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.
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: Wet-lab researchers and bioinformaticians
Keywords: Genetics, Genomics. Nucleic acids analysis
Language: English
Skill level: Beginner
Type of training: face-to-face / in person
Credential awarded: letter of participation
Venue of workshop: UCT Med-school, Anatomy Building, Health Teaching Lab 1
Dates for the workshop: 20 May 2019
Workshop organisers: Ben Moore, Nicola Mulder, Sumir Panji, Verena Ras
Registration opens: 15 April 2019
Registration closes: 12 May 2019
Notification date: 16 May 2019 (accepted participants)
Link to application form: https://is.gd/ensembl
Link to EBI page for additional information: https://www.ebi.ac.uk/training/events/2019/ensembl-browser-workshop-university-cape-town-20th-may-2019
Participation: People who will be using or are using the Ensembl genome browser for their research, or would like to learn more about how to use the Ensembl browser. Selection will be done via an application process.
Workshop Sponsors: H3ABioNet and Ensembl
Objectives: After this workshop participants should be able to:
- view genomic regions and manipulate the view to add features they are interested in.
- explore information about genes and their sequences, and gene data in bulk using BioMart.
- analyse genomic variants and associated phenotypes and their own variation data using the VEP.
- view homologous genes and genomic regions, functional elements involved in gene regulation and their activity in different cell types.
Syllabus and Tools:
Morning: Introduction to Ensembl and Ensembl genes. Viewing genes and locations in the browser. Data export with BioMart.
Afternoon: The afternoon sessions depend on the participants' interest. We can cover genetic variation, comparative genomics and gene regulation, depending on what you express an interest in when you register.
Prerequisites: None
Feedback from previous courses: "There are probably quite few people out there who all assume that Ensembl today is the same as it was years ago. It is not. With many new features and datasets incorporated/interlinked, it offers data exploration like never before. This course was a very useful update on what Ensembl has become" Browser workshop, CRUK, April 2016
"Very useful workshop, certainly one of the most informative and useful I have attended. Delivered by someone who was extremely familiar with the website and its capabilities, not someone who had used it a couple of times and proclaimed themselves to be an expert." Browser workshop, Cardiff, March 2014
If you think you'd like to host a similar course at your institute, you can find out more on the Ensembl workshops page.
Training Materials Availability:
Training materials used for this course were not directly produced by H3ABioNet but may be accessed here: http://training.ensembl.org/events/2019/2019-05-20-CapeTown. Please note, these materials may be governed by different sharing/re-use policies, and you are encouraged to follow the policies of the external providers regarding material re-use and/or sharing.
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