The Bioinformatics Roadshow - Maine, USA
The Ensembl project (http://www.ensembl.org) provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This 1-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 following modules will be covered:
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 retrieval with BioMart: retrieving complex / large datasets using the data retrieval tool BioMart
Comparative genomics: orthologues and paralogues, protein families, whole genome alignments and syntenic regions
Variation: sequence variants, structural variants, Variant Effect Predictor
Custom annotation: uploading / attaching your own data (BED, GFF, BAM, VCF files) to Ensembl
Most modules consist of a presentation and demo, 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.
Note: Most examples and exercises in the workshop will be focused on human as this is by far the most richly annotated species. However, most of what is taught in the workshop can be applied to other species in the Ensembl browser (http://www.ensembl.org), as well as to the species in the Ensembl Genomes browser, that contains genomes of invertebrates, protists, plants, fungi and bacteria (http://www.ensemblgenomes.org).
The only prerequisite for this workshop is general knowledge of molecular biology / genomics and a familiarity with web browsers.
|30 October 2012|
|09:30-09:30||Introduction to Ensembl||Bert Overduin, EMBL-EBI|
|16:30-17:00||Wrap-up, questions and answers and feedback|
The course is only available for delegates based at The Jackson Laboratory, please contact Martha Abbott (Martha.email@example.com) for further information. There will be a maximum of 24 places available.