Curator

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 role
The postholder has two key responsibilities. First, for running a containerised pipeline for absorbing all TB genomic data from the ENA, incorporating new genomes as they arrive in the ENA. This pipeline must register every step in a database, in order to produce a full audit trail.

Second, to curate the above data, as well as associated phenotype and geographical data for those samples which have it. The current prototype contains 40,000 strains and we expect this to grow to over 80,000 during the project.

You have
Python
familiarity with Linux
some experience of microbial genomics
You might also have
mySQL
mongoDB
Familiarity with BIGSI
Familiarity with dev ops (Kubernetes)
Familiarity with Docker/singularity
Nextflow (preferred) or snakemake

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 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.

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 please visit our website.

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.