EBI EMBO Practical Course on Comparative Genomics and SNP analysis using the Ensembl Genome Browser

Wed, 19th April - Fri 21st April 2005

The EMBL-EBI acknowledges the European Molecular Biology Organisation for funding this event.

Date: 19th - 21st April 2006

Location: Principe Felipe Centro de Investigacion, València, Spain

Tutors: Xose Fernandez, Lisa Mullan, Frank Dudbridge

Presentations used on this course are available as PDF downloads from the appropriate section of the timetable. The course photo is also available as a JPG image should you wish to download it.

Ensembl (http://www.ensembl.org) is a genome browser offering access to genome annotation for currently 21 species of eukaryote. It is a collaborative effort between the EMBL-EBI and Sanger Institute.

This three day course will give instruction on the theory behind the Ensembl data and the use of this data for life science research. It will focus on human data and look at the variety of ways in which this data has been annotated within the Ensembl pipeline. Deviations from this norm will be mentioned for other species where appropriate. The aim is to present Ensembl as a research tool and illustrate this with examples from comparative genomics and SNP identification.

In addition, participants will be introduced to other resources designed for comparative genomics, including HapMap and the tools from our host institute. Lectures will introduce participants to research solutions involving the taught material.

You will be informed of the success of your application by Monday, 6th March 2006.

The EBI regrets there will not be any travel bursaries for this event.

Schedule

Day One

Time	EMBO Course Programme
09.30 - 09.45	Welcome
09.45 - 10.30	Lecture: Introduction to Ensembl
10.30 – 11.45	Practical: Exploring Ensembl
11.45 - 12.00	Refreshment Break
12.00 - 12.30	Lecture: Comparative Proteomics in Ensembl
12.30 - 13.45	Practical: Orthology/Parology identification, Family clustering
13.45 - 14.45	Lunch Break
14.45 – 15.15	Lecture: Comparative Genomics in Ensembl
15.15 - 16.45	Practical: Identification of relevant non-coding elements, synteny
16.45 - 17.00	Refreshment Break
17.00 - 18.00	Research Lecture - Joaquin Dopazo
19.30	Dinner

Day Two

Time	EMBO Course Programme
09.30 - 10.15	Lecture: Variation in Ensembl
10.15 - 11.45	Practical: SNP's, Linkage disequilibrium
11.45– 12.00	Refreshment Break
12.00 - 12.30	Lecture: HapMap
12.30 - 13.45	Practical: Haplotype Maps
13.45 - 14.45	Lunch Break
14.45– 15.15	Lecture: SNP and Mutation databases
15.15 - 16.45	Practical: SNP retrieval using the Sequence Retrieval System
16.45 - 17.00	Refreshment Break
17.00 - 18.00	Research Lecture - Eduardo Eyras
19.30	Dinner

Day Three

Time	EMBO Course Programme
09.30 - 10.15	Lecture: Relevant tools at Prince Felipe C.I.
10.15 - 11.45	Practical: Investigation of further tools
11.45– 12.00	Refreshment Break
12.00 - 13.45	Demonstration & Pratical : Annotation pipeline
13.45 - 14.45	Lunch Break
14.45– 15.15	Lecture: Distributed Annotation System
15.15 - 17.00	Practical: Displaying personal web-based annotation tracks in Ensembl interface

Accommodation

Accommodation for this course will be at the NH Express Hotel Las Artes, Valencia, Spain, situated an approximate 10 minute walk from the course.

The hotel address is:

Av Instituto Obrero 26,
46013 Valencia
Tel +34 96 335 6062
fax +34 96 333 4683

The course location address is:

Centro de Investigacion Principe Felipe
Avd. Autopista del Saler 16,
46013 Valencia
Spain

Tel: +34 963289680
Fax: +34 963289801

and we will be in the ciudad de las artes y las ciencias.

Comparative