Introduction to Integrative Omics
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Date:
Monday 7 - Thursday 10 March 2016Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Friday 18 September 2015Application deadline:
Thursday 31 December 2015Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£500Registration closed
Overview
With the increase in the volume of data across the whole spectrum of biology, more researchers are looking to integrate data of different types to inform hypotheses and biological questions. This may also include public domain data, which can provide added value to data derived through researcher’s own work. This course will provide participants with biological examples of data integration, and the challenges that researchers face. The course will focus on the use of public data resources and open access tools for enabling integrated working, with an emphasis on data visualisation.
Audience
This course is aimed at biologists with experience of working with at least one type of omics data. Computational biologists are welcome to attend but please note that the course will not cover computational approaches for data integration.
Syllabus, tools and resources
During this course you will learn about:
- Data standards, curation and ID mapping
- Quality control for data integration
- Analysis and visualistion: Cytoscape, Ondex/QTLNetMiner, InterMine
- Challenges and best practice for working in an integrated manner with genomic, transcriptomic, and proteomic data
Outcomes
At the end of the course you should be able to:
- Discuss motivations for working in an integrated manner
- Comprehend the importance of data standards and the collection of metadata
- Identify challenges for bring different data types together
- Use a range of bioinformatics tools to integrate and visualise biological data
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Monday 7th March 2016 | ||
| 08:45 - 09:00 | Registration | |
| 09:00 - 09:30 | Welcome and introduction | Annalisa Mupo, EMBL-EBI |
| 09:30 - 10:30 | Introduction to data integration – Why, how, promise and pitfalls | Lee Larcombe, Elixir-UK |
| 10:30 - 11:00 | Break | |
| 11:00 - 12:30 | Group activity: designing a data integration study | Brandon Invergo, EMBL-EBI |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 14:45 | Quality issues – data standards, curation, ontologies and metadata | Sandra Orchard, EMBL-EBI |
| 14:45 - 16:00 | A brief introduction to the nature of different data types | Tamás Korcsmáros, TGAC-UK |
| 16:00 - 16:30 | Tea/coffee break | |
| 16:30 - 17:30 | Keynote I – Integration in public resources: Expression Atlas | Amy Tang, EMBL-EBI |
| 17:30 - 19:00 | Poster session I | |
| 19:00 | Evening meal on campus | |
| Day 2 - Tuesday 8th March 2016 | ||
| 09:30 - 11:00 | Using integrative omics: a case study | Bissan Al-Lazikani, Institute of Cancer Research |
| 11:00 - 11:30 | Tea/coffee break | |
| 11:30 - 12:30 | Open tools for data integration – hands on example with InterMine | Rachel Lyne, University of Cambridge |
| 12:30 - 14:00 | Lunch and poster session II | |
| 14:00 - 16:00 | Open tools for data integration – hands on example with InterMine cont… | Rachel Lyne, University of Cambridge |
| 16:00 - 16:30 | Tea/coffee break | |
| 16:30 - 17:30 | Keynote Lecture II | Laurent Gatto, University of Cambridge |
| 18:00 | Evening meal on campus | |
| Day 3 - Wednesday 9th March 2016 | ||
| 09:00 - 10:30 | Data integration using Ensembl | Benjamin Moore, EMBL-EBI |
| 10:30 - 11:00 | Tea/coffee break | |
| 11:00 - 12:30 | Open tools for data integration – hands on example with Ondex/QTLNetMiner hands on | Keywan Hassani-Pak, Rothamsted Research-UK |
| 12:30 - 13:30 | Lunch - | |
| 13:30 - 15:00 | Open tools for data integration – hands on example with Ondex/QTLNetMiner cont… | Keywan Hassani-Pak |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 16:30 | Open tools for data integration – hands on example with Ondex/QTLNetMiner cont… | Keywan Hassani-Pak |
| 16:30 - 17:00 | ID mapping | Pablo Porras, EMBL-EBI |
| 17:00 - 18:00 | Keynote Lecture III | Aleksej Zeleniak, University of Cambridge |
| 18:30 | Evening meal on campus | |
| Day 4 - | ||
| 09:00 - 10:30 | Hands-on data integration with Cytoscape | Pablo Porras / David Fazekas |
| 10:30 - 11:00 | Tea/coffee break | |
| 11:00 - 12:30 | Hands-on data integration with Cytoscape cont… | Pablo Porras / David Fazekas |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | Hands-on data integration with Cytoscape cont… | Pablo Porras / David Fazekas |
| 15:30 - 16:00 | End of course wrap up and feedback | |
| 16:00 | Bus to Cambridge train station | |