H3ABioNet

Pan African Bioinformatics Network for H3Africa

Ensembl Browser Workshop- University of Cape Town, 6th June 2016

Workshop dates: Monday 6th June 2016

Venue: Health Teaching Labs 1-2, Basement of Anatomy Building, UCT Medical School, Anzio Rd, Observatory, Cape Town, South Africa

Workshop organisers and sponsors: Ben Moore, Nicola Mulder, CBIO@UCT

Workshop trainers and support: Ben Moore, CBIO@UCT

Course Overview: The Ensembl project at 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 hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information. Our sister project at www.ensemblgenomes.org can also be covered if participants are working with bacteria, plants, fungi, protists or (invertebrate) metazoa.

Intended Audience: The workshop is primarily targeted at wetlab researchers, and we customise the course for species of interest and to include total beginners to our browser up through frequent users.

Prerequisites: Participants should complete the application form to attend the workshop. Participants should have a general knowledge of molecular biology / genomics and a familiarity with web browsers. As there is no workshop fees, participants must take care of their own catering needs.

Workshop format: Most modules consist of a presentation and demo, followed by an opportunity to complete exercises and explore Ensembl with assistance. 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 www.ensemblgenomes.org.

Syllabus: Morning

  • Introduction to Ensembl: origin, goals and organization of the Ensembl project
  • Genes and Transcripts: 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

Afternoon: two or three of the following modules will be covered, depending on the interest of the participants.

  • Comparative genomics: gene trees, orthologues and paralogues, whole genome alignments and syntenic regions
  • Variation: sequence variants, structural variants, Variant Effect Predictor
  • Regulation: annotation of regulatory elements using data from ENCODE, Roadmap Epigenomics and BLUEPRINT projects.
  • Custom annotation: uploading / attaching your own data (BED, GFF, BAM, VCF files) to Ensembl
  • Advanced access: other ways to access Ensembl data (MySQL, Perl API, REST API)

Objectives:

  • Learn about the data types in Ensembl
  • Learn how to view data in the Ensembl browser
  • Learn how to mine Ensembl data using BioMart

Workshop materials:

Attachments:
Download this file (Exercise_BM2.txt)Exercise_BM2.txt[ ]0.1 Kb
Download this file (Exercise_BM3.txt)Exercise_BM3.txt[ ]0.2 Kb
Download this file (Exercise_BM5.txt)Exercise_BM5.txt[ ]0.2 Kb
Download this file (Exercise_V4.vcf)Exercise_V4.vcf[ ]319 Kb