Genomic sequence and annotation databases and browsers

Ensembl was created alongside the publication of the first draft of the human genome in 2001 to distribute this goldmine of information to scientists across the world. It quickly became and remains one of the most important reference databases in genomics, following the rapid development of the field. Its initial mission included finding all of the genes in the human genome. A year later, the mouse genome was published and we developed tools to directly compare genomes across species. Over the following decade, sequencing capacity increased exponentially (faster that Moore's Law in fact) and large surveys started examining more species and more individuals within each species. Our mission therefore expanded to store these datasets and statistics efficiently. Finally, in recent years, sequencing has been used to study the biochemical activity of the DNA molecule within the different tissues of an individual, prompting us to extend yet again our remit.

At the same time, Ensembl is an evolving software development project. Over 15 years, we moved from a central relational MySQL database with a Perl API and static web pages, to an array of storage technologies with a RESTful interface and an interactive front-end. We have dedicated portals for the large clades on the tree of life (known as Ensembl Genomes). Our annotations are produced through centuries of CPU time, coordinated by our powerful eHive analysis workflow manager.

Today, we are a team of nearly 60 full time staff, housed at the European Bioinformatics Institute, and we collaborate with many external contributors around the world, in particular via our Github repositories where you can see us work day-to-day. We are at the intersection of two exciting and rapidly expanding fields, and there is no lack of interesting directions to push the project.

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Technologies

  • perl
  • mysql
  • java script

Topics

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Genes, Genomes and Variation 2018 Projects

  • Tony Yang
    Automated Processing of Primary Genome Analysis
    Develop an automated system that performs analyses on newly sequenced genomes.
  • Nabil Ibtehaz
    Transcript Comparisons
    In Comparative Genomics we compare an unknown gene with some other known genes, for better inference of biological properties of that unknown gene....
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2018