Operations Bioinformatician - European Genome-phenome Archive
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: 5 (monthly salary starting at £2,631.99 after tax)
Closing Date: 23 June 2019
Reference Number: EBI01434
We are looking to recruit an enthusiastic Operations Bioinformatician to work in the European Genome-phenome Archive (EGA) Team at the European Bioinformatics Institute (EBI), located on the Wellcome Genome Campus near Cambridge (UK).

The successful applicant will work in a team of user support personnel and developers as part of the EGA project (https://ega-archive.org) a leading controlled access resource for human genetic and phenotypic data. The EGA receives submission of a wide range of data, including whole-genome and exome sequencing, genotype array data, GWAS results, and phenotypic data in a variety of formats. The EGA is a collaboration between the EBI and the Centre for Genomic Regulation (CRG) in Barcelona, and is an ELIXIR Core Data Resource. The EGA collaborates with many groups at EMBL-EBI such as the European Variation Archive, the European Nucleotide Archive, and BioSamples, as well as many external groups and consortia in Europe and worldwide. The EGA is a driver project for the Global Alliance for Genomics and Health (GA4GH) which aims to promote open and interoperable standards for sharing genetic variation.

Your role

The main responsibility of the operations bioinformatician will be supporting the EGA helpdesk, by streamlining pipelines and processing of genomic and phenotypic files and metadata for archiving and distribution, optimising standard operating procedures, and generating regular reports for the EGA management. You will work with software developers in the implementation of Extract, Transform, and Load (ETL) pipelines and APIs for the management, transfer and analysis of genetic data. The team is managed using agile methodologies using a mix of the RT ticketing system, JIRA, and Confluence in a collaborative environment.

You will:
  • Help ensure the data in EGA is FAIR (Findable, Accessible, Interoperable, and Re-usable), by helping to develop procedures to unify data representation at EGA.
  • Work with both national and international collaborators gaining expertise in software engineering and biological data modelling.
  • Work with, teach, and learn from a great team that is fun, devoted to personal growth, and committed to building something meaningful, lasting and impactful.
  • Be expected to occasionally travel to meetings and conferences to represent EGA.

You have

A postgraduate degree in bioinformatics, computer science, computational biology or equivalent industry experience. Additional qualifications or experience in software development or engineering would be advantageous, as would experience in running and maintaining complex bioinformatics pipelines.

You must have the following skills:
  • Expertise in one or more of: Java, Python, Bash shell
  • Experience in using relational databases and SQL
  • Familiarity with working in unix environments and compute clusters
  • Working knowledge of genome sequencing and genetic variation data
  • Experience with interacting/processing/analysing bioinformatics datasets
  • Excellent written and verbal communication skills

You might also have

Experience in:
  • Issue tracking systems (JIRA, RT or other)
  • Version control systems (Git, Subversion or other)
  • Experience of working in a professional or academic context in multi-person team on production projects
  • Understanding or experience of web technologies
The successful candidate must be capable of working both independently and within a closely interacting team, in an international collaborative high pressure environment. They will be required to follow standard operating procedures (SOPs), work methodically, and understand the importance of privacy and security with respect to human genetic and phenotypic data. An ability to work to tight deadlines and under pressure is essential.

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 20 member states and 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 BST on the date listed above.