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 crystal_seminar@um.edu.my and include the information on the registration form by 19th November. For workshop details, please contact Dr Amonida Zadissa at amonida@sanger.ac.uk or Dr Giulietta Spudich at gspudich@ebi.ac.uk.

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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