Using the Ensembl Genome Browser (ONLINE LIVE TRAINING) Beginners
The Ensembl Project provides an interface and an infrastructure for accessing genomic information, including genes, variants, comparative genomics and gene regulation data, covering over 300 vertebrate species. 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.
If you do not have a University of Cambridge Raven account please book or register your interest here.
- Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
- Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
- Further details regarding eligibility criteria are available here.
- Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
- Knowledge of basic genetics and basic bioinformatics terminology is very helpful for this course
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
Tea/Coffee Breaks around 11am and 3pm
| Time | Topics |
| 09:30 | Introduction to Ensembl |
| Exploring genomic regions | |
| Genes and transcripts | |
| 12:30 | Lunch break |
| 13:30 | Variation data and the Variant Effect Predictor (VEP) |
| Regulation | |
| Comparative Genomics | |
| BioMart | |
| Wrap Up |
- Free for registered University of Cambridge students
- £ 60/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.
- £ 60/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
- £ 120/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
Events available