[ensembl-dev] Reminder: Workshop on Gene Annotation 1-2 Nov
gspudich at ebi.ac.uk
Tue Oct 18 16:59:35 BST 2011
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 bert at ebi.ac.uk in order to attend.
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.
Two genebuilders from Ensembl will lead the workshop, and it is an
excellent chance to understand and explore the Ensembl annotation pipeline.
Giulietta (Ensembl Outreach)
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.
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.
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,
* Overview of the different Ensembl APIs
* Obtaining the Ensembl API (cvs checkout)
* Core database schema
* Tracking jobs in the pipeline
* Runnable and RunnableDB modules
* Creating a genebuild database
* Loading an assembly into the database
* Running algorithms first on the commandline and then using the
* Understanding how the pipeline code interacts with the algorithms
and the database
* Understanding the pipeline's job tracking system
* Visualisation of results with Apollo.
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 <mailto:bert at ebi.ac.uk>) for
more details or to register.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Dev