API course tomorrow

Posted on April 2, 2013 by Emily (Outreach)

Due to some last minute cancellations, we have spaces on our Ensembl API course in Cambridge, tomorrow (3rd April) until Friday (5th April).

If you’re in Cambridge, know Perl and would like to learn about using the Ensembl Perl API, register here:

http://www.training.cam.ac.uk/event/564960

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Take our Browser Workshop … Online!

Posted on March 27, 2013 by Giulietta (Outreach)

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.

 

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What’s coming in Ensembl release 71

Posted on February 18, 2013 by Thomas Maurel (Production)

Ensembl release 71 is scheduled for release in April 2013. We expect this release to include, among other things:

  • SIFT scores for all possible changes to the proteome in human, mouse, zebrafish, pig, cow, chicken, rat and dog
  • New “clinically associated” summary track on Region in Detail for human
  • VISTA Enhancers updated for human and mouse to the latest release (28/1/2013).
  • New DNA methylation data
    • New whole genome bisulphite sequencing (WGBS) sperm data set for human
    • Several reduced representation bisulphite sequencing (RRBS) sets for mouse
  • Import of COSMIC version 63 and update of COSMIC structural variants
  • Updated gene sets
    • Human and zebrafish, with manual annotation from HAVANA
    • Anole lizard, including RNAseq
  • Updated cDNA alignments for human and mouse
  • Phenotype data for some farm animals
  • New assemblies
    • Chicken (Gallus_gallus4.0), including RNAseq
    • C. elegans (WBcel235)

For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.

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Ensembl Genomes release 17

Posted on February 7, 2013 by Denise (Outreach)

The Ensembl Genomes project is pleased to announce release 17 of Ensembl Genomes.

Our latest release brings over 6,000 bacterial genomes into Ensembl for the first time ever!  Users can browse these data interactively on the web with our graphical interface. Programmatic access is available through the Perl and RESTful Ensembl APIs, and through publicly accessible mysql databases. Full data dumps such as DNA sequence and protein sequence in FASTA format, annotations in GTF format, and mysql dump files are also provided on our FTP sites.

Due to this sheer number of new genomes in Ensembl Bacteria in release 17, BioMart access is no longer possible and we are now working on alternative and more powerful data retrieval tools.

An increased number of bacteria (over 120 genomes) has now been used for comparative genomics analyses across a wider range of non-bacterial genomes (from both Ensembl and Ensembl Genomes projects). This is known as Pan-taxonomic Compara and can be visualised in the gene views on the browser or accessed through the Compara database.

In addition to the thousands of new bacterial genomes, we also have six new genomes in Ensembl Fungi and one new genome in Ensembl Protists. We have also improved existing genomes and added new variation, comparative genomics and transcriptomics data for several species.

The significant milestones of this release are:

* Protein families are now classified based on PANTHER and HAMAP matches. Gene trees are provided for several but not for all bacterial genomes

* Pan–taxonomic compara now contains 123 key bacterial genomes

* Gene families are now populated by dividing all proteins on all genomes by HAMAP and PANTHER classification provided by InterPro

* Six new genomes: Komagataella pastoris, Sporisorium reilianum, Pyrenophora teres, Pyrenophora tritici-repentis, Glomerella graminicola and Melampsora larici-populina

* New EST alignments for Melampsora larici-populina, Glomerella graminicola and Leptosphaeria maculans

* Mycosphaerella graminicola has been renamed to Zymoseptoria tritici

* Updated gene sets for Anopheles gambiae

* Updated gene sets for Drosophila pseudoobscura (FlyBase version 2.30) and Drosophila simulans (FlyBase version 1.4)

* Updated cross-references for all 12 drosophilid species

* A missing chromosome in beetle (Tribolium castaneum) was also reinstated, and its gene models updated

* New and extensive variation dataset for Hordeum vulgare (barley)

* Triticum aestivum (wheat) EST and RNA-seq alignments in the syntenic context of Brachypodium are now available

* New wheat sequence search facility based on extensive genomic and transcriptomic data aligned to Brachypodium

* Solanum tuberosum (potato) EST and RNA-seq alignments are also now available

* New pairwise alignments between several plant genomes.

* A new genome of a flagellated protozoan parasite, Giardia lamblia, is now available

  • Software migration to Ensembl 70

Have fun!

The Ensembl Genomes Team

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Ensembl browser workshops in the US East Coast

Posted on February 1, 2013 by Denise (Outreach)

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

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Variants in regulatory regions

Posted on January 24, 2013 by Anja (Variation)

From release 70 we store and display information on the type of consequence a variant has on overlapping regulatory regions (Ensembl regulatory features and Ensembl motif features) for human and mouse.

Web display
Consequence types for variations overlapping regulatory features in region in detail view
One of the major benefits of this is that we can highlight the predicted consequence types for a variant overlapping regulatory regions in the region in detail view. The Variation – Genes and regulation page gives more information on the type of consequence a single variant has on a specific regulatory region.

