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Bioinformatics Engineer

Organization
EMBL-EBI
Job Location
Wellcome Genome Campus
Hinxton
CB10 1SD
United Kingdom
Salary
5 (monthly salary starting at £2,676.73 after tax)
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.  For more information about pay and benefits click here.

Job Description

After receiving funding from the UK government to cover an 18 month project, we are assembling a team to pilot our prototype software providing DNA-based diagnostics and global surveillance information for tuberculosis (“Mykrobe Atlas”). We will trial it in Buenos Aires with collaborators at the Malbran Institute, with an intention of scaling it up as a global service in the future.

The new EMBL-EBI team (4 new members: architect/server-side API, dev ops, bioinformatic/analytics back-end, data curator) will work with two existing team members who built the current version, and a secondee from Buenos Aires. At the other end, in Buenos Aires, another developer will use the service “in the field”, working with the local expert group to use the information for patients. The EMBL-EBI team will work alongside the Iqbal research group, comprising 8 researchers (backgrounds in biology, computer science, and maths) from across the world.

The goal is to deliver a working system (with minimal features) to the customer (secondee mentioned above, onsite in same office) within 2 months of project start. This will be followed by multiple iterative loops of improving user-interface, analytics and performance, with direct customer feedback, both locally (EMBL-EBI) and then in Buenos Aires.Your roleThe postholder will be responsible for the asynchronous analysis (bioinformatics) jobs run as a result of user queries or data uploads. These containerised jobs will all run on a (Kubernetes) cluster, and are mostly pre-defined, mature and heavily tested (Mykrobe and SNP calling).

The role requires a mix of maintenance of existing jobs and development of new ones (e.g. Global SNP distance measurement). Working in tandem with senior bioinformatician and sharing user testing with the full team. End-to-end user-testing of the overall system is a secondary responsibility of this post.

Requirements

You have: 

  • Experience of running processes on a cluster, and considerations when scaling up: RAM, I/O, local versus network attached disk.
  • Experience of microbial bioinformatics: SNP analysis, VCF files, programmatic parsing of phylogenetic trees (eg with the APE package or equivalent)
  • Python

You might also have

  • Familiarity with dev ops (e.g. Docker, Kubernetes, Continuous Delivery and Deployment)
  • Familiarity with public health applications of microbial bioinformatics and sequencing.
  • Familiarity with mongoDB
How to Apply

To view a copy of the full job description please visit our website. 

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.

About Our Organization

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 27 member states and two 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.

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