Introduction to Omics data integration
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Date:
Tuesday 7 - Friday 10 March 2017Venue:
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Wednesday 05 October 2016Application deadline:
Friday 13 January 2017Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£500 (fee includes 3 nights accommodation)Registration 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 who have some experience of working with at least one type of omics data, and computational biologists / bioinformaticians who wish to gain a better understanding of the biological challenges when working with integrated datasets. No programming or command line experience is required to attend this course, but please note this course does not cover statistical 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, Genestack/KnetMiner, InterMine, Open Targets, Omics DI
- 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 - | ||
| 08:45 - 9:15 | Registration | |
| 09:15 - 09:30 | Welcome and introduction | Melissa Burke |
| 09:30 - 10:30 | Introduction to data integration – Why, how, promise and pitfalls | Lee Larcombe |
| 10:30 - 11:00 | Tea/coffee break | |
| 11:00 - 12:30 | Group activity: designing a data integration study | Brandon Invergo |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | Quality issues – data standards, curation, ontologies and metadata | Sandra Orchard |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 17:00 | A brief introduction to the nature of different data types | Tamás Korcsmáros |
| 17:00 - 18:00 | Keynote – Integration in public resources: Expression Atlas | Amy Tang |
| 19:00 | Evening meal | |
| Day 2 - | ||
| 09:00 - 10:00 | Open Targets | Denise Carvalho-Sliva |
| 10:00 - 10:30 | Tea/coffee break | |
| 10:30 - 11:30 | Open Targets – hands on example | Denise Carvalho-Sliva |
| 11:30 - 12:30 | Omics discovery index | Yasset Perez-Riverol |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | Open tools for data integration – hands on example with InterMine | Rachel Lyne |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 16:30 | Open tools for data integration – hands on example with InterMine | Rachel Lyne |
| 16:30 - 17:30 | Case study lecture | Evangelia Petsalakis |
| 18:30 | Evening meal | |
| Day 3 - | ||
| 09:00 - 10:30 |
ID mapping |
Pablo Porras |
| 10:30 - 11:00 | Tea/coffee break | |
| 11:00 - 12:30 |
GENESTACK platform for omics data analysis and integration |
Keywan Hassani-Pak, Ajit Singh, Misha Kapushesky, Kevin Dialdestoro |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | KnetMiner App for network mining and candidate gene discovery | Keywan Hassani-Pak, Ajit Singh, Misha Kapushesky, Kevin Dialdestoro |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 17:00 | Metabolomics and data integration | Thomas Lawson |
| 17:00 - 18:00 | The IMPC: Large-Scale Phenotyping Analysis to Provide insight into Human Disease | Terry Meehan |
| 19:00 | Evening meal | |
| 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 | Pablo Porras, David Fazekas |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | Hands-on data integration with Cytoscape | Pablo Porras, David Fazekas |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 16:00 | Course wrap-up and feedback | Melissa Burke |
| 16:00 | Bus to Cambridge train station | |