Bioinformatician / Scientific Programmer

Competitive Salary
12 Aug 2017
09 Sep 2017
Contract Type
Full Time
Bioinformatician / Scientific ProgrammerLocation:EMBL-EBI Hinxton near Cambridge, UK Staff Category:Staff Member
Contract Duration:2 years and 4 months
Grading:5 (monthly salary starting at GBP2,507 after tax). For more information about pay and benefits click hereClosing Date:13th August 2017
Reference Number:EBI_00941
Job Description

The Protein Data Bank in Europe Team (PDBe; is part of the worldwide Protein Data Bank organisation (wwPDB;, which maintains the global archive of structural data on biomacromolecules - the PDB. The PDBe Team also maintains a number of databases that support deposition and advanced search services for structural biologists and the wider scientific community. The Team consists of an international and inter-disciplinary mix of professionals: scientists, software engineers, and database engineers. The PDBe and CS3DB teams form the Molecular and Cellular Structure cluster within the EBI.

We are looking for a bioinformatician to integrate value-added information on enzymes and catalytic binding sites with the PDB structure data and make it available programmatically and via PDBe website. The work will involve close collaboration with the Thornton research group and with UniProt and ChEMBL teams, all co-located at the EBI.

The tasks for this post include:

  • to identify the data that will be integrated into PDBe infrastructure and define formats and ontologies for its standardisation;
  • to design and develop a process for data integration;
  • to design and develop reusable web components to display this data on the PDBe website;
  • to integrate the data in the PDBe search system;
  • to extend the existing PDBe REST API by developing new calls to export this data (Current API: );
  • to interact with other EMBL-EBI teams which are participating in this data sharing project, primarily Thornton research group;
  • Contribute to the biocuration work at PDBe.

The successful candidate will report to the project manager for the Data and Integration team at PDBe, Aleksandras Gutmanas. This is an opportunity for the right person to develop an excellent understanding of complex biological data (structure, sequence and enzyme chemistry), how it relates to each other and how it can be standardised, and then develop robust mechanisms for data integration, visualisation and access.

At EMBL-EBI, we help scientists realise the potential of 'big data' in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 22 member states and two associate member states and proud to be an equal-opportunity employer. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

Qualifications and Experience

We are looking for a bioinformatician with strong software engineering skills. The post holder should be able to work both independently and in close collaboration with the rest of PDBe team members and with other teams at EMBL-EBI. Excellent communication and interpersonal skills as well as excellent knowledge of English are therefore required.

You should hold a Master's degree or Bachelor's degree and minimum 2 years' work experience in Bioinformatics, Computer Science or related subjects. Strong knowledge of structural biology, protein sequencing or enzyme chemistry is expected. The ideal candidate would have a PhD in Bioinformatics or related fields.

You should have excellent knowledge of Python (scripting, data integration, REST API development) and a basic understanding of SQL (querying). Ideally you will have experience in Web technologies (JavaScript - Web component development with Polymer and Angular 2, Front end development - Responsive design templates, HTML/CSS) or Apache Solr.


EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises 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.

We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise - something you probably won't find anywhere else.

If you've ever visited the campus you'll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, caf??s and restaurant and a library.

Application Instructions

To apply please submit a covering letter and CV, with two referees, through our online system.

Additional Information

Applications are welcome from all nationalities - visa information will be discussed in more depth with applicants selected for interview.

EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.

This position is limited to the project duration specified.

Applications will close at 23:00 GMT on the date listed above.

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