One of the biggest headaches when working with insertions and deletions is how many different ways you can represent the same variant. If you’re looking to find out if there’s already known allele frequencies or phenotypes at a locus, you want to make sure that you find the right one. The VEP can take that headache away through normalisation of variants.
Author: Emily (Outreach)
For the third year in a row, we’re lucky to have student developers working with us as part of Google Summer of Code. We’ve got three GSOC-ers this year, working on some really exciting projects: Zeyu Tony Yang, working on primary genome analysis, Nabil Ibtehaz, working on transcript-level orthology and Somesh Chaturvedi, working on retrieving reference sequences with APIs.
GSOC is a project set up by Google that places students in open source projects to take on a short independent coding project, and pays them for it. We have to pass rigorous selection criteria to be allowed to offer projects on GSOC, and the students have to be selected by both Google and us to take part. It means the GSOC-ers are the Top Gun of student developers. We think this is a really great opportunity, both for open source projects like us, who get a fresh pair of eyes to take a look at something that we’ve maybe put on the back-burner, and for the students, who get experience working on a real-world coding project during their university summer break.
As of Ensembl release 93, which is due at the end of the month, the Gene Variant Image view will be retired for human. We have elected to retire this page because we feel that the density of known genetic variation is too great for this view to be informative in its current form.
Some Variant Effect Predictor (VEP) jobs are small, just ten or fewer variants, and that’s easy. Some VEP jobs are big, if you do variant calling on one whole human genome, that’s five million variants! The more variants you have, the more computing power the VEP needs to process them, which can make it slow. But there are ways to speed it up.
The VEP (Variant Effect Predictor) is our most popular tool and is incredibly useful for annotating genetic variants with the genes they hit and what effect they have on them. But did you know you can filter your results? Both in the web interface and using the script?
We think conferences are great opportunities to use talks and posters to tell people about all the cool stuff we’re developing, provide training with workshops and learn more about what’s going on in our fields of interest. Ensembl team members attend many conferences a year and 2018 is no exception, we’re planning to attend twenty (so far)!
This month we’re meeting Carla from our comparative genomics team (which we call compara).
We’re holding an Ensembl Perl API course at the Genome Campus in the UK in April. The course give you chance to learn how to access the database directly from the people who produce the databases and write the APIs themselves. It is aimed at bioinformaticians and wet-lab scientists who are familiar with Object Oriented Perl.
This four-day course costs only £140, which includes daily transport to the campus from Cambridge city centre and refreshments (the fee is to cover only these expenses).
Please visit the course page for more details on the content and how to apply.