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Hello all,<br>
<br>
The Ensembl Gene Annotation workshop at CSHL is coming up! Although
this workshop is free of charge, you have to register by sending an
email to <a class="moz-txt-link-abbreviated"
href="mailto:bert@ebi.ac.uk">bert@ebi.ac.uk</a> in order to
attend. <br>
<br>
Please register so we know the numbers. If there is not enough
interest, we won't hold the workshop, so please pass this on to any
interested colleagues who will be around CSHL at the beginning of
November.<br>
<br>
Two genebuilders from Ensembl will lead the workshop, and it is an
excellent chance to understand and explore the Ensembl annotation
pipeline.<br>
<br>
Regards,<br>
Giulietta (Ensembl Outreach)<br>
<br>
Workshop details:<br>
<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>
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.
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