[ensembl-dev] Automatic gene annotation workshop in Malaysia

[Amonida Zadissa]

Dear all,

Ensembl is holding a workshop on automatic gene annotation at CRYSTAL,
University of Malaya [1] in Kuala Lumpur on the 5th and 6th December,
2011.

The 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.

Registration: For registration please send your information to Azrina
at crystal_seminar at um.edu.my and include the information on the
registration form [2] by 19th November. For workshop details, please
contact Amonida at amonida at sanger.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.

Thanks,
Amonida

[1] http://crystal.um.edu.my/CRYSTAL/index.php?pageid=1
[1] http://crystal.um.edu.my/CRYSTAL/index.php?pageid=24#tabs-2