Networks and Pathways
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Date:
Monday 14 - Friday 18 May 2018Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Monday 13 November 2017Application deadline:
Friday 16 February 2018Participation:
Open application with selectionContact:
Johanna LangrishRegistration fee:
£605 (Including Accommodation)Registration closed
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 | Application of network analysis in research | Evangelia Petsalaki |
| 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 | Thawfeek Mohamed Varusai |
| 10:30 - 11:00 | Tea/coffee break | |
| 11:00 - 13:00 | Reactome analysis tools | Thawfeek Mohamed Varusai |
| 13:00 - 13:45 | Lunch | |
| 13:45 - 15:00 | Case study | Glyn 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 | |