Scientific Programmer/Bioinformatician

Hinxton, Cambridgeshire, UK
Competitive Salary
May 18, 2018
May 18, 2018
Contract Type
Full Time
Job Type
Scientific Programmer/BioinformaticianLocation:EMBL-EBI Hinxton near Cambridge, UK Staff Category:Staff Member
Contract Duration:3 years initially (renewable)Grading:5 or 6 (monthly salary starting at £2,552 or £2,855 after tax). For more information about pay and benefits click hereClosing Date:24th June 2018
Reference Number:EBI_01224Job 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 Scientific programmer/Bioinformatician with a strong background in Structural Biology to further develop the wwPDB validation pipeline for structure data. The wwPDB validation pipeline is a critical component of the OneDep data deposition and biocuration system. The successful candidate will work closely with other members of the global OneDep team to implement better validation metrics for bound ligands and will be responsible for the day-to-day maintenance of the validation pipeline. The candidate will also be involved in maintaining and developing the SIFTS ( project, which is a critical component of Bioinformatics infrastructure providing the “glue” between PDB structure data and sequence information from UniProt and other databases. Major bioinformatics resources use these data to reliably link PDB structure information with other biomedical resources.

The tasks for this post include:

  • to implement improvements to the wwPDB validation pipeline, particularly pertaining to validation of small molecules;
  • to maintain the wwPDB validation pipeline;
  • to help maintain the OndeDep deposition and biocuration processes;
  • to develop and maintain SIFTS infrastructure;
  • to extend the existing PDBe REST API by developing new calls to export additional SIFTS data (Current API:;
  • to interact with other EMBL-EBI and external teams

The successful candidate will report to the coordinator for the Data Enrichment and Integration team at PDBe, Aleksandras Gutmanas. This is an opportunity for the right person to contribute to the wwPDB mission of archiving high quality structure data as well as develop an excellent understanding of complex biological data and developing data integration infrastructure.

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 23 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 Scientific programmer or a Bioinformatician with strong software engineering skills. You should be able to work both independently and in close collaboration with the wwPDB OneDep and PDBe team members. You will also interact with other teams at EMBL-EBI and other external collaborators. Excellent communication and interpersonal skills as well as excellent knowledge of English are therefore required.

You should hold a PhD in Structural biology, Bioinformatics or Chemistry and should have a minimum 2 years’ work experience in Structural biology, Bioinformatics or related subjects. A strong knowledge of Structural biology is expected.

You will have an excellent knowledge of Python (scripting, data integration, REST API development), and a basic understanding of SQL (querying). Some understanding of biomedical ontologies and RDF is desirable but not a requirement of the role.

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, cafés 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.

The initial contract is for a period of three years with the possibility of a fixed-term extension.

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

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