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
Contact:Felix Viana de la Iglesia
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.
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:
- Data management: the problems we face in poor reproducibility of published research results, and how to alleviate them with some simple data management tips
- 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)
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.
|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|