Ensembl is holding a workshop titled, ‘Introduction to automatic gene annotation’ aimed at developers. The workshop runs on 29-30th of October 2013 at Cold Spring Harbor Laboratory, New York.

Registration for this workshop is free, but participants will need to cover their own accommodation and meal expenses. Please contact Bert (bert@ebi.ac.uk) for more details or to register.

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 system.

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 Ensembl genebuild system, 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 Ensembl Analysis and Pipeline APIs
  • Obtaining the Ensembl API (cvs checkout)
  • Core database schema
  • Tracking jobs in the system
  • 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.

Related Cold Spring Harbor Conference:
Genome Informatics 2013, 30 October to 2nd November, Cold Spring Harbor, New York. Please click here for full details.

download_apiIn May the Ensembl team will again provide a 3-day Ensembl Perl API workshop on the Wellcome Trust Genome Campus in Hinxton, United Kingdom. Although this workshop is primarily meant for campus employees, external participants are also more than welcome to attend.

The workshop itself is free of cost. You should note though that our campus is located a bit in the middle of nowhere and that you have to make your own arrangements for accommodation and/or travel. A similar workshop will be given again end of the year at the University of Cambridge (27-29 November 2013).

For more information and to register please mail me (bert@ebi.ac.uk).

3-DAY ENSEMBL API WORKSHOP
Time: 22-24 May 2013, 9:30-17:00
Place: Teaching room, EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Instructors: Magali Ruffier, Thomas Juettemann, Anja Thormann, Matthieu Muffato, Javier Herrero
Cost: none

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. 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.

Important
This workshop is NOT intended to teach you either Perl or basic 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.

We’d like to announce our new, filmed browser workshop.

Take it for free on EBI’s Train Online platform!

http://www.ebi.ac.uk/training/online/course/ensembl-video-workshop

You can either go through the whole day course top to bottom, or pick your favourite module.  It’s complete with filmed presentations, exercises and answers, and links to more information.

Ensembl (many thanks to Emily Pritchard for putting this together) worked with EBI’s Outreach and Training team’s Mark Adams (who filmed the workshop and did all the slide and video processing).

We’re hosting a live webchat to take questions about any aspect of the course, so join us there on either date:

  • Wed 3 April 4-5pm (GMT+1)
  • Wed 17 April 4-5pm

Like the course? You might want to fly one of us out there to teach at your institute!

Questions/comments are very welcome at our helpdesk.

 

The Ensembl Outreach team is considering the possibility of going to the East Coast of the US in May to deliver Ensembl browser workshops soon after the Biology of Genomes conference in Cold Spring Harbor (May 7th-11th, 2013).

Our browser workshops are highly interactive consisting of presentations intermingled with live demos and hands-on exercises. They can be highly customised to the audience needs, which is ideally in the range of 20-30 attendees.

Ensembl workshops are delivered free of charge but we ask our hosts to pay for our instructor’s expenses which typically include flights, accommodation and subsistence.

For more details, please refer to the page below:

http://www.ensembl.info/workshops/

If you would like Ensembl to come to your academic institution or want additional details, please contact the Outreach Project Leader Giulietta Spudich (gspudich@ebi.ac.uk) or me (denise@ebi.ac.uk).

Kind regards,

Denise

Ensembl Outreach

  • Are you new to Ensembl and want some help on using the browser?
  • Have you used Ensembl before, and want to learn more about it?
  • Do you want to get data quickly using BioMart?

These Online Tutorials are helpful for beginners looking for pointers in browsing their favourite gene, variation or region of interest, or those looking to further develop their skills.

The Quick Tour. A good place for beginners, this gives a brief overview of the kinds of data you can find on Ensembl and where to look for it. There are also links throughout to more detailed tutorials. This is only a thirty minute course so don’t expect to be an Ensembl expert at the end of it!

The Beginner’s Ensembl Course. This is a good place for beginners, or for Ensembl users wanting to expand their knowledge about the browser. In total, this three-hour overview covers Ensembl genes, variation, comparative genomics, and regulation. You’ll learn where the data comes from and how to access it.

 

Video Tutorials. These videos range from 2 minute clips to 20 minute overviews on a particular topic in Ensembl. This is a good place for anyone from beginners to frequent users to increase knowledge and understanding of the wealth of data and resources Ensembl provides. All of our videos are found on our YouTube channel, and our YouKu channel if you’re accessing Ensembl from China.

Looking for more? Have a look at our tutorials page.

Don’t forget, we run customised browser and API workshops if you want an Ensembl expert to take you first-hand through the site.

Can’t find what you’re looking for? Just contact us and let us know!

An example of output and documentation from the Ensembl REST ServiceWe are pleased to announce the beta release of our programming language agnostic REST API, for Release 68 data, at beta.rest.ensembl.org. Our initial release provides access to:

  • Sequences (genomic, cDNA, CDS and protein)
  • VEP (Variant Effect Predictor)
  • Homologies
  • Gene Trees
  • Assembly and coordinate mapping

Data can be retrieved in JSON, XML and a variety of bioinformatical formats such as FASTA. Each endpoint is fully documented with live service responses and example clients in Perl, Python, Ruby and the Unix command line.

Since 2006, Perl has been the only language to have a supported API. Third party alternatives are available but can lag in their support of new data. The REST service has been developed using Catalyst and the Perl API providing a stable base for development and provides access to all of Ensembl’s functionality. Using the Perl API also means that any Ensembl compatible resource can provide data using the same REST server. Our sister project, Ensembl Genomes, has already taken advantage of this feature and are hosting release 15 data at test.rest.ensemblgenomes.org.

Development is on-going so please let us know about any features you would like to see in a future release. Please send any feedback to helpdesk.

 

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.