[ensembl-dev] Automatic gene annotation workshop in Cambridge, 4-5 September 2012

[Amonida Zadissa]

Ensembl is holding a workshop titled, 'Introduction to automatic
gene annotation' aimed at developers. The workshop runs on 4-5 of
September 2012 at Department of Genetics, University of Cambridge,
UK. 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.

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.

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.