The Ensembl Outreach team is currently looking into the possibility of giving browser and / or API workshops in the Western US in 2013. Ideally, this would be after the Plant and Animal Genome Conference in San Diego (12-16 January), so in the second half of January.

Our workshops are highly interactive and consist of presentations alternated with lots of hands-on exercises. The ideal group size is between 20-30 participants for a browser workshop and between 10-20 participants for an API workshop.

We don’t charge academic institutions any fee for our workshops, but we expect the host to pay for our instructor’s expenses (i.e. accommodation, domestic travel and subsistence).

If you are potentially interested in hosting a workshop or want more information, please contact me at bert@ebi.ac.uk.

Bert Overduin
Ensembl Outreach

Ensembl is holding a workshop titled, ‘Introduction to automatic
gene annotation’ aimed at developers. The workshop runs on 4-5 of
September 2012 at Department of Genetics, University of Cambridge,
UK. 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.

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.

Topics to be presented:

  • Introduction to the GeneBuild pipeline, including data input types, generating protein-coding transcript models, and adding UTR to these model
  • 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

Practical sessions:

  • 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 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@ebi.ac.uk) for more details or to
register.

Related Wellcome Trust Conference:
Genome Informatics 2012, 6-9 September, Cambridge. Please click here for full details.

 

Variant Call Format (VCF) has become the standard portable data format for variation data. Ensembl provides various tools for handling VCF files, such as the ability to upload and view VCF data on the genome browser, and the Variant Effect Predictor (VEP) for predicting the functional consequence of variants.

We now provide an easy-to-use Perl script, import_vcf.pl, that allows you to create and populate an Ensembl Variation database from a VCF file.

Using the script you can create a database that is ready for use on your own Ensembl website mirror, as well as with Ensembl’s Perl API. Through these you have access to our powerful tools such as:

You can either build a new database from scratch, or add data on top of an existing database (for example, a copy of one of our databases downloaded from our FTP servers).

All you need is the Ensembl API modules, and a MySQL server that you can write to!

The script is located in the ensembl-variation API module, in the scripts/import/ sub-directory.

Click here for full documentation.

We still have some places available at our Ensembl API workshop that will be given from Wednesday 21 until Friday 23 March 2012 at the University of Cambridge.

Description:

This 3-day workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers the core, compara, variation and functional genomics (regulation) databases and APIs. For each of these the database schema and the API design as well as its most important objects and their methods will be presented. This will be followed by practical sessions in which the participants can put the learned into practice by writing their own Perl scripts. There are no costs for the workshop.

Prerequisites:

This workshop is NOT intended to teach you either Perl or molecular biological and genetic concepts! To be able to attend you should be able to code in Perl and be familiar with basic molecular biology and genetics. A basic knowledge of Ensembl is advantageous.

Schedule:

Wednesday 21 March 2012:

09:30 – 14:30: Core API (Kieron Taylor)
14:30 – 17:00: Functional Genomics API (Nathan Johnson)

Thursday 22 March 2012:

09:30 – 11:30: Functional Genomics API (Nathan Johnson)
11:30 – 17:00: Variation API (Will McLaren)

Friday 23 March 2012:

09:30 – 17:00: Compara API (Matthieu Muffato / Stephen Fitzgerald)

Registration:

You can register for the workshop here.

Hi,

I am working in Ensembl Outreach, and I’d like to point you to some new videos we have on our YouTube channel.  These 5 videos were requested from clinical researchers at the Erasmus MC in Rotterdam.

The Ensembl Overview takes you through some Ensembl data and analysis, with a focus on where the gene set comes from, and sequence variations.

Four short clips between two and five minutes each show you:

We’d like to know what other videos you want to watch.  Drop me an email, or add as a comment to this post.  Thanks!

Giulietta (Ensembl Outreach)

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

Practical sessions:

  • 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 crystal_seminar@um.edu.my and include the information on the registration form by 19th November. For workshop details, please contact Dr Amonida Zadissa at amonida@sanger.ac.uk or Dr Giulietta Spudich at gspudich@ebi.ac.uk.

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.

Join us for 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 (preferabley 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, 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

Practical sessions:

  • 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 pipeline’s job tracking system
  • Visualisation of results with Apollo.

Would you like to join us? Please contact Bert (bert@ebi.ac.uk) for more details or to register.

 

The team is looking forward to supporting our users in Japan!  For the next two weeks, one of our Ensembl outreach officers, Jana, will be teaching full day workshops at the DBCLS and Showa Pharmaceutical University in Tokyo, RIKEN in Yokohama, Osaka University in Osaka, and the OIST in Okinawa.  James from the EBI will also be introducing other EBI resources and tools such as Array Express, the Atlas, and Reactome.

More information can be found here.  We look forward to hearing from new and continuing Ensembl users in Japan!

The Ensembl Outreach team is looking into the possibility to give browser and/or API workshops in the US West and Midwest in 2012. For academic institutions these workshops would be free of charge, but we would expect hosts to reimburse our travel, accomodation and subsistence expenses. Browser workshops are typically one day, API workshops can be one or more days. The ideal group size is around 20 participants. If you are potentially interested to host a workshop or want more information, please contact Bert Overduin.

The Ensembl Outreach team is currently looking into the possibility of giving some 1-day Ensembl browser workshops in the North Eastern US (New England and NY area) in the second half of November 2011. Academic institutions would only have to pay the instructor’s expenses (i.e. accommodation and subsistence) and the domestic travel costs, but we would not otherwise charge for the workshops. The possibility of a 1-day API workshop, covering the core and variation APIs, is also discussable.

For more information about our workshops, please have a look here.

Interested? Please contact me for more details at bert@ebi.ac.uk.