The Bioinformatics Roadshow - Faroe Islands
This programme is aimed at bench-based researchers using genomics and/or transcriptomics-based methodologies in their research. It provides an introductory overview of some of the most commonly used, publicly accessible resources for nucleotide sequences, assembled genomes and functional genomics data. Delegates will gain hands-on practice of using these data resources, interspersed with some lectures. We will make every effort to use examples of relevance to research in the Faroe Islands (human variation; aquaculture). The practical exercises use web-browser-based tools and assume no previous training in bioinformatics.
What will I learn?
After this course you should be able to…
- Navigate the EMBL-EBI website and use EBI search to access and retrieve data.
- Appreciate the depth and variety of tools and databases available at the EBI.
- Understand the basics of genome annotation in Ensembl with a focus on vertebrates and other eukaryotes.
- Have practical experience of data mining approaches based on BioMart.
- Understand how to view comparative genomics data (gene trees and homologies) and sequence variation data in Ensembl (including structural variation).
- Understand the differences between the major nucleotide sequence databases.
- Browse the ENA database in detail, understanding the structure of a database entry.
- Understand the different ways to access sequence data and when it’s appropriate to use them.
- Know how to browse and retrieve data from the ArrayExpress public repository of transcriptomics data and from the Gene Expression Atlas.
- Understand how to query for condition-specific gene expression patterns as well as perform broader exploratory searches for biologically interesting genes, samples or correlations.
|Day 1 - 28 November 2012|
|09:00||Welcome and Introduction to the EBI||Tom Hancocks|
|09:30||The FarGen Project||Bogi Eliasen|
|10:00||Exploring the EBI - Faroe Islands Case Study||Tom Hancocks|
|11:00||Ensembl browsing (practical)||Bert Overduin|
|13:30||Ensembl browsing & BioMart (practical) - Excercises||Bert Overduin|
|16:00||Ensembl variation and comparative genomics (practical)||Bert Overduin|
|17:30||The 1000 Genomes Project (lecture)||Bert Overduin|
|Day 2 - 29 November 2012|
|09:00||Nucleotide sequence archives: ENA and EGA (lecture and practical)||Marc Rosello|
|11:00||Nucleotide sequence archives cont. (practical) - Guidance, Questions||Marc Rosello|
|13:30||ArrayExpress and Gene Expression Atlas (practical)||Emma Hastings|
|16:00||ArrayExpress and Gene Expression Atlas cont. (practical)||Emma Hastings|
|16:30||Wrap up and course evaluations||Tom Hancocks|
Please follow the link to complete the feedback survey: https://www.surveymonkey.com/s/faroe
For further information, to register interest, or enquire about hosting a roadshow - please contact the EMBL-EBI Events Team, T: +44 (0)1223 494444.