Bioinformatics & Functional Genomics in Zebrafish

Date:

 Monday 15 Thursday 18 October 2018

Venue: 

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

Application opens: 

Monday June 18 2018

Application deadline: 

Friday July 27 2018

Participation: 

Open application with selection

Contact: 

Charlotte Pearton

Registration fee: 

£600

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