Job Details
Software Developer, Proteomics Resources


EMBL-EBI Hinxton near Cambridge, UK

Staff Category:

Staff Member

Contract Duration:

3 Years


5 (monthly salary starting at £2,552 after tax). For more information about pay and benefits click here

Closing Date:

22nd November 2017

Reference Number:

Job Description
Are you a motivated software developer who wants to work with biological data? We are looking for an enthusiastic Full Stack Java Developer to join the Proteomics Team at the European Bioinformatics Institute (EMBL-EBI). The team is responsible of the maintenance and further development of the popular PRIDE (PRoteomics IDEntifications) database and related resources such as PRIDE Cluster. PRIDE is a world-leading international proteomics database, a founding member of ProteomeXchange (PX) Consortium, that is capturing large-scale mass spectrometry (MS)-based proteomics data from the scientific community, and currently managing hundreds of TBs of data. In addition, we are a major contributor to international standardisation efforts under the umbrella of the Proteomics Standards Initiative.

The successful candidate will be involved in the design and development of scalable Restful web services for PRIDE and ProteomeXchange resources using cutting-edge open source frameworks and Big Data technologies. A significant part of these efforts will be devoted to the implementation of new data standards and standard interfaces developed by the Proteomics Standards Initiative in the context of a project funded by the NIH.
As the Proteomics Software Developer you will:
  • Design/develop interfaces for proteomics resources (e.g. PRIDE Archive, ProteomeXchange and PRIDE Cluster).
  • Build and development of a scalable and responsive backend system that enables the interaction with thousands of users and the retrieval of millions of mass spectra, peptide and proteins evidences.
  • Support the optimization of web application components for maximum speed and scalability when working with “big data”.
  • Collaborate with other developers in the team to redesign/re-implement backend components for more responsive UI interfaces and a better user experience across our resources.
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
You should have a degree in computer science and be able to demonstrate a minimum of 3 years’ experience in software development, ideally in a life science environment. You will have a minimum of 3 years’ experience in software development in an International environment. Experience in bioinformatics would be desirable. Experience in mass spectrometry proteomics would be a major advantage.
If successful, you will work in a highly international, team-oriented environment and collaborate closely with external partners. Excellent communication skills are essential. The ability to work independently, under time pressure, and the dedication to communicate openly are necessary skills.
The following skills are requirements of the role:
  • Proficient programmer in Java.
  • Proficient understanding of REST APIs and knowledge of how to interface with them.
  • Proficient understanding of indexing and database technologies and how to interact with them (e.g. SolR, Lucene, Elasticsearch, MongoDB, Neo4J).
  • Good understanding of asynchronous request handling, and partial results updates on Restful web services.
  • Good understanding of Spring Framework (Spring Batch, Spring Boot).
  • Good understanding of technologies such as JSON, XML, NoSQL and relational databases.
  • Good understanding of code versioning tools, such as Git.
  • Experience with other backend languages such as Python or Scala.
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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