February 2019
08:45 Arrival  
09:00-10:00 Open Targets introduction and hands on Denise Carvalho-Silva
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 Guiridice
12:00-12:45 Lunch
12:45-13:30 Poster session All
13:30-15:30 TBC TBC
15:30-16:00 Tea/Coffee Break  
16:00-17:00 Introduction to Networks and Pathways Pablo Porras
17:00-18:00 Keynote lecture TBC
18:00 End of day  
19:00 Dinner at the Red Lion Pub, Hinxton  
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