Senior Software Developer
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 2 years and 6 months
Grading: 6 (monthly salary starting at £2,994,54 after tax)
Closing Date: 8 January 2020
Reference Number: EBI01559
The Samples, Phenotypes and Ontologies team are looking to recruit an enthusiastic, highly motivated software developer to join them. You will be working on the Human Cell Atlas (HCA - Data Coordination Platform (DCP) funded by the Chan-Zuckerberg Initiative.  The HCA-DCP will enable scientists to share, organise and analyse cellular-resolution data that the Human Cell Atlas community can use to create comprehensive reference maps of all human cells.

You will be part of a cross-functional team of bioinformaticians and software developers, building tools and services to support data contributors to the HCA-DCP.  We are looking for a full stack developer with an interest in building systems that can deal with complex data. Our mission is to provide software and tools to assist scientists in making their data Findable, Accessible, Interoperable and Reusable (FAIR) via the HCA-DCP. In this role, you will work to develop the EBI’s “Semantics as a Service” platform that provides terminology standards and ontologies to the HCA-DCP data ingestion system.

You’ll be developing a knowledge graph of biological concepts used in single-cell research. This knowledge graph will be used to support the semantic annotation of metadata submitted to the DCP, and ensure data coming into the DCP is interoperable for downstream querying and analysis. You will explore novel ways to integrate the knowledge graph with machine learning methods to predict and automate the markup of datasets with ontologies. You will also develop systems that improve how the knowledge graph can be used in data search and visualisation. Our goal is to ensure that all data submitted by the HCA community is well annotated and semantically interoperable, providing a high-quality resource for the entire scientific community.

The position is a fantastic opportunity to gain hands-on experience at working on a project with major scientific impact in a world-leading bioinformatics institute.  

Your role

Under the supervision of the Samples, Phenotypes and Ontologies Coordinator, you will join a team of software developers building the EBI’s Semantics as a Service platform. Your role will include the following duties and responsibilities:
  • Develop and maintain the pipeline that constructs the set of ontology and terminology standards used by the HCA;
  • Build services on our existing knowledge graph to assist contributors to the HCA in annotating their data to appropriate standards;
  • Devise new services for the automated prediction and mapping of data being submitted to the HCA;
  • Develop tools to support data validation against the standards used by the HCA;
  • Develop user-interface widgets for the presentation of data in the knowledge graph;
  • Assist in the development of a semantic search engine that utilises the structure of our knowledge graph to support data discovery through query expansion;
  • Develop a robust CI/CD strategy for deploying the ontology service in cloud environments;
  • Ensure the HCA metadata schema conforms to FAIR principles and identify areas that require further fairification.

You have

  • BSc in Computer Science, Bioinformatics or related. Equivalent, demonstrated professional experience will be considered.     
  • Proven experience in collaborative development projects
  • Minimum 5 years’ experience developing full stack applications in Java
  • A reliable, independent worker
  • Thorough and organised. You can follow up where results diverge from expectations, and assess and address those differences
  • Good communication and interpersonal skills, both oral and written
  • Ability to work to tight deadlines
  • Ability to interpret and contribute to technical documents
  • Proficiency in written and spoken English

You might also have

  • Knowledge of biology, biochemistry, genomics or bioinformatics
  • Experience working within an agile framework
  • Evidence of delivering training and support to users in a similar project
  •  Knowledge of single-cell experimental technologies
  • Experience of the Spring framework
  • Experience with any of Neo4j, MongoDB, Elasticsearch, Apache Solr
  •  An understanding of graph databases, knowledge graphs, ontologies and taxonomies
  • Practical experience of working with ontology formats such as OBO, RDF and OWL.
  • Experience with Docker, Kubernetes and deploying applications in cloud environment
  • Experience of writing scientific papers and reports
  • Ability to establish and drive multi-person plans  towards a successful outcome

Why join us

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 over 27 member states and two associate member states. 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.

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. For more information about pay and benefits click here

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.

What else you need to know

To view a copy of the full job description please click here

To apply please submit a covering letter and CV through our online system.

Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. 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.