<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi again,<div><br></div><div>In addition to two Genebuilders, Will McLaren from our Variation team will also be attending the Genome Informatics conference. </div><div><br></div><div>If you'd like to get in touch with Will to chat about any variation challenges your team might have, he has a poster about the Variant Effect Predictor (VEP) and his email address is : <a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a> .</div><div><br></div><div><a href="mailto:wm2@ebi.ac.uk"></a>Thanks,</div><div>Bronwen</div><div><br></div><div><br></div><div><br><div><div>On 4 Oct 2011, at 09:59, Bronwen Aken wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div 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. <span style="color: rgb(255, 0, 0);">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.</span></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></div></blockquote></div><br></div></body></html>