EMBL-EBI Bioinformatics Workshop, Institute of Neuroscience, Alicante

Date:

  Wednesday 27 September 2017

Venue: 

Institute of Neuroscience (INA) - San Juan de Alicante, 03550,  Alicante,  Alicante, Spain

Application opens: 

Monday August 14 2017

Application deadline: 

Monday August 14 2017

Participation: 

By invitation

Registration closed

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Course Overview

This course will provide participants with an introduction to EMBL-EBI and its public resources, with a focus on functional genomics (e.g. microarray expression profiling, RNA-seq, ChIP-seq). The course will focus on providing skills in the effective use of functional genomics databases: ArrayExpress (one of the ELIXIR core data resources) and ExpressionAtlas. These will include searching, retrieving and interpreting data relevant to their research areas of interests. Activities will include interactive presentations by the trainer, demonstrations and practical exercises to give the trainees hands on experiences.

Please note this course does not cover microarray or sequence data analysis.

Audience

This course is for wet-lab researchers of any career stage, who have minimum or no prior experience in bioinformatics, who want to explore, and use EMBL-EBI resources for their research. No knowledge of programming is required, but the trainer expects an undergraduate level knowledge of biology and/or biochemistry.

Modules and resources

During this course you will learn about:

  • ArrayExpress: a public archive of functional genomics data (e.g. expression microarrays, RNA-seq, ChIP-seq), often deposited as a pre-requisite of journal publication
  • Expression Atlas: a public resource of systematically analysed gene and protein expression data from manually curated studies across many species (not limited to model organisms)

Learning outcomes

After this course you should be able to:

  • Recall some public data services that EMBL-EBI provides
  • Describe the source of data in ArrayExpress database, and how to search for data of interest effectively
  • Distinguish between Expression Atlas and ArrayExpress, as well as search for and interpret expression information using Expression Atlas.
  • Discuss the value of biocuration in safeguarding reproducibility of research data

Programme

Time Topic Trainer
Day 1 - 27th September 2017
09:00 - 09:15 Welcome and Introduction to EMBL-EBI resouces Amy Tang
09:15 - 10:45 ArrayExpress – archive of functional genomics data sets Amy Tang
10:45 - 11:15 Tea and Coffee   
11:15 - 12:45 Expression Atlas – a public resource for looking up gene/protein expression  Amy Tang
12:45 Wrap up and feedback Amy Tang
  End of course