Networks and Pathways

Date:

 Monday 14 Friday 18 May 2018

Venue: 

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

Application opens: 

Monday November 13 2017

Application deadline: 

Friday February 09 2018

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£605 (Including Accommodation)

Overview

This course will provide life scientists with training on exploring and using protein interaction bioinformatics resources. The content examines the data repositories, resources and tools available to explore and analyse large datasets. The principles of biological network and pathway analysis will be introduced and explained using relevant case studies. 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.

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 course is aimed at bench-based biologists, who are involved in, or embarking on, 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, Complex Portal, Reactome, SignaLink 2
• Network analysis tools: Cystoscape and selected apps: BINGO, MCODE, ClueGO
• Ontologies, identifiers and data standards: GO, PSICQUIC, IMEx, HUPO

Outcomes

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

Programme

Time Topic Trainer
Day 1 - Monday 14 May 2018
12:00 - 13:00 Registration and lunch  
13:00 - 13:30 Welcome, introduction 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 Tea/coffee break  
16:00 - 17:30 IntAct molecular interaction database Livia Perfetto & Birgit Meldal
17:30 - 18:30 IntAct Complex Portal Hema Bye-A-Jee
18:30  End of day  
19:00 Evening meal   
Day 2 - Tuesday 15 May 2018
09:00 - 10:00 Computational analysis of protein post- translational networks Pedro Beltrao 
10:00 - 11:00 IntAct molecular interaction database Livia Perfetto & Birgit Meldal
11:00 - 11:30 Tea/coffee break   
11:30 - 12:30 Identifier mapping Pablo Porras 
12:30 - 13:30 Lunch and poster session   
13:30 - 15:00 Network analysis & Cytoscape  Pablo Porras
15:00 - 15:30 Tea/coffee break  
15:30 - 18:00 Network analysis & Cystoscape Pablo Porras
18:00  End of day  
19:00 Evening meal    
Day 3 - Wednesday 16 May 2018
09:00 - 10:30 Network analysis & Cytoscape Pablo Poras
10:30 - 11:00 Tea/coffee 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 
15:30 - 16:00 Tea/coffee break  
16:00 - 17:00 Network medicine - applications of pathways and networks  Tamas Korcsmaros 
17:00 - 17:30 Discussion session Tamas Korcsmaros 
17:30 - 18:30 Case study Cancer Networks Rob Ewing
18:30 End of day  
19:00 Evening meal  
Day 4 - Thursday 17 May 2018
09:00 - 10:30 Reactome Reactome team 
10:30 - 11:00 Tea/coffee break  
11:00 - 13:00 Reactome analysis tools  Reactome team 
13:00 - 13:45 Lunch  
13:45 - 15:00 Case study Glynn Bradley
15:00 - 16:00 Networks, complexes and pathways Matt Rogon
16:00 - 16:30 Tea/ coffee break   
16:30 - 18:30 Networks, complexes and pathways Matt Rogon
18:30 End of day  
19:00 Dinner  
Day 5 - Friday 18 May 2018
09:00 - 10:30 Methods for accessing data Pablo Porras, Matt Rogon, Anjali Shrivastava & Noemí del Toro
10:30 - 11:00 Tea/coffee 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 Lunch  
14:00 End of course  
14:15 Shuttle service to Cambridge train station