Genome 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

  • mysql
  • perl
  • javascript

Topics

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Genes, Genomes and Variation 2017 Projects

  • Stefan Dvoretskii
    Data file search API
    The Ensembl and Ensembl Genomes projects provide genomic data for over 40 thousands genomes. Considering even the increasing number of this data, it...
  • Sourabhreddy Medapati
    Enabling large file format support in Genoverse
    The motive is enable support for large binary file formats in Genoverse, a genome browser that is written in javascript. This project would involve...
  • Rachel Slater
    Gene Visualisation in Mixed Reality with Microsoft HoloLens.
    This project would involve building an application allowing genes to be visualised in ‘mixed reality’ with the Microsoft HoloLens. Mixed reality...
  • Chanaka De Silva
    Project Proposal Ensembl Track Database Mentors : Andy Yates, Stephen Trevanion
    Ensembl is a data warehousing and data sets project which helps to analyse advanced biological data. Simple this application displays a 1 dimensional...
  • Arpit Agarwal
    Strain Differential
    The objective of the project is to get a scrollable web view for gene variations after changing the reference strain of genome data in real time. The...
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2017