EMBL-EBI Bioinformatics Workshop

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.

Course Organizers:

Cymon Cox is a senior researcher at CCMAR in Faro. He is the leader of the Plant Systematics and Bioinformatics group.

Affiliation: Fundação para a Ciência (FCT) / CCMAR, Faro, PT

Amy Tang studied Human Genetics at the University of Nottingham for her bachelor degree. She did her PhD at the Brockdorff's lab, then at MRC Clinical Sciences Centre / Imperial College London, working on the epigenetic control of X-chromosome inactivation in mouse early development. The project was split 50:50 into wet-lab and bioinformatics, this is when she first got interested in bioinformatics. After a short postdoc in the same lab, she returned to study at Imperial for a MSc in Bioinformatics and Systems Biology, which helped her move laterally from wet-lab to bioinformatics.

Amy now leads the curation efforts for ArrayExpress and Expression Atlas databases in the Gene Expression Team, promoting reproducible research by maintaining curation quality, and also by driving the development of the user-friendly ArrayExpress data submission tool Annotare. To allow users make the most out of the databases and to educate researchers on best practices for reproducible research, she also manages all training activities for the Team, delivering most of the hands-on courses on functional genomics resources at EMBL-EBI and worldwide. Through listening to Annotare submitters' needs and gathering feedback at training courses, she also acts as users' advocate and works with software developers to improve user experience of ArrayExpress and Expression Atlas websites.

Before joining EMBL-EBI, Amy was a senior bioinformatician in the Ensembl GeneBuild team, curating gene models for key model organisms such as mouse and rat.

Affiliation: EMBL-EBI, UK

Adelino V. M. Canário is a full professor at University of Algarve (Portugal) is a specialist in fish physiology. He is the Director of the Centre of Marine Sciences (ccmar.ualg.pt) since 1994 and leads the Comparative and Molecular Endocrinology research group. He teaches Cell Biology to undergraduate students and Reproductive Biology to graduate students. He coordinates courses for graduate students on Molecular and Cellular Biology Techniques and marine Genomics. He is the promoter of 2 ongoing PhDs and has supervised to completion 12 PhDs (8 in the last 5 years). He is internationaly recognized expert in his field with over 140 published articles (H=26) in regulation of calcium homeostasis, fish reproductive physiology, hormone-behavour relationships, chemical communication and genomics. He has coordinated and participated in European Commission funded research including recently Marine Genomics Europe, Assemble and EMBRC (ESFRI infrastructure).

Affiliation: Fundação para a Ciência (FCT) / CCMAR, Faro, PT

Grace Mugumbate Scientific Training Officer - Training

Affiliation: EMBL-EBI, UK

Course Lecturers:

Steven Jupe is a Knowledge Database Curator/Developer for the Hermjakob team at the EML-EBI.

Affiliation: EMBL-EBI, UK

Amy Tang (Bio above)

Affiliation: EMBL-EBI, UK

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

Program:

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