Senior Software Developer
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: 6 (monthly salary starting at £3,063 after tax)
Closing Date: 6 August 2020
Reference Number: EBI01640
MGnify is EMBL-EBI’s microbiome data analysis resource, which performs the archiving, assembly and analysis of metabarcoding, metagenomics and metatranscriptomics data. This resource is produced by the Microbiome Informatics Team, led by Rob Finn, and provides access to one of the largest collections of publicly available analysed microbiome data.

The field of microbiome research is rapidly growing and evolving, and new tools and approaches are perpetually being developed by the wider scientific community.  As new data types increase in popularity, the range of MGnify analyses grow accordingly, either through the iterative development of existing pipelines or through the introduction of entirely new analysis pipelines.  

These new analysis data types need to be propagated to our data stores and made accessible via the MGnify APIs and website.  An example of this is the development of our metagenome assembled genomes catalogue, building upon the human gut catalogue produced by the Finn Research Team (Almeida et al, Nature 2019). Due to the growing demand for metagenomic assembly and analysis the team is increasingly using Cloud computing solutions, in combination with the EMBL-EBI high performance computing cluster. Thus, the team has adopted the use of workflow descriptions, coupled with containers, to enable the deployment of the MGnify pipelines.  

Your role

The successful post-holder will be responsible for maintaining the core production pipelines, integrating developments produced by the wider team, and ensuring that new features and data types are propagated into the MGnify data models. Where possible, they will identify areas for increased automation and areas where processes can be optimised to increase scalability. The postholder will be responsible for the develop of the execution framework for seamless deploying the MGnify workflows on a hybrid computing architecture (as described), ensuring their efficient and timely execution and the propagation of results in the MGnify data stores.

This project will also interface with other EMBL-EBI resources, particularly ENA, Ensembl, and BioSamples, and as such the postholder will be required to liaise with developers in those groups to ensure correct data syncing across resources. In collaboration with the rest of the team, the postholder will be expected to interact with users of MGnify, answering helpdesk questions and by developing training materials for virtual, online and in-person training. They will also be expected to present at team and collaborator meetings.  

You have

  • Educated to PhD level in a computational or related discipline or have a demonstrable equivalent level of experience.
  • Experience writing robust, high-quality Python code in a production environment, using revision control tools and agile development techniques.
  • Experience working with cloud computing solutions
  • Work knowledge of workflows (e.g. Common Workflow Language or Nextflow) and associated execution engines, and their use in running large scale production pipelines
  • Relational databases (MySQL and/or PostgreSQL), programmatic access, schema design and optimisation.
  • Attention to detail and ability to problem solve when problems arise
  • Knowledge of metagenomics, metatranscriptomics and/or genomics analysis.
 

You might also have

  • Background in bioinformatics and experience in genomic annotation
  • Knowledge of tool containerisation using Singularity and/or Docker
  • Experience with NoSQL databases, ideally MongoDB
  • Willingness to mentor junior team members
  • Experience leading small scientific projects
 

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 27 member states and two associate member states.

We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 850 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.

3 year staff member contract renewable up to 9 years of service

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.

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