[ensembl-dev] Workshop: Introduction to Automatic Gene Annotation

[Bronwen Aken]

Dear all,

Ensembl is planning a workshop titled, ‘Introduction to Automatic Gene Annotation’, aimed at developers. 

Date: 29 - 30 October 2013
Venue: Racker Room, Cold Spring Harbor Laboratory, NY

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. The workshop will follow the same format as previous years. 

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

Requirements:
	• Experience in object-oriented programming
	• Good familiarity with Perl, a Unix/Linux environment, and MySQL 
	• Knowledge of the Ensembl core API 
	• 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) for more details or to register.

Thanks,
Bronwen