Scientific Programmer Bioimaging & EMPIAR

European Bioinformatics Institute (EMBL-EBI)
Job Location
Wellcome Trust Genome Campus
CB10 1SD
United Kingdom

The remuneration package includes a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation.

EMBL-EBI staff also enjoy excellent sports facilities, a free shuttle bus to Cambridge and other nearby centres, an activve sports and social club and an attractive working environment set in 55 acres of parkland

Job Description

We are looking to recruit an experienced and motivated Scientific Programmer to join the Protein Data Bank in Europe (PDBe) team at the European Bioinformatics Institute (EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK.

The Protein Data Bank in Europe (PDBe; is a world leader in archiving and dissemination of 3D biomacromolecular structure data. Together with our international partners, PDBe accepts and curates depositions of structural data for the two global archives, PDB and EMDB. PDBe also maintains a number of databases that support advanced search services for structural biologists and the wider scientific community. The team consists of an international and inter-disciplinary mix of professionals (scientists and IT specialists).

PDBe has recently launched EMPIAR (, an archive of raw 2D image data from electron microscopy and electron tomography experiments. We now plan to extend and improve the archival, integration and dissemination of cellular imaging data from a range of other modalities including 3D scanning electron microscopy (3D-SEM), soft X-ray tomography (SXT) and correlative light and electron microscopy (CLEM). We are therefore seeking to recruit an enthusiastic scientific programmer with outstanding programming skills to join the EMPIAR development team.

The post will involve the development of:

  1. data models to represent meta-data from the different imaging modalities;

  2. software for reading/writing and manipulating image data;

  3. software for depositing, archiving, curating and distributing image data.

    This is a unique opportunity for the right individual to make an impact on the future of structural biology where access to integrated information across a range of length scales and from a variety of biological data resources will enable exciting new knowledge discovery.

  4. The EBI is part of the European Molecular Biology Laboratory (EMBL) and is Europe's leading provider of information services to biological researchers in academia and industry.


Applicants should hold an MSc or PhD in physics, mathematics, (bio-)chemistry, biology or similar, involving the application of computational methods in the life sciences. Applicants should have at least two years experience with professional scientific software development (design, implementation, and maintenance).

Applicants should be fluent in one or more higher-level programming languages (e.g., C++, Java, Fortran), in scripting languages (esp. Python) and in SQL. Experience in developing web-based applications (especially using the Python Django framework) and databases is highly desirable. Also desirable are a familiarity with building advanced JavaScript-driven and HTML5 graphical user interfaces and with data modelling concepts and tools (e.g., XML, XSD, RDF and OWL). A background in, or a good level of understanding of imaging in biology would be advantageous.

Excellent written and oral communication skills (reflected in the cover letter), fluency in English, ability to work in a team and with international collaborators, and attention to detail are required. The position requires occasional travel, mainly in the UK and Europe.

How to Apply

Please apply online through

About Our Organization

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. We provide a dynamic, international working environment and have close ties with both the University of Cambridge and the Wellcome Trust Sanger Institute

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