Networks and Pathways

Date:

 Monday 22 Friday 26 May 2017

Venue: 

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

Application opens: 

Thursday December 01 2016

Application deadline: 

Tuesday February 28 2017

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£605.00

Registration closed

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Overview

This course will provide life scientists 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 their own data using the approaches covered in the course.

Audience

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, 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

 

Additional information

We are grateful for support from the BBSRC-funded MIDAS project (grant no. BB/L024179/1) and the National Institutes of Health-funded HeartBD2K project (1U54GM114833-01). Delegates will receive training on services made possible or enhanced by these projects.

 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. 

Included within the Registration Fee:

* 4 night's accommodation at the Holiday Inn Express, Duxford (Whittlesford) - Arriving Monday 22 May 2017, Departure Friday 26 May 2017

* Breakfast, Lunch, Tea/Coffee and Evening Meals

* Shuttle service from the Holiday Inn Express to EMBL-EBI each morning, and the return journey in the evening

* Use of the Training Room

* All Course Materials

* Return Shuttle Service to Cambridge Train Station at the end of the course

Programme

Time Topic Trainer    
Day 1 -  Monday 22 May 2017
12:00-13:00  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 Sandra Orchard     
14:45-15:30 PSICQUIC Pablo Porras    
15:30-16:00 Tea/Coffee break      
16:00-17:30 IntAct molecular interaction database Sandra Orchard    
17:30-18:30 IntAct Complex Portal  Birgit Meldal & Hema Bye-A-Jee    
18:30 End of day
19:00 Dinner at Hinxton Hall      
20:30 Shuttle service to the Holiday Inn Express, Duxford (Whittlesford)      
Day 2 - Tuesday 23 May 2017
08:30 Shuttle service to the Wellcome Genome Campus      
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 Tea/Coffee break      
11:30-13:00 Identifier mapping Pablo Porras    
13:00-14:00 Lunch and poster session      
14:00-15:30 Network analysis & Cytoscape Pablo Porras    
15:30-16:00 Tea/Coffee break       
16:00-18:30 Network analysis & Cytoscape Pablo Porras    
18:30 End of day      
19:00 Dinner at Hinxton Hall      
20:30 Shuttle service to the Holiday Inn Express, Duxford (Whittlesford)      
Day 3 - Wednesday 24 May 2017
08:30 Shuttle service to the Wellcome Genome Campus      
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 Keynote: Cancer Networks Rob Ewing    
18:30 End of day      
19:00 Dinner at Hinxton Hall      
20:30 Shuttle service to the Holiday Inn Express, Duxford (Whittlesford)      
Day 4 - Thursday 25 May 2017
08:30 Shuttle service to the Wellcome Genome Campus      
09:00-10:30 Reactome Steve Jupe    
10:30-11:00 Tea/Coffee break      
11:00-13:00 Reactome analysis tools Steve Jupe    
13:00-13:45 Lunch       
13:45-15:00 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 Tea/Coffee 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      
21:00 Shuttle bus to the Holiday Inn Express, Duxford (Whittlesford)      
Day 5 - Friday 26 May 2017
08:30 Shuttle service to the Wellcome Genome Campus      
09:00-10:30 Methods for accessing data Pablo Porras, Matt Rogon & Max Koch    
10:30-11:00 Tea/Coffee break      
11:00-13:00 Methods for accessing data Pablo Porras, Matt Rogon & Max Koch    
13:00-13:15 Course feedback and wrap up Tom Hancocks    
13:15-14:00 Lunch      
14:00 End of couse      
14:15 Shuttle service to Cambridge Train Station