Functional Insights Into Biological Data Through Network Analysis


 Monday 13 Friday 17 May 2019


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

Application opens: 

Tuesday 13 November 2018

Application deadline: 

Friday 22 February 2019


Open application with selection


Johanna Langrish

Registration fee: 

£660 - (Including Accommodation)

Registration closed

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The omics era of biological research requires more systemic approaches to data analysis and a move away from the single gene/protein perspective. Network and pathway analysis tools use the information available in protein-protein interaction and pathway databases to enrich biological data and allow us to understand biological entities, not only as individual components, but also as complex, interacting systems.

This course will provide life scientists with training on biological network and pathway analysis and protein interaction bioinformatics resources. The principles of biological network and pathway analysis will be introduced and explained using relevant case studies. The course also explores the data repositories, resources and tools available to explore and analyse large datasets from a network perspective.Participants will also have the opportunity to either learn how to access public repositories via programmatic methods or spend time analysing data using the approaches covered in the course.


This introductory course is aimed at bench-based biologists, who are involved in, or embarking on projects that will use network and pathway analysis or protein interaction data. For example, you may be using these tools in the interpretation of biological datasets or as part of a systems biology approach. The course requires no prior knowledge of pathway analysis or computer programming skills. Preference will be given to those actively involved in or commencing interaction/pathway-based projects.

Syllabus, tools and resources

During this course you will learn about:

  • Molecular interaction and pathway databases: IntAct, Complex Portal, Reactome, SignaLink 2
  • Network analysis tools: Cystoscape and selected apps: BINGO, MCODE, ClueGO
  • Ontologies, identifiers and data standards: GO, PSICQUIC, IMEx, HUPO


After this course you should be able to:

  • Use network and pathway analysis tools to enrich biological data
  • Overlay expression data using appropriate identifiers to visualise biological networks and pathways
  • Discuss some properties and features of biological networks, protein interaction data, and relevant data standards

Browse, search and access protein interaction and network data stored in publicly available repositories

Additional information

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. 


Day 1 – Monday 13 May 2019
12:00-13:00 Arrival, registration and lunch  
13:00-13:30 Welcome, introductions and networking Melissa Burke
13:30-14:00 Introduction to EMBL-EBI  Melissa Burke
14:00-14:45 Introduction to molecular interactions Livia Perfetto
14:45-15:30 PSICQUIC Pablo Porras
15:30-16:00 Break  
16:00-17:30 IntAct molecular interaction database IntAct Team
17:30 End of day  
18:30 Dinner at the Conference Centre  
Day 2 – Tuesday 14 May 2019
08:45 Arrival  
09:00-10:00 Keynote presentation Evangelia Petsalaki
10:00-11:00 IntAct Complex Portal  Hema Bye-A-Jee
11:00-11:30 Break  
11:30-12:30 Identifier mapping Pablo Porras
12:30-13:30 Lunch and posters  
13:30-15:00 Network analysis & Cytoscape Pablo Porras
15:00-15:30 Break  
15:30-18:00 Network analysis & Cytoscape Pablo Porras
18:00 End of day  
19:00 Dinner at the Conference Centre Hinxton Hall Restaurant
Day 3 – Wednesday 15 May 2019
08:45 Arrival  
09:00-10:30 Network analysis & Cytoscape Pablo Porras
10:30-11:00 Break  
11:00-13:00 From pathways to networks - visualization challenges and solutions Tamas Korcsmaros
13:00-14:00 Lunch  
14:00-15:30 Extending pathways - data integration Tamas Korcsmaros & David Fazekas
15:30-16:00 Break  
16:00-17:00 Network medicine - applications of pathways and networks Tamas Korcsmaros
17:00-17:30 Discussion session Tamas Korcsmaros & David Fazekas
17:30-18:30 Keynote: Cancer Networks Rob Ewing
18:30 End of day  
19:00 Dinner at the Conference Centre Hinxton Hall Restaurant
Day 4 – Thursday 16 May 2019
08:45 Arrival  
09:00-10:30 Reactome Thawfeek Mohamed Varusai
10:30-11:00 Break  
11:00-13:00 Reactome analysis tools Thawfeek Mohamed Varusai
13:00-13:45 Lunch  
13:45-15:00 Application of interaction data in Target discovery:
Causal Network Analysis
Glyn Bradley
15:00-16:00 Networks, complexes and pathways Matt Rogon
16:00-16:30 Break  
16:30-18:30 Networks, complexes and pathways Matt Rogon
18:30 End of day  
19:00 Dinner at the Red Lion Pub, HInxton  
Day 5 – Friday 17 May 2019
08:45 Arrival  
09:00-10:30 Methods for accessing data Pablo Porras, Matt Rogon Anjali Shrivastava & Noemí del Toro
10:30-11:00 Break  
11:00-13:00 Methods for accessing data Pablo Porras, Matt Rogon Anjali Shrivastava & Noemí del Toro
13:00-13:15 Course feedback and wrap up Melissa Burke
13:15-14:00 Break  
14:00 End of course  
14:15 Shuttle to Cambridge Station