The Health Sciences Library and CCTSI were pleased to host training in the Ensembl genome database on January 24th. A video recording of the training session is now available! Please remember that anytime you need assistance with Ensembl, you can contact firstname.lastname@example.org
The Ensembl project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This one-day workshop provided background information for Ensembl users. The workshop is primarily targeted at wetlab researchers.
The workshop consisted of the following modules. Most modules consisted of a presentation and demo, followed by ample opportunity to do exercises.
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
Regulation: “best guess” set of regulatory elements, segmentation tracks
Variation: sequence variants, structural variants
Custom annotation: visualizing your own data (from bam and vcf files etc.) in Ensembl
Note: Most examples and exercises in the workshop focused on human as this is by far the richest annotated species. However, most of what is taught in the workshop can be applied to other species in the Ensembl browser 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 and genomics and a familiarity with web browsers.
[Lynne M. Fox, Education Librarian]