European Bioinformatics Institute (EMBL-EBI)

European Bioinformatics Institute (EMBL-EBI)

Hinxton, GB

Software developer (back-end) – contribute to a renown Genetic Data Platform

We are looking to recruit an enthusiastic software developer to work in the Genetic Data Platform group that is delivering EMBL-EBI’s role in the AMP-T2D Knowledge Portal and the INTERVENE project, addressing human genetic variation data in common diseases and using this data for the calculation of polygenic risk scores.

The AMP-T2D Knowledge Portal aims to make T2D-relevant genetic association data more easily accessible. The portal draws genetic associations and functional genomic data from a federated database with nodes at the Broad Institute Data Coordinating Center (DCC), the European Bioinformatics Institute (EBI), and the University of California San Diego (UCSD). It provides access to these data through application programmatic interfaces (APIs) and a web-portal with visualizations built by the Broad and the University of Michigan (UM).

The INTERVENE consortium is a 5-year EU funded project that aims to develop and test next generation tools for disease prevention, diagnosis and personalised treatment utilizing the first US-European pool of genomic and health data and integrating longitudinal and disease-relevant -omics data into genetic risk scores. INTERVENE will build a new European platform that will allow researchers and clinicians to easily calculate genetic scores with the goal to enable a wide adoption of genetic risk scores as a gold standard in clinical research. EMBL-EBI’s role is to deliver this federated platform and to integrate this with controlled access datasets.

The successful applicant will work in a team of Bioinformaticians and Software Developers to deliver EMBL-EBI’s contributions to these projects. The team is part of the Molecular Archives cluster, and sits within both the Samples, Phenotypes and Ontologies and the European genome-phenome archive (EGA). The team collaborates closely with the NHGRI-EBI GWAS Catalog, the PGS Catalog (a collaboration between University of Cambridge and EBI), the Broad Institute and the Finnish IT Center for Science (CSC).

Your role

You should be a strong programmer who is excited and interested by complex data integration and presentation problems. You’ll need to be flexible enough to learn new languages to find the right tool for the right problem. You’ll be responsible for the development and maintenance of software using a variety of tools, frameworks and technologies. You should also be keen to advance your knowledge of the latest industry standard toolkits to help continuously innovate the platform. You should be enthusiastic about full-stack development, as you’ll be expected to develop, test and deploy tools from database to user interface.

Molecular Archives Teams practice agile development methodologies, so you should have experience in working in agile teams, or be keen to learn.

You will also need to be capable of working with non-technical biologists to maintain a strong focus on the biological requirements of the platform, and ideally have familiarity with conducting user experience testing to ensure that the resource is tailored to our users’ requirements. If you have a biological background, or have worked in a bioinformatics environment in the past, you’ll have a distinct advantage but training in this area will be provided if required.

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.

Main Duties and Responsibilities

  • Developing and maintaining platform software using a combination of technologies;
  • Liaising with users to gather requirements and translating these into technical specifications and test plans;
  • Work as part of a team that follows the Agile model of software development involving sprints in which user requirements are prioritised via issue tracking software;
  • Configuring and deploying software using version control and continuous integration tools;
  • Investigating new technologies which could be utilised in platform and within the wider SPOT/EGA teams;
  • Representing the team at meetings and conferences of both a biological and technical nature held with collaborators and by external organisations;
  • Understand the role of ontologies and semantic web technologies in order to develop applications capable of semantically enriching the raw genetic data by annotation to ontologies.

You have

  • Degree in either computer science or Bioinformatics;
  • 4 years’ experience developing software and contributing to a production system or service;
  • Demonstrate a good understanding of all aspects of full stack development, including Java 8, JavaEE, Spring boot, SQL, Python;
  • Experience in creating well documented RESTful APIs;
  • Experience of containerisation with Docker and deployment in Kubernetes on different cloud environments;
  • 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

  • Experience of production software development processes and be comfortable using Git-like workflows and Continuous Integration/Deployment (CI/CD) strategies.
  • Previous experience with NoSQL databases such as MongoDB, Neo4j, Solr, or Elastic search
  • Prior experience of working with ontologies or semantic web technology

What else you need to know

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

This is a project-limited contract foreseen for 3 years (or until end 2025).

At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ and individuals from all nationalities. Visa exemptions will be offered to international candidates and details will be discussed during interview. We believe in science without borders and this continues after Brexit.

This role is based in Hinxton, UK and you will be required to relocate once it is safe to do so if you are currently based abroad. More info on how we are recruiting in this period is available on our page: Recruitment and Onboarding during Covid19.

This position is full-time (39h per week). While this position cannot be entirely remote, flexible working (alternative work schedule, flexible hours) can be possible. Many members of the team have families and dependants and we value the importance of a good work-life balance. EMBL-EBI makes progress every year towards building a more diverse workforce, making it an ideal place for smart, curious people across cultures, genders, ethnicities, and lifestyles.

About European Bioinformatics Institute (EMBL-EBI)

EMBL-EBI is a worldwide leader in bioinformatics. 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 encourage personal and professional development and are committed to ensuring our employees feel valued, supported and empowered to reach their potential at work.Surrounded by picturesque South Cambridgeshire countryside, our Campus provides employees with a relaxed atmosphere where the pursuit of scientific discovery and meaningful work, underpin every role. In addition, our employees have access to a wide range of benefits including: