Networks and Pathways

Date:

 Monday 9 - Friday 13 June 2014

Venue: 

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

Application opens: 

Thursday 09 January 2014

Application deadline: 

Friday 04 April 2014

Participation: 

Open application with selection

Contact: 

Rebecca Greenhaff

Registration fee: 

£615

Registration closed

Overview

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 (i) learn to access public repositories programmatically, or (ii) to analyse your own data.

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, Reactome

  • Network analysis tools: Cytoscape and selected plug-ins (BINGO)

  • 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

AllBio sponsored travel bursaries are available for applicants currently working in EU based institutions on research that is non-human / non-medical in nature. Please fill the relevant boxes within the application if you wish to be considered for a travel bursary.

Programme

Time Topic Trainer
Monday 9 June
12:00-13:00 Registration and Lunch  
13:00-13:30 An Introduction to the EBI Laura Emery
13:30-14:15 Introduction to Molecular Interactions Sandra Orchard
14:15-14:45 Tea/coffee break  
14:45-15:30 PSICQUIC Sandra Orchard and Pablo Porras
15:30-17:30 IntAct molecular interaction database Sandra Orchard
17:30-18:30 The IntAct complex portal Birgit Meldal
19:00 Dinner at the Wellcome Trust Centre  
Tuesday 10 June
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  
11:30-12:15 Identifier mapping Pablo Porras
12:15-14:00 Lunch & Posters  
14:00-15:30 Network analysis & Cytoscape Pablo Porras
15:30-16:00 Tea/coffee break  
16:00-17:30 Network analysis & Cytoscape Pablo Porras
19:00 Dinner at the Wellcome Trust Centre  
Wednesday 11 June
09:00-11:00 Network analysis & Cytoscape Pablo Porras
11:00-11:30 Tea/coffee break  
11:30-13:30 From pathways to networks - visualization challenges and solutions Tamás Korcsmáros
13:30-14:30 Lunch  
14:30-15:30 Extending pathways - data integration Tamás Korcsmáros
15:30-16:00 Tea/coffee break  
16:00-17:30 Network medicine - applications of pathways and networks Tamás Korcsmáros
17:30-18:30 Network analysis of genotyping data relating to severe dengue Benno Schwikowski
19:00 Dinner at the Wellcome Trust Centre  
Thursday 12 June
09:00-10:30 Reactome Steve Jupe
10:30-11:00 Tea/coffee break  
11:00-13:00 Reactome analysis tools Steve Jupe
13:00-14:00 Lunch  
14:00-15:00 Networks, complexes and pathways José Villaveces
15:00-15:30 Tea/coffee break  
15:30-17:30 Networks, complexes and pathways José Villaveces
17:30-18:30 TBC Julio Saez-Rodriguez
19:00 Dinner at the Wellcome Trust Centre  
Friday 13 June
09:00-10:30 Data/computational access Pablo Porras/Rafael Jimenez and José Villaveces
10:30-11:00 Tea/coffee break  
11:00-12:30 Data/computational access Pablo Porras/Rafael Jimenez and José Villaveces
12:30-13:00 Course feedback and wrap up Laura Emery
13:00 Course Ends      COURSE FEEDBACK  
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

At EMBL-EBI, we manage the world’s public biological data and make it freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. Set on the beautiful Wellcome Genome Campus near Cambridge in the UK, we support scientists throughout the world in seeking solutions to challenges in healthcare, agriculture and the environment.

/training/events/0000/files/content.ebi.ac.uk/venues/south_building_exterior.jpg

In association with

How to apply

Registration is now closed for this course.

Application deadline

04 April 2014

Number of places

30 places

Registration closed

Organisers

Laura Emery

Sandra Orchard

Trainers

Laura Emery - EMBL-EBI, UK

Sandra Orchard - EMBL-EBI, UK

Pablo Porras Millan - EMBL-EBI, UK

Birgit Meldal - EMBL-EBI, UK

Pedro Beltrao - EMBL-EBI, UK

Tamas Korcsmáros - Earlham Insititute, UK

Benno Schwikowski - Institut Pasteur, France

Steve Jupe - EMBL-EBI, UK

Jose Villaveces - EMBL-EBI, UK

Julio Saez-Rodriguez - EMBL-EBI, UK

Rafael Jimenez - EMBL-EBI, UK

Materials & attachments

Networks and Pathways