ENSEMBL Training Courses - variation.
Location:
Oeiras, PORTUGAL27 May 2008 - 12:30am
30 May 2008 - 6:00pm
Etc/GMT
Deadline:
Tuesday, 6 May 2008In 2008 we are organizing two training courses on ENSEMBL, with emphasys on its use to study variation.Â
What is ENSEMBL?
The current Ensembl genome browser represents the present state of the art with respect to genome annotation and data management. Current genome annotation includes SNPs and in-dels, as well as protein domains and functional classes such as provided by GO (Gene Ontology). Protein coding gene annotation is provided by the GeneWise program, and SNP-based data mining by the Ensembl BioMart tool.
ENSGEN08 The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This two day workshop offers participants the possibility of gaining lots of hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information. The workshop is primarily targeted at wetlab researchers. The workshop consists of the following modules. Most modules consist of a presentation, followed by the opportunity to do exercises. Participants are encouraged to bring problems/questions about their research to try to tackle these during the workshop using Ensembl. * Introduction to Ensembl : origin, goals and organization of the Ensembl project * Worked example: guided tour of the most important pages of the Ensembl website * Data mining with BioMart: retrieving datasets using the data mining tool BioMart * Evaluating genes and transcripts: how are Ensembl gene and transcripts predictions made? * Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions * Variations: SNPs, haplotypes, linkage disquilibrium * Advanced access & DAS: uploading your own data, other ways of accessing Ensembl dataÂ
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ENSAPI08 Ensembl uses MySQL relational databases to store its information. A comprehensive set of Application Programme Interfaces (APIs) serve as a middle-layer between underlying database schemes and more specific application programmes. The APIs aim to encapsulate the database layout by providing efficient high-level access to data tables and isolate applications from data layout changes. This 2-day workshop is aimed at developers interested in exploring Ensembl beyond the website. Participants will be expected to have experience in writing simple Perl scripts and a background in object oriented programming techniques. Being familiar with databases (MySQL) would be an advantage. The workshop covers various Ensembl databases and APIs. For each of them the database schema and the API design as well as its most important objects and their methods will be presented. This will be followed by practical sessions in which the participants can put the learned into practice by writing their own Perl scripts. If there is demand amongst the participants a session on directly querying the core database using SQL queries can also be included. Ensembl Variation databases and API
Technological advances are leading to the widespread availability of multi-species variation data, dense genotype data, and large-scale resequencing projects. The study of human variation has significantly advanced through resources already available from projects such as the HapMap. To address these challenges within Ensembl, we have designed and tested a database solution and API designed to support variation data, dense genotyping and resequencing data from thousands of individual genome sequences.
Technological advances are leading to the widespread availability of multi-species variation data, dense genotype data, and large-scale resequencing projects. The study of human variation has significantly advanced through resources already available from projects such as the HapMap. To address these challenges within Ensembl, we have designed and tested a database solution and API designed to support variation data, dense genotyping and resequencing data from thousands of individual genome sequences.
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More information: http://gtpb.igc.gulbenkian.pt
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