Ensembl Browser Workshop, Universidad Icesi, 2nd-3rd December 2019

Date:

 Monday 2 Tuesday 3 December 2019

Venue: 

Universidad Icesi - Calle 18 No 122-135, Cali,  VAC, Colombia

Application opens: 

Thursday 04 July 2019

Application deadline: 

Monday 25 November 2019

Participation: 

First come, first served

Registration fee: 

Universidad Icesi students and collaborators, and attendees of the 'XVII Congreso Colombiano de Parasitología y Medicina Tropical', $50.000 Colombian pesos. Other participants, $60.000 Colombian pesos.

Course Overview

The Ensembl project at www.ensembl.org provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 2-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.

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. 

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.

Audience

Wet-lab researchers and bioinformaticians

Learning outcomes

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.

Programme

Time Topic Trainer

Day 1 - Monday 2nd December

Introduction & Ensembl Browser Workshop

 
08:00 - 09:00 Participant introductions and project presentation

Gloria Giraldo-Calderon

Diego Eccheverri

09:00 - 09:45 An introduction to Ensembl Benjamin Moore
09:45 - 10:30 Exploring Genomic Regions Benjamin Moore
10:30 - 10:45 Tea/coffee break  
10:45 - 12:30 Genes and Transcripts Benjamin Moore
12:30 - 13:30 Lunch  
13:30 - 15:00 Variation data and the VEP Benjamin Moore
15:00 - 15:15 Tea/coffee break  
15:15 - 15:45 Comparative genomics Benjamin Moore
15:45 - 16:15 Finding features that regulate gene expression Benjamin Moore
16:15 - 16:50 BioMart Benjamin Moore
16:50 - 17:00 Wrap-up and Feedback  

 

Day 2 - Tuesday 3rd December

GroupProjects

 
08:00 - 10:30 Group work on projects

Gloria Giraldo-Calderon

Diego Echeverri

Benjamin Moore

10:30 - 10:45 Tea/coffee break  
10:30 - 12:30 Group work on projects

Gloria Giraldo-Calderon

Diego Eccheverri

Benjamin Moore

12:30 - 13:30 Lunch

 

13:30 - 15:00 Group work on projects and presentation

Gloria Giraldo-Calderon

Diego Eccheverri

Benjamin Moore

15:00 - 15:15 Tea/coffee break  
15:15 - 16:50 Group work on projects and presentation

Gloria Giraldo-Calderon

Diego Eccheverri

Benjamin Moore

16:50 - 17:00 Wrap-up and Feedback