Using the Ensembl Genome Browser (ONLINE TRAINING)

Beginners

PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information.

This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

• Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
• Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
• Further details regarding eligibility criteria are available here

• Knowledge of basic genetics and basic bioinformatics terminology is very helpful for this course

Number of sessions: 1

Bioinformatics, Data retrieval, Database search, Gene structure, Gene transcripts

After this course, participants should be able to:

• View genomic regions and manipulate the "default" view by adding features of interest.
• Explore information about genes and their sequences, and download gene annotations using BioMart.
• Analyse genomic variants and associated phenotypes using the VEP.
• View homologous genes, genomic regions, and functional elements in different cell types.

During this course you will learn about:

• 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
• Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions
• Variation: SNPs and other polymorphisms, haplotypes, linkage disquilibrium, structual variants like CNVs

Presentations, demonstrations and practicals

• Free for registered University of Cambridge students
• £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
• It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
• £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
• £ 100/day for all Industry participants. These charges must be paid at registration
• Further details regarding the charging policy are available here

Participants are encouraged to bring problems/questions about their research to try to tackle these during the workshop using Ensembl

1

A number of times per year

• Ensembl REST API workshop (ONLINE LIVE TRAINING)

• Bioinformatics
• Specialised Research Topics