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Scientific Programmer EMPIAR 3D Browser

Employer: European Bioinformatics Institute (EMBL-EBI)
Posted: June 9, 2014
Expires: August 5, 2014
Requisition number: EBI_00397

Science jobs from European Bioinformatics Institute (EMBL-EBI):
We are seeking an enthusiastic scientific programmer to join the Protein Data Bank in Europe team at the European Bioinformatics Institute (EMBL-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 obtained funding from UK research councils to extend and improve the archival, integration and dissemination of 3D cryo-electron microscopy (EM) and tomography (ET) data. For this project, called EMPIAR, we require a scientific programmer with outstanding programming skills.

The post of "Scientific Programmer EMPIAR 3D Browser" will involve the development of:

1. software for interactive browsing of integrated 3D structural data at scales from molecules to cells from the PDB and EMDB archives; 2. software for adding biologically meaningful annotations to predefined regions of interest ("segmentations") of 3D EM and ET data

Interview for this post will be held on either the 15th or 16th July 2014.

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.

The EBI is part of the European Molecular Biology Laboratory (EMBL) and is a world-leading bioinformatics centre, We provide a dynamic, international working environment and our staff enjoy many benefits including excellent sports facilities, a free shuttle bus to Cambridge and other nearby centres, an active sports and social club and an attractive working environment in 55 acres of land. EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.

The successful candidate should hold an MSc or PhD in computer science, bioinformatics, physics, mathematics, (bio)chemistry, biology or similar, with an emphasis on 3D image processing and visualisation as well as have at least two years experience with professional scientific software development (design, implementation and maintenance). A background in, or a good level of understanding of structural biology would be advantageous.

In addition, you should be fluent in one or more higher-level programming languages (esp. Java or C++) and in scripting languages (esp. Python). Experience in 3D rendering and visualisation, developing web based applications (esp. using the Python Django framework), code parallelisation and optimisation, HTML5, OpenGL or equivalent, and GPUs, is highly desirable. A familiarity with building advanced JavaScript-driven graphical user interfaces (using frameworks like jQuery and YUI) would be highly beneficial.

Excellent oral and written communications 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.

This position requires occasional travel, mainly in the UK or Europe.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

We welcome applications from all nationalities. Visa information will be discussed in more depth with applicants selected for interview

Don't forget to mention NatureJobs when applying.

Apply for European Bioinformatics Institute (EMBL-EBI)
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