<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><p>Hi all,</p><p><br></p><p>Ensembl is holding a workshop titled, “Introduction to automatic gene annotation”. This workshop, running 1-2 November at CSHL, is aimed at developers. 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 pipeline. This meeting will therefore follow the same format as the 2007-2010 automatic gene annotation workshops.</p><p>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. We will be working from a Virtual Machine and participants are expected to bring their own laptops (preferably Mac) to work from – more details will be provided on registration.</p><p>Topics to be presented:</p><ul><li>Introduction to the GeneBuild pipeline, including data input types, generating protein-coding transcript models, and adding UTR to these models</li><li>An introduction to assembly structure (toplevel, contigs, scaffolds, chromosomes)</li><li>Overview of the different Ensembl APIs</li><li>Obtaining the Ensembl API (cvs checkout)</li><li>Core database schema</li><li>Tracking jobs in the pipeline</li><li>Runnable and RunnableDB modules</li></ul><p>Practical sessions:</p><ul><li>Creating a genebuild database</li><li>Loading an assembly into the database</li><li>Running algorithms first on the commandline and then using the pipeline</li><li>Understanding how the pipeline code interacts with the algorithms and the database</li><li>Understanding the pipeline’s job tracking system</li><li>Visualisation of results with Apollo.</li></ul><p>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 (<a href="mailto:bert@ebi.ac.uk">bert@ebi.ac.uk</a>) for more details or to register.</p><div><br></div><div>Cheers,</div><div>Bronwen</div><div><br></div></body></html>