Software Developer (Back-End, Gwas Catalog)

European Bioinformatics Institute (Embl-Ebi) | Hinxton

Date listed

1 month ago

Employment Type

Full time

Glassdoor Rating

4/5 (59 reviews)

The Samples, Phenotypes and Ontologies team is part of the Molecular Archives Cluster and shares projects such as the GWAS (Genome-Wide Association Study) Catalog with the Genes, Genomes and Variation Cluster. We also collaborate closely with EMBL-EBI colleagues.

The GWAS Catalog is a manually curated, high-quality repository of all published genome-wide association studies and has been running since 2008. It is considered the “go-to” resource for looking up findings relating human genotype to phenotype associations. GWAS studies give scientists insight into the association between small variations in the human genome, and biological traits, phenotypes or diseases. The GWAS Catalog is responsible for collecting these data and making them Findable, Accessible, Interoperable and Reusable (FAIR) so they can be served back to the community for analysis and discovery.  We’re looking for an experienced software developer to join the GWAS Catalog development team and help take our infrastructure to the next level.  You’ll be working on the full software stack as a DevOps engineer and have the opportunity to influence the design and development of the system to meet future challenges in this exciting era of genomic science.

You should be a strong Java 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 the GWAS Catalog software using a variety of tools, frameworks and technologies, including Spring, Thymeleaf and Bootstrap.  You should also be keen to advance your knowledge of the latest industry standard toolkits to help continuously innovate the Catalog.  You should be enthusiastic about full-stack development, as you’ll be expected to develop, test and deploy tools from database to user interface.

The Samples, Phenotypes and Ontologies Team practices 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 GWAS Catalog, and ideally have familiarity with conducting user experience testing to ensure that the Catalog 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.

Your role

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 will involve:

  • Developing and maintaining NHGRI-EBI GWAS Catalog software using a combination of technologies;
  • Developing new applications to complement and replace the existing NHGRI-EBI GWAS Catalog infrastructure—this might include developing a new curation interface, or building a pipeline for mapping GWAS data to other genomic resources like Ensembl or dbGaP;
  • 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;
  • Configure and deploy software using version control and continuous integration tools;
  • Investigating new technologies which could be utilised in NHGRI-EBI GWAS Catalog development and within the wider SPOT team;
  • Representing the SPOT/NHGRI-EBI GWAS 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 GWAS data by annotation to ontologies—prior experience of working with ontologies or semantic web technologies would be desirable.

You have

  • A good understanding of all aspects of full stack development, including Java 8, JavaEE, Spring boot, SQL, Web MVC, HTML5, CSS, Thymeleaf, ES6 and modern javascript frameworks;
  • Experience in creating well documented RESTful APIs and Graph QL APIs;
  • Experience of containerisation with Docker and deployment in Kubernetes on different cloud environments;
  • Experience of software development processes and be comfortable using Git-like workflows and Continuous Integration/Deployment (CI/CD) strategies;
  • 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

  • Previous experience with NoSQL databases such as MongoDB, Neo4j, Solr, or Elastic search;
  • Prior experience of working with ontologies or semantic web technology.

Why join us

Our supportive culture encourages personal and professional development and we are committed to ensuring our employees feel valued, supported and empowered to reach their potential at work.

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