[ensembl-dev] Workshop on automatic gene annotation

Bronwen Aken ba1 at sanger.ac.uk
Fri Oct 14 14:02:26 BST 2011

Hi again,

In addition to two Genebuilders, Will McLaren from our Variation team will also be attending the Genome Informatics conference. 

If you'd like to get in touch with Will to chat about any variation challenges your team might have, he has a poster about the Variant Effect Predictor (VEP) and his email address is : wm2 at ebi.ac.uk .


On 4 Oct 2011, at 09:59, Bronwen Aken wrote:

> Hi all,
> Ensembl is holding a workshop titled, “Introduction to automatic gene annotation”. This workshop, running 1-2 November at CSHL, is aimed at developers.  Two Ensembl developers will present sessions on how to  create your own core database, including the loading of a genome assembly into a database and the running of simple analyses using the Ensembl genebuild pipeline. This meeting will therefore follow the same format as the 2007-2010 automatic gene annotation workshops.
> Participants will be expected to have experience in programming and a background in object-oriented programming. A good familiarity with Perl, a Unix/Linux environment, and MySQL are essential to follow the workshop and the programming examples. Knowledge of the Ensembl core API is also essential.  We will be working from a Virtual Machine and participants are expected to bring their own laptops (preferably Mac) to work from – more details will be provided on registration.
> Topics to be presented:
> Introduction to the GeneBuild pipeline, including data input types, generating protein-coding transcript models, and adding UTR to these models
> An introduction to assembly structure (toplevel, contigs, scaffolds, chromosomes)
> Overview of the different Ensembl APIs
> Obtaining the Ensembl API (cvs checkout)
> Core database schema
> Tracking jobs in the pipeline
> Runnable and RunnableDB modules
> Practical sessions:
> Creating a genebuild database
> Loading an assembly into the database
> Running algorithms first on the commandline and then using the pipeline
> Understanding how the pipeline code interacts with the algorithms and the database
> Understanding the pipeline’s job tracking system
> Visualisation of results with Apollo.
> Registration for this workshop is free, but participants will need to cover their own accommodation and meal expenses. Would you like to join us? Please contact Bert (bert at ebi.ac.uk) for more details or to register.
> Cheers,
> Bronwen

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