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GA4GH Bioinformatician / Software Developer

EMBL-EBI
Hinxton, Cambridgeshire, England, UK
Jobs in UKJobs in EnglandFull-time

Staff category
Staff member

Contract duration
2 years

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

Reference number
EBI_01240

Job description
The Samples, Phenotypes and Ontologies team are looking for an enthusiastic, highly motivated GA4GH Bioinformatician/Java software developer to join the BioSamples database team. This post offers the challenges and excitement of working at the forefront of genomics and clinical data science.

The project:

The BioSamples database (http://www.ebi.ac.uk/biosamples) at EMBL-EBI is a resource that integrates biological samples from a wide variety of sources to provide a single location to apply standards and ontologies to sample data. It has grown from 14,000 samples in 2010 to over 5 million samples in 2017. It plays a key role in biological knowledge to the raw data, stored in the many archive databases at EBI and outside. The GA4GH initiative underlies the foundation of data sharing and processing for genomic medicine. The Clinical & Phenotypic work stream of GA4GH is designing datamodels to ensure sample, individual and technical metadata is completely interoperable and can be used by research groups across the globe.

The Biosamples team is a multidisciplinary team of bioinformaticians and programmers with experience in ontologies, databases, backend java technologies and user interfaces.

Your role:

As a GA4GH Bioinformatician/software developer for BioSamples you will be in charge of making the BioSamples metadata available to GA4GH members, and retrieve associated raw data from other EMBL-EBI archives such as ENA and EGA.

You will use many techniques, including big data techniques, to explore and analyse sample data. This will include: data mining, analysis and the presentation of results in a clear manner with a view to processing, cleaning, and verifying the integrity of data stored in BioSamples, with a specific focus on human diseases. In this role, you’ll be building tools to automate the capture, validation and storage of ontology- and metadata-rich descriptions of biological samples. This will involve development of automated data validation and curation tools. You will also need to identify and support evolving user requirements, as well as develop training materials in collaboration with the EMBL-EBI training team.

You’ll be working locally within the SPOT team at EBI alongside developers, bioinformaticians and ontologists. Internationally you will be part of the GA4GH consortium and be involved in regular conference calls with diverse partners. You will have the opportunity to travel to face to face meetings. For example, our next plenary will be in Basel early October 2018.

Qualifications and experience
You will have:

– An undergraduate degree in a Biomedical Science, with a masters degree in bioinformatics or a computer science. Demonstrated equivalent experience will also be considered.
– Previous experience of software development in at least one programming language
– A desire to engage with both the user community and project collaborators, which requires good communication skills and ability to work as part of a team of people with a range of skills and a diversity of backgrounds.
– Interest in integrating data to solve biological problems, specifically in genomics with a view towards human health

You might also have:

– Experience with collaborative projects and/or Agile software development
– Data formats for expressing biological data and data management
– UI Design
– Semantic technologies such as ontologies and RDF

Benefits
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.

How to apply
To apply please submit a covering letter and CV, with two referees, through our online system.

Please apply online via www.embl.org/jobs.

Closing date: 27 July 2018

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.

This position is limited to the project duration specified.

Applications will close at 23:00 GMT on the date listed above.

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