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Java Software Engineer at European Bioinformatics Institute (EMBL-EBI) (Hinxton, UK)

The Samples, Phenotypes and Ontologies team are looking for an experienced software developer  to join their group. You will be working on a project specific to the Open Targets initiative to help develop the infrastructure behind the high-profile GWAS Catalog. The GWAS Catalog is a manually curated, high quality repository of all published genome wide association studies that has been running since 2008. It is considered the “go-to” resource for looking up findings relating human genotype to phenotype associations.

Open Targets is a platform for target identification and prioritisation and performs large-scale biological data analysis and integration using EFO as the core ontology for the semantic annotation of data about disease and phenotype. GWAS Catalog data makes up a very important part of the Open Targets platform.

If you’re an experienced developer with an interest in helping solve big biological problems about the genetic basis of disease, this job is perfect for you! Most of the GWAS Catalog infrastructure is written in Java, so you’ll need previous Java experience, but we also have data pipeline services developed in Python and we make use of modern javascript frameworks for our user interfaces. We make good use of tools and frameworks like Spring and Docker to deliver our resources. SPOT is a multitalented team, so you should also be flexible enough to learn new languages to find the right tool for the right problem. You should be enthusiastic about full-stack development, as you’ll be expected to develop, test and deploy tools from database to user interface. You should be keen to advance your knowledge of the latest industry standard toolkits to help continuously innovate the catalog.

In this role, we’ll be asking you to help develop the infrastructure that manages the data in the GWAS Catalog - this means you’ll be building tools and pipelines to capture new data from submitters, and to serve it back to the community through the Open Targets platform, via APIs. Individual GWAS datasets can be very large - tens or hundreds of gigabytes - and we’re storing billions of records, so this requires someone who can get creative to build solutions to these sort of big data problems.

Qualifications and Experience

The Samples, Phenotypes and Ontologies team follows agile techniques in our approach to development, so if you’re the sort of person who likes to work in sprints, has worked with tools like Jira in the past to prioritise user requirements, or have ever tried pair-programming or code reviews, then you’ll be a good fit for our team. All of our software is built and published using continuous integration and version control, so you should at least be familiar with GitHub, and you should be confident in making your code public for others to install and run.

Our ideal candidate will be self-motivated and capable of working both independently and with a closely interacting team of scientists in an international academic environment. This post offers the challenges and the excitement of working at the forefront of genomics and clinical data, and as such requires an eager individual with excellent communication skills.

This position represents a fantastic opportunity to get hands-on in applying your software engineering skills to a resource with major scientific impact in a world-leading bioinformatics institute. It comes with the chance to work with a strong team of curators and developers at the interface of big data architecture and expert biologists to help deliver services with real scientific impact and a variety of clinical applications.

by via developer jobs - Stack Overflow

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