EMBL-EBI Bioinformatics workshop, Centre for Marine Sciences (CCMAR), Faro

Date:

 Monday 2 Tuesday 3 October 2017

Venue: 

Centre for Marine Sciences (CCMAR) - Universidade do Algarve, Campus de Gambelas. Edif.7, 8005-139,  Faro, Portugal

Application opens: 

Wednesday August 30 2017

Application deadline: 

Tuesday September 05 2017

Participation: 

First come, first served

Contact: 

Cymon Cox

Registration fee: 

€50

Registration closed

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Course Overview

In this course, participants 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). 

During the course,participants will acquire skills in the effective use of functional genomics databases: ArrayExpress (one of the ELIXIR core data resources) and Expression Atlas.  Such skills will include searching, retrieving and interpreting data relevant to their research areas of interests.  There will be interactive presentations, demonstrations and practical exercises to give trainees hands on experiences.To complement the sessions on functional genomics, there will be brief presentations on some related EMBL-EBI resources: EBI metagenomics and Reactome

Since many EMBL-EBI resources are built to facilitate reproducible research, there will also be a session discussing the obstacles and barriers to data reproducibility in the research environment, illustrated by real-life examples.  Participants will learn about some handy data management techniques that help to alleviate reproducibility problems, many of which have already been implemented for over a decade at EMBL-EBI.

Please note this course does not cover microarray, sequencing, metagenomic or network data analysis.

Audience

This course is aimed at wet-lab researchers 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:

  • EMBL-EBI data services: an overview of the free databases and data services covering a wide range of subject areas across biological sciences.
  • 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)
  • Data management: the problems we face in poor reproducibility of published research results, and how to alleviate them with some simple data management techniques

Learning outcomes

After this course, you should be able to:

  • Define some of the public data services EMBL-EBI provides
  • Explore functional genomics data in ArrayExpress effectively, and submit your own data with ease.
  • 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 - 2nd October 2017
09:00 - 09:30 Welcome and Introduction to EBI resources Amy Tang
09:30 - 10:30 ArrayExpress  Amy Tang 
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 ArrayExpress  Amy Tang 
12:30 - 13:30 Lunch   
13:30 - 14:30 ArrayExpress and data submission Amy Tang 
14:30 - 15:00 Tea/coffee break   
15:00 - 16:00 An introduction to EBI Metagenomics  Amy Tang 
16:00 - 17:00 Data management for reproducible research Amy Tang 
17:00 End of Day 1  
Day 2 - 3rd October 2017 
09:00 - 10:30 Expression Atlas   Amy Tang 
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 Expression Atlas   Amy Tang 
12:30 - 13:30 Lunch  
13:30 - 15:00 Expression Atlas & RNAseq-er API  Amy Tang 
15:00 - 15:30 Tea/coffee break  
15:30 - 16:30 Reactome (webinar)  Steve Jupe 
16:30 - 17:00 Wrap up and feedback Amy Tang 
17:00 End of course