Automatic gene annotation workshop in Cold Spring Harbor, 29-30th October

Ensembl is holding a workshop titled, ‘Introduction to automatic gene annotation’ aimed at developers. The workshop runs on 29-30th of October 2013 at Cold Spring Harbor Laboratory, New York.

Registration for this workshop is free, but participants will need to cover their own accommodation and meal expenses. Please contact Bert ( for more details or to register.

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 system.

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 Ensembl genebuild system, 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 Ensembl Analysis and Pipeline APIs
  • Obtaining the Ensembl API (cvs checkout)
  • Core database schema
  • Tracking jobs in the system
  • 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

Would you like to join us? Please contact Bert ( for more details or to register.

Related Cold Spring Harbor Conference:
Genome Informatics 2013, 30 October to 2nd November, Cold Spring Harbor, New York. Please click here for full details.