The Ensembl “Geek for a Week” experience is a way for Ensembl software developers and our scientific collaborators to work in an intensive environment for short periods of time on the Wellcome Genome Campus in Hinxton, UK. Visiting “Geeks” will be assigned a desk within the Ensembl team at the EMBL-EBI and have an opportunity to work on their project with direct access to the developers who built the tools and the Ensembl scientists using these for data analysis. Here, we meet Yeorgia Argirou, who joined us in November 2022 as a “Geek for a Week”.
Yeorgia is currently doing a Doctoral Career Development Fund (DCDF) to develop her bioinformatic skills. Prior to this she was doing her PhD with NIAB, the University of Cambridge, and industrial partner KWS, looking at the effects of novel genetic diversity in hybrid wheat.
A set of genes in the current version of the Arabidopsis thaliana genome in Ensembl Plants have translation errors, which have resulted in them incorrectly being labelled as non-coding. To find the underlying reasons why these gene models were incorrect, the genomic sequences from Ensembl were compared with data from TAIR and Uniprot entries. The Ensembl MySQL database was then updated with the necessary edits / frameshifts to produce successful translations.
Although this was a short project, I developed lots of new skills and knowledge. I had used Ensembl before but not extensively. However, this project improved not only my knowledge of how to use Ensembl, but also of what goes on behind the scenes. This included learning MySQL which I had no knowledge of before and familiarising myself with the Ensembl MySQL database. In addition to this I used resources that I had previously not used or had limited use of such as TAIR and Uniprot.