ATT: EMBL-EBI Bioinformatics workshop | - CCMAR -

ATT: EMBL-EBI Bioinformatics workshop

Segunda, 2 Outubro, 2017 a Terça, 3 Outubro, 2017
Centre for Marine Sciences (CCMAR) - Universidade do Algarve, Campus de Gambelas. Edif.7, 8005-139, Faro, Portugal

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.

(registration closed)


Cymon Cox

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.

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


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





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
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
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 (TBC)
16:30 - 17:00 Wrap up and feedback Amy Tang
17:00 End of course  



(registration closed)