Bioinformatics & Functional Genomics in Zebrafish
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Date:
Monday 15 - Thursday 18 October 2018Venue:
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Monday 18 June 2018Application deadline:
Friday 03 August 2018Participation:
Open application with selectionContact:
Marina PujolRegistration fee:
£600Registration closed
Overview
Zebrafish are widely used to study development, toxicity and disease, and functional genomics is used throughout the field to identify new pathways and mechanisms and for comparison to other model systems and humans. In this hands-on course, participants will learn how to design functional genomics experiments and how to manage and analyse such datasets from zebrafish and to compare these to other species. The course will be relevant to researchers working on a wide range of topics, but will use a number of cancer datasets as the basis for hands-on analysis. The final day will provide participants with an opportunity to apply the tools and resources introduced during the previous teaching sessions by undertaking a short problem solving session.
Audience
This course is aimed at researchers currently working with zebrafish and generating gneomic and functional data. No prior bioinformatics knowledge is required, but knowledge of R and web-based packages would be beneficial. Trainees with limited experience of R will be provided with pre-course preparation materials to increase their R knowledge.
Outcomes
At the end of the course you will be able to:
- Design and implement RNA-Seq experiments using Zebrafish
- Know and apply common approaches and tools used in the analysis of zebrafish expression data
- Undertake basic data visualisation
- Query RNA-Seq datasets for gene signatures
- Undertake cross species comparison of gene datasets
Programme
Day 1 – Monday 15th October 2018 |
||
|---|---|---|
| 12:00 - 13:00 | Lunch and Registration | |
| 13:00 - 13:30 | Welcome and introduction | EBI Training team |
| 13:30 - 14:30 | Good experimental design - general considerations | Elisabeth Busch-Nentwich |
| 14:30 - 15:00 | Break | |
| 15:00 - 16:00 | Data and Metadata submission | Nancy George and Anja Fullgrabe |
| 16:00 - 17:00 | Case study - Zebrafish data in Expression Atlas | Nancy George and Anja Fullgrabe |
| 17:00 - 17:30 | Discussion | All |
| 18:30 | Dinner | |
Day 2 – Tuesday 16th October 2018 |
||
|---|---|---|
| 09:00 - 10:30 | Introduction to Ensembl | Ensembl Outreach |
| 10:30 - 11:00 | Break | |
| 11:00 - 12:30 | Introduction to BioMart | Ensembl Outreach |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | Comparing species using Biomart | Ensembl Outreach |
| 15:00 - 15:30 | Break | |
| 15:30 - 17:00 | Ensembl and Biomart Practical cotd. | Ensembl Outreach |
| 17:00 - 17:30 | Discussion | All |
| 18:30 | Dinner | |
Day 3 – Wednesday 17th October 2018 |
||
|---|---|---|
| 09:00-10:00 | Gene Ontology | George Georghiou |
| 10:00-10:30 | Break | |
| 10:30-12:30 | Reactome | Thawfeek Varusai |
| 12:30-13:30 | Lunch | |
| 13:30-17:30 | Cytoscape | Livia Perfetto |
| 18:30 | Dinner | |
Day 4 – Thursday 18th October 2018 |
||
|---|---|---|
| 09:00 - 10:30 | Short project - applying tools and resources introduced. | TBC |
| 10:30 - 11:00 | Break | |
| 11:00 - 13:00 | Short project - applying tools and resources introduced (Cotd.) | TBC |
| 13:00 - 14:00 | Lunch | |
| 14:00 - 15:00 | Presentation and discussion of project results | All |
| 15:00 - 15:30 | Feedback and wrap-up | EBI Training team |
| 15:30 | Course end | |