EMBL-EBI Bioinformatics workshop, SENC Neuroscience Congress, Alicante

Date:

  Thursday 28 September 2017

Venue: 

ADDA (Auditorio de la Diputación de Alicante) - Paseo de Campoamor, 03010,  Alicante,  Alicante, Spain

Application opens: 

Wednesday August 16 2017

Application deadline: 

Friday September 15 2017

Participation: 

First come, first served

Registration closed

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Course Overview

This course is designed to highlight the importance of data reproducibility and introduce researchers to EMBL-EBI bioinformatics resources.

The course is divided into two parts:

Part I: The open lecture, open to anyone registered for the SENC meeting, will illustrate the obstacles and barriers to data reproducibility with real-life examples, and suggest how the problems can be addressed by some data management techniques, many of which have already been implemented for over a decade at EMBL-EBI.

Part II: In the hands-on sessions, selected participants (see How to apply) will receive an introduction to EMBL-EBI and its public data resources, with a focus on functional genomics (e.g. microarray expression profiling, RNA-seq, ChIP-seq).  Participants will acquire skills in the effective use of functional genomics databases: ArrayExpress (one of the ELIXIR core data resources) and Expression Atlas. 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 trainees hands on experiences.

Please note this course does not cover microarray or sequencing 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

  • arrayexpress-public-database-functional-genomics
  • expression-atlas-gene-expression-across-species-and-biological-conditions

Learning outcomes

After this course, you should be able to:

  • Highlight a few common reasons why research data is not reproducible
  • Discuss the value of biocuration and data management practice in safeguarding reproducibility of research data
  • 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.

Programme

Time Topic Trainer
Day 1 - 28th September 2017
11:30 - 12:30 Part I: Data management for reproducible research Amy Tang
17:30 - 18:30 Part II: ArrayExpress – archive of functional genomics data sets Amy Tang
18:30 - 19:30 Part II: Expression Atlas – a public resource for looking up gene/protein expression Amy Tang
19:30 Course feedback and wrap up Amy Tang
  End of course