[ensembl-announce] Reminder: Workshop on Gene Annotation 1-2 Nov

[Giulietta]

Hello all,

The Ensembl Gene Annotation workshop at CSHL is coming up!  Although 
this workshop is free of charge, you have to register by sending an 
email to bert at ebi.ac.uk in order to attend.

Please register so we know the numbers.  If there is not enough 
interest, we won't hold the workshop, so please pass this on to any 
interested colleagues who will be around CSHL at the beginning of November.

Two genebuilders from Ensembl will lead the workshop, and it is an 
excellent chance to understand and explore the Ensembl annotation pipeline.

Regards,
Giulietta (Ensembl Outreach)

Workshop details:

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 <mailto:bert at ebi.ac.uk>) for 
more details or to register.
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