Ensembl and friends at PAG XXVII

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Excited for PAG? So are we! You can find several representatives of Ensembl at the conference, if not during our talks, workshops and posters then at the EBI booth 309 where we can chat with you about your data and how to use Ensembl.

A full schedule of talks, posters and demonstrations from researchers and staff at the EBI, is at the end of this blog. Here we highlight where you can find members of Ensembl during the conference.

Sunday 13th January

8:00-12:40: Workshop, Genome annotation resources at the EBI

  • 8:00 – 9:00 “Browsing genes and genomes with Ensembl and Ensembl genomes”
Presenter: Erin Haskell, Ensembl
Twitter: @ensembl and @mycoacia
Session ID: W505

Summary: A brief introduction to Ensembl and Ensembl genomes, highlighting new data added in 2018, covering the basics of the data and using the browser as well as how to use the popular tools, the Variant Effect Predictor (VEP) and BioMart. This session consists of presentations and live demonstrations in the browser. Workshop materials can be found online at the Ensembl training portal.

  • 09:00 – 09:30 “Manual gene annotation in Ensembl”
Presenter: Jane Loveland, GENCODE Project
Twitter: @GencodeGenes
Session ID: W506
Summary : The Human and Vertebrate Analysis and Annotation (HAVANA) team at the European Bioinformatics Institute (EBI) are part of the Ensembl team and undertake manual annotation of vertebrate genomic sequence. Recently the project has annotated whole genomes and chromosomes for zebrafish, pig and rat and specific regions of interest, such as the Major Histocompatibility Complex (MHC), for selected organisms.

Monday 14th January

10:00-11:30: Poster, “Visualising the Wheat Genome in Ensembl Plants”

Presenter: Guy Naamati, Ensembl Plants
Poster number: PE1008
Summary : Ensembl Plants was very fortunate to be the first place to offer the new IWGSC RefSeq v.1.0 genome assembly, the first chromosome level assembly of bread wheat. An important feature of Ensembl Plants is the Genome Browser which allows visualization and analysis of plant genomic sequences including gene annotation, genetic variation and comparative genomics. This assembly and visualization adds to tremendous advancements in wheat research in the last few years, and Ensembl Plants remains an optimal platform to visualize and analyze this important genome. Visit Guy’s poster for a chat about what Ensembl can offer in regard to browsing the new wheat genome.

13:50 – 14:10: Talk, “Exploring your data in Ensembl” 

Presenter: Erin Haskell, Ensembl
Twitter: @ensembl and @mycoacia
Session ID: C10

Summary: Ensembl has a wealth of data, but did you know you can upload your own data to compare it to the reference genomes we offer? In this session we will show you how you can upload and configure your own experimental data in Ensembl, to aid with analysis. We will demonstrate direct file upload and introduce resources for uploading files by URL, which is necessary for larger file sizes. We will also cover how to search the Track Hub Registry for additional datasets available for display in the Ensembl browsers. Workshop materials can be found online at the Ensembl training portal.

15:00 – 16:30: Poster, “Ensembl updates for farm animals” 

Presenter: Thibaut Hourlier, Ensembl
Twitter: @ensembl
Poster ID: PO0463

Summary: 2018 was a bumper year for new species in Ensembl, where we have doubled the number of vertebrate species we provide annotations for. Three major species, chicken, horse, and cow  had their assembly updated during the last year. At the same time, we annotated donkey for its closeness to horse. Salmonids are a group of fish of great agricultural importance. We annotated a set of salmonids containing the Atlantic salmon, the coho salmon, the chinook salmon  and rainbow trout. Visit Thibaut’s poster to have a chat about the annotation of these new species.

 

Tuesday 15th January

09:30 – 10:30: Booth demonstration, Using Ensembl

Presenter: Erin Haskell, Ensembl
Twitter: @ensembl and @mycoacia

Summary: There are several live demo session at the EBI booth (#309), and our slot is on the Tuesday morning coffee break. Pop along with your coffee for a chat about your data and what you would like to know how to do in Ensembl. Live demonstrations in the browser and expert help. Please come along for a chat if you are interested in hosting your own Ensembl workshop.

15:30 – 15:50: Talk, “Visualizing the IWGSC Refseq v1.0 Wheat Assembly in Ensembl Plants”

Presenter: Guy Naamati, Ensembl Plants
Session ID: W682
Summary: Another opportunity to hear about the new wheat genome assembly in Ensembl. Guy’s talk will take place in the IWGSC – Wheat Genome Manual and Functional Annotation session.

Schedule of EBI talks, posters and demonstrations