Ensembl Browser Training

Registration deadline: 

Ensembl Browser Training

The Africa Society of Human Genetics in collaboration with Ensembl is calling for country Society Members to select two of their members to participate in the Ensembl Browser Training on the 7th of September, 2020. Only 30 training slots are available.

The selected country representatives should register via the link below by 15 August, 2020

Course Content

The workshop consists of a series of modules, listed below. Most modules consist of a presentation and a demonstration of the tools, followed by the opportunity to do exercises. Participants are encouraged to bring problems/questions about their research and we will try to tackle these during the workshop using Ensembl. The exact mix of modules can be varied, depending on the preferences of the participants.

  • Introduction to Ensembl: origin, goals and organisation of the Ensembl project
  • Genebuild: how are Ensembl gene and transcripts predictions made?
  • Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions
  • Variation: SNPs and other polymorphisms, haplotypes, linkage disequilibrium, structural variants like CNVs
  • Regulation: Sequences that may be involved in gene regulation, and integration of ENCODE data
  • Data export with BioMart: retrieving genomic information using a web interface (no programming required).

Learning outcomes

At the end of this course 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 involvedin gene regulation and their activity in different cell types.

Programme

Times can be adjusted to suit the timetable of the institute (extra modules can be added depending on the final list of participants).

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

*Optional modules depending on the interests of the participants

Prerequisites

  • It is aimed at wet-lab scientists and bioinformaticians.
  • Participants should have degree-level understanding of molecular biology/genetics and be proficient at using web browsers.
  • Be interested in being a facilitatorin future Ensemblbrowser training workshops.
  • Be keen and available to be anEnsemblBrowserTrainer after more in-person training has been provided
  • Evidence of being active in the genetic/genomic research fields
  • Access to a stable internet to attend the training (liaise with AfSHG National Societies -see contact at the bottom).
  • Maximum 1-page CV (Personal/Contact details, Educational Qualifications, Work/Research Experiences, Publications, Future Plans (Highlight Training)

Requirements

  • Computer room with a computer for each participant
  • OR Participants
  • Each computer should have a (reasonably fast) internet connection and an up-to-date internet browser installed (preferably Chrome or FireFox)
  • A computer for the instructor, connected to a projector, with an internet connection
  • Booklet printing for all the participants (Distributed Classroom)
  • Access to Zoom & Slash
  • Material shared in advance
Opening/Closing dates: 
Monday, September 7, 2020