Networks and Pathways


 Monday 9 Friday 13 May 2016


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

Application opens: 

Friday December 18 2015

Application deadline: 

Friday March 04 2016


Open application with selection


Frank O’Donnell

Registration fee: 


Registration closed

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This practical course is specifically intended to give life scientists training on how to explore and use protein interaction bioinformatics resources. This course looks at the data repositories, resources and tools available to explore and analyse large datasets. Principles of biological network and pathway analysis will be introduced and case studies presented. Additionally, there will be the option to either spend time learning how to access public repositories programmatically, or to analyse your own data using the methods covered in the course.



This course is aimed at bench-based biologists, who are involved in or embarking upon protein interaction and/or pathway related projects. 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, Reactome
  • Network analysis tools: Cytoscape and selected plug-ins (BINGO)
  • Ontologies, identifiers and data standards: GO, PSICQUIC, IMEx, HUPO


After this course you should be able to:

  • Discuss some features of protein interaction data, properties of biological networks, and relevant data standards
  • Browse, search and access protein interaction and network data stored in publicly available repositories
  • Use bioinformatics tools to analyse biological networks and pathways
  • Overlay expression data using appropriate identifiers to visualise biological networks and pathways


Time Topic Trainer
Day 1 - Monday 9 May
12:00-13:00 Registration and lunch  
13:00-13:30 Welcome and introduction to EMBL-EBI Tom Hancocks
13:30-14:15 Introduction to molecular interactions Sandra Orchard
14:15-15:00 PSICQUIC Sandra Orchard & Pablo Porras
15:00-15:30 Break  
15:30-17:30 IntAct molecular interaction database Sandra Orchard
17:30-18:00 IntAct Complex Portal Hema Bye-A-Jee
18:00-19:00 Poster session and drinks reception  
19:00 End of day  
19:30 Evening meal at Hinxton Hall Restaurant  
Day 2 - Tuesday 10 May
09:00-10:00 Computational analysis of protein post-translational networks Pedro Beltrao
10:00-11:00 IntAct molecular interaction database Sandra Orchard
11:00-11:30 Break  
11:30-13:00 Identifier mapping Pablo Porras
13:00-14:00 Lunch and posters  
14:00-15:30 Network analysis & Cytoscape Pablo Porras
15:30-16:00 Break  
16:00-18:30 Network analysis & Cytoscape (Cont.) Pablo Porras
18:30 End of day  
19:30 Evening meal at Hinxton Hall Restaurant  
Day 3 - Wednesday 11 May
09:00-10:30 Network analysis & Cytoscape (Cont.) Pablo Porras
10:30-11:00 Break  
11:00-13:00 From pathways to networks - visualization challenges and solutions Tamás Korcsmáros
13:00-14:00 Lunch  
14:00-15:30 Extending pathways - data integration Tamás Korcsmáros
15:30-16:00 Break  
16:00-17:00 Network medicine - applications of pathways and networks Tamás Korcsmáros
17:00-17:30 Discussion Tamás Korcsmáros
17:30-18:30 Keynote: Cancer Networks Rob Ewing
18:30 End of day  
19:30 Evening meal at Hinxton Hall Resturant  
Day 4 - Thursday 12 May
09:00-10:30 Reactome Steve Jupe
10:30-11:00 Break  
11:00-13:00 Reactome analysis tools Steve Jupe
13:00-14:00 Lunch  
14:00-15:00 Keynote: Predictive and mechanistic logic models of signalling networks

Julio Saez-Rodriguez

15:00-16:00 Networks, complexes and pathways Matt Rogon
16:00-16:30 Break  
16:30-18:30 Networks, complexes and pathways (Cont.) Matt Rogon
18:30 End of day  
19:30 Evening meal at the Red Lion Pub, Hinxton  
Day 5 - Friday 13 May
09:00-10:30 Data & computational access Pablo Porras & Matt Rogon
10:30-11:00 Break  
11:00-12:30 Data & computational access (Cont.) Pablo Porras & Matt Rogon
12:30-12:45 Course feedback and wrap up Tom Hancocks
12:45-13:15 Lunch  
13:30 Coach to Cambridge Railway Station