Training – Page 2 – Ensembl Blog

Free Ensembl Browser and REST API virtual workshops in March

26th February 2021 by Michal Szpak·Comments Off

Update: registration is now closed as all of the available places on the virtual Ensembl browser and REST API workshops have been filled. If you would like to be added to the waiting list, please e-mail the Ensembl Helpdesk.

We’ve got another round of the free virtual Ensembl workshops covering the genome browser and the REST API. The Browser workshop will be held between Tuesday 16th March – Thursday 18th March 2021 (9am-1pm) and the REST API workshop will be held between Tuesday 23rd March – Thursday 25th March 2021 (9am-11:30am). Read on for more information and registration instructions.

Open: Ensembl Browser and REST API virtual workshops

6th January 2021 by Ben (Outreach)·2 Comments

Registration is now open for two free virtual Ensembl workshops covering the genome browser and the REST API. The Browser workshop will be held between Tuesday 26th January – Thursday 28th January 2021 (2pm-5pm) and the REST API workshop will be held between Wednesday 3rd February – Friday 5th February 2021 (2pm-4:15pm). More information and registration instructions can be found below.

Training in the Time of Pandemic

20th November 2020 by Michal Szpak·Comments Off

Were you planning on attending or hosting an Ensembl workshop in 2020, but your plans got cancelled due to the SARS-CoV-2 pandemic? All is not lost, as we’re still providing live virtual training and here’s how it works.

Get training, virtually

21st October 2020 by Emily (Outreach)·Comments Off

You’re invited to join us for a free, open, virtual training course, 30th November – 2nd December. The course will be held using the Blackboard training platform.

Cool stuff the Ensembl VEP can do: annotating structural variants

27th March 2020 by Astrid (Outreach)·Comments Off

The Ensembl VEP does not only allow you to annotate short variants, such as SNPs and short insertions or deletions, but also some types of structural variants.

Cool stuff the Ensembl VEP can do: install using Docker

28th February 2020 by Emily (Outreach)·Comments Off

We know that installing the VEP is not always trivial – there are dependencies and modules that you may or may not have already, and your existing setup may require different module versions. It’s also designed for a Linux system and installing on, for example, Windows, can be complex. To get around this, the VEP and all its dependencies are available in a Docker image, so that you can install everything with just a few simple commands.

Reaching under-served

30th January 2020 by Michal Szpak·Comments Off

Outreach is, by its definition, tied to identifying and serving under-served populations. How does Ensembl address that? We provide services to communities who might not otherwise have access to those services through scientific outreach in low-middle income countries (LMIC) and by public engagement in groups that might lack science exposure. We provide training materials, tutorials and helpdesk support, spread awareness on social media and run webinars, as well as classroom workshops around the world. Our resources are open source and open access, freely available to anyone.

Cool stuff the Ensembl VEP can do: write your own plugin

24th January 2020 by Emily (Outreach)·Comments Off

Plugins can be an excellent way to extend the functionality of the VEP. They can be used to look-up information in external databases or use the Ensembl API to add to or filter your VEP output. Many plugins have already been written, both by us and external groups, but with a bit of Perl you can easily write your own.

Cool stuff the Ensembl VEP can do: external gene regulation annotation

22nd November 2019 by Emily (Outreach)·Comments Off

The interpretation of non-coding variants is more challenging than that of coding variants as less prediction methods and reference data are available. On top of the annotation provided for human and mouse in the Ensembl Regulatory Build, the Ensembl Variant Effect Predictor (VEP) also integrates two other human-specific datasets providing information about how variants can affect gene expression. The plugins, satMutMPRA and FunMotifs, are available for use with command-line VEP. One provides detailed information on the impact on expression of variants in the regulatory regions of disease-associated genes; the other an alternative set of genome-wide transcription factor binding motifs.

Cool stuff the Ensembl VEP can do: transcript selection

25th October 2019 by Emily (Outreach)·Comments Off

By default VEP will tell you the consequences for every transcript affected by a variant. You may wish to prioritise your analysis to only the most important or well supported transcripts for each gene, and VEP provides information to help you do that.

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Category: Training