We are delighted to inform you that CRYSTAL, University of Malaya will be hosting a workshop on Ensembl gene annotation on the 5th and 6th December, 2011.
This 2-day workshop is aimed at developers and bioinformatics programmers. The workshop will consist of 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.
Prerequisite: Participants will be expected to have experience in writing Perl programs. A background in object oriented programming techniques and familiarity with databases (MySQL) are essential to follow the workshop. Knowledge of the Ensembl core API is also essential.
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, scaffolds, chromosomes)
- 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 pipeline
- Understanding how the pipeline code interacts with the algorithms and the database
- Understanding the pipelines job tracking system
- Visualisation of results with Apollo.
This workshop will be conducted by Dr Amonida Zadissa and Magali Ruffier of the Ensembl team, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
Registration: For registration please send us your information via email to firstname.lastname@example.org and include the information on the registration form by 19th November. For workshop details, please contact Dr Amonida Zadissa at email@example.com or Dr Giulietta Spudich at firstname.lastname@example.org.
Please note: the number of participants is limited to 15. The organisers shall select the participants based on the information provided in the registration form. Only successful applicants will be notified.