The Gulbenkian Training Programme in Bioinformatics
GTPB ENSEMBL Courses in 2008 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. |
ENSEMBL08 course websiteIMPORTANT DATES
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Instructors: |
Giulietta Spudich is trained in biochemistry and molecular biology. Her PhD work focused on protein structure and folding, and her postdoctoral research explored protein-protein and protein-lipid interactions. She moved to the world of genomics and bioinformatics in 2006, where she now works for Ensembl Outreach and Training. She gives worldwide courses in exploring genomes with Ensembl and BioMart. |
Daniel Rios has a background in Computer Science (Universitat Politecnica de Catalunya), and finished his degree in Sweden (Kungliga Tekniska Hogskolan). He entered in the bioinformatics world developing a tool to allow scientists to curate SNP data submitted to HGVbase, Human Genome Variation database, at the Karolinska Institutet. He joined the Ensembl project in 2004 working in the Functional Genomics team. During his time at EBI, he has been involved in the development of the new database schema and API to support variation data, including data produced with new resequencing technologies, and has taught several API workshops in Europe. |
Affiliation: European Bioinformatics Institute, Hinxton, Cambridge, UK |
Course description:
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 data
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Course Timetable: |
ENSGEN08 | Browsing Genes and Genomes with Ensembl |
May 27th | Ensembl and BioMart Day 1 |
09:30 - 11:00 | Introduction to genome browsing with Ensembl |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 | Hands-on (browsing) and introduction to data retrieval with BioMart |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 | Hands-on (BioMart) and Comparative Genomics |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 | Hands-on (Comparative) and summary |
May 28th | Advanced Ensembl Day 2 |
09:30 - 11:00 | The Ensembl gene set |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 | Variations |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 | Tying together Ensembl and BioMart.
Adding your data with DAS |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 | Summary and other EBI resources |
ENSAPI08 | Ensembl API access, Programming workshop |
May 29th | Hands-on practise with the Ensembl API Day 1 |
09:30 - 11:00 | What is an API.
Introduction and main objects within the API. The Registry |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 | Using several coordinate systems.
Slices and Features in Ensembl |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 | Genes, Transcripts, Exons and Translations |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 | Coordinate transformations.
References to external databases |
May 30th | Hands-on practise with the Ensembl Variation API Day 2 |
09:30 - 11:00 | Introduction to variation data, database schema and API.
The Variation object |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 | Population, Individuals and Alleles |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 | VariationFeature and TranscriptVariations |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 | New resequencing data: StrainSlice, AlleleFeature and ReadCoverage objects |
Pre-requisites:
Basic Molecular Biology and Biochemistry. Elementary computing skills.
For the ENSAPI08 course, the applicants should have basic knowledge in PERL scripting. |
Instituto Gulbenkian de Ciência,
Apartado14, 2781-901 Oeiras, Portugal