Gene annotation workshop in Kuala Lumpur

We are delighted to inform you that CRYSTAL, University of Malaya will be hosting a workshop on Ensembl gene annotation on the 5th and 6th December, 2011.

This 2-day workshop is aimed at developers and bioinformatics programmers. The workshop will consist of 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.

Prerequisite: Participants will be expected to have experience in writing Perl programs. A background in object oriented programming techniques and familiarity with databases (MySQL) are essential to follow the workshop. 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 pipelines job tracking system
  • Visualisation of results with Apollo.

This workshop will be conducted by Dr Amonida Zadissa and Magali Ruffier of the Ensembl team, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

Registration: For registration please send us your information via email to and include the information on the registration form by 19th November. For workshop details, please contact Dr Amonida Zadissa at or Dr Giulietta Spudich at

Please note: the number of participants is limited to 15. The organisers shall select the participants based on the information provided in the registration form. Only successful applicants will be notified.

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