API
We store the data in two new tables: regulatory_feature_variation and motif_feature_variation. Both are populated in a similar way to the transcript_variation table. You can find further information on the table structures on our Variation database schema description page.

You can access the data using the Ensembl Variation Perl API. Please check the API documentation for examples of how to use the RegulatoryFeatureVariationAdaptor and the MotifFeatureVariationAdaptor. These new modules allow you to fetch MotifFeatureVariations or RegulatoryFeatureVariations on a VariationFeature, MotifFeature or RegulatoryFeature. This is in addition to the existing functionality for getting all RegulatoryVariationFeatures and MotifFeatureVariations using the VariationFeatureAdaptor.

If you have any questions please email helpdesk.

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Comparative Genomics Project Leader

Posted on January 21, 2013 by Fiona, on behalf e! Variation

Are you interested in joining the Ensembl project based in the UK, near Cambridge? The Comparative Genomics team currently has an open position for a Project leader.

The Ensembl Compara team develops new and established methods for:

  • whole genome sequence alignment,
  • assignment of gene families,
  • annotation of orthologs and paralogs.

The comparative genomics project leader will set the direction and priorities of Ensembl Compara and will participate in major international genomics projects. Additional responsibilities include working to develop effective data displays, hiring and training staff and participation in the overall leadership of the Ensembl project.

For full details, see the job description. If you have any queries about this position feel free to contact Paul Flicek (flicek@ebi.ac.uk). All applications must be sent via the website above before 25 January.

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Ensembl 70 has been released!

Posted on January 17, 2013 by Thomas Maurel (Production)

We are pleased to announce release 70 of Ensembl.

What’s new in e!70?

  • New web features (sharing and streamlined interface to add your data to Ensembl).
  • Updated patches for the Human assembly (GRCh37.p10) and inclusion of patches for the Mouse assembly (GRCm38.p1).
  • Reanalysed Human BodyMap data from Illumina using the recently updated RNASeq pipeline. The BodyMap BAM files can be downloaded from our ftp site.
  • Imported HGMD-PUBLIC sequence variation data from release 2012.3 with regulatory data for Human.
  • Updated HAVANA manual curation for Human and Mouse.
  • A new regulatory build for Mouse including a much broader coverage for the Embryonic Fibroblast (MEF) build and additional data on other cell types.
  • New assemblies for Rat (Rnor 5.0) and Cat (Felis catus 6.2) and a new geneset for Fruitfly (FlyBase version 5.46).

Sharing pages and images and other web integration

Sharing is now enabled on Ensembl views. We have added a share icon in the toolbar above configurable images and a share button in the left menu on each page. Click on the share icon or button to send the link to a collaborator or colleague.  This works with uploaded data, and is a quick way to share your own data track with others. More information can be found in our FAQ.

We have merged the web interfaces for uploading your data and attaching it via a URL into a single form that changes as you select options. Click “Add your Data” to get started.

For the convenience of our Chinese users, if your IP address is based in China you will be served the Youku versions of our video tutorials instead of the YouTube ones.

Sequence Variation

We have new Human structural variants from COSMIC release 61. Sequence variation for Mouse and Cow have been updated to dbSNP 137. Rat and Cat have been remapped to the new assembly. Also we have imported HGMD-PUBLIC sequence variation data from release 2012.3 with regulatory data for Human.

New Assemblies

We are happy to introduce two major assembly update for this release.

Rattus norvegicusThe Norway rat (Rattus norvegicus) genome, Rnor_5.0 was provided by the Rat Genome Sequencing Consortium. Rat models have been used to advance medical research in many areas like cardiovascular diseases, psychiatric disorders, neural regeneration, diabetes, cancer, wound and bone healing. Drug development also relies on rat models to demonstrate therapeutic efficacy and assess toxicity of drug compounds prior to human clinical trials.

The Felis_catus-6.2 assembly of the cat (Felis catus) genome was Felis catusproduced by the International Cat Genome Sequencing Consortium. The domestic cat is a significant model organism for biomedical research, especially in infectious disease research, and has aided human disease in research fields including neuroscience, behavioural biology, reproductive physiology and endocrinology.

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File-based tracks – scheduled downtime

Posted on January 11, 2013 by Ensembl

Owing to urgent storage maintenance work at the Wellcome Trust Sanger Institute some Ensembl data will be unavailable on the morning (UK time) of Monday 14th January, as it is served from data files on disk rather than from databases. This includes some human and mouse regulation data (e.g. DNA methylation) and all RNAseq tracks (for all species with this data, including human, mouse, zebrafish, chimp and orangutan).

Only www.ensembl.org and archives from version 62 onwards will be affected – this data will still be available on our FTP site and mirror websites if you need it during this period.

Thank you for your patience.

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Learn Ensembl Online

Posted on January 3, 2013 by Emily (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! helpdesk@ensembl.org

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