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Tue 2 May 2017
09:30 - 17:30

Venue: Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

Provided by: Bioinformatics


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Bookings cannot be made on this event (Event is completed).


Other dates:


Mon 12 Mar 2018


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CRUK: Using the Ensembl Genome Browser
Beginners

Tue 2 May 2017

Description

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.

Materials for this event are available here.

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.

Target audience
  • 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 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
Prerequisites
  • Knowledge of basic genetics and basic bioinformatics terminology is very helpful for this course
Sessions

Number of sessions: 1

# Date Time Venue Trainer
1 Tue 2 May 2017   09:30 - 17:30 09:30 - 17:30 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE Victoria Newman
Topics covered

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

Aims

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
Format

Presentations, demonstrations and practicals

Timetable

Time Topics Speaker(s)
09:30-10:30 Introduction to Ensembl and the Region in Detail View Victoria Newman
10:30-10:50 Tea/Coffee Break
10:50-12:00 Genes and transcript annotation Victoria Newman
12:00-12:30 BioMart Victoria Newman
12:30-13:30 Lunch Break
13:30-15:00 Variation data and the VEP Victoria Newman
15:00-15:20 Tea/Coffee Break
15:20-16:10 Comparative Genomics Victoria Newman
16:10-17:15 Regulatory Data Victoria Newman
17:15-17:30 Wrap Up

Registration Fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, 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
Notes

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

Duration

1 day

Frequency

A number of times per year

Theme
Databases and Services

Booking / availability