Software Developer
Location:EMBL-EBI Hinxton near Cambridge, UK
Staff Category:Staff member
Contract Duration:3 years
Grading:6 (monthly salary starting at £2,2,805 after tax). For more information about pay and benefits click here
Closing Date:12th February 2017
Reference Number:EBI_00835

Job Description

The EBI Metagenomics Portal and MG-RAST are the world-leading platforms offering free-to-use analysis services for the characterisation of metagenomics sequences. The Metagenomics Exchange is a new collaboration between these platforms, aiming to promote data exchange, discovery and cross talk between the resources and their analysis pipelines. Metagenomics analysis is challenging in terms of scale of data and diversity of data.

We are seeking an experienced software developer to work on this project, specifically working on the EBI metagenomics resource. The post-holder will be involved in implementing pipeline components, evaluating different storage solutions, investigating different cloud deployment approaches for running the pipeline and the application of workflow technologies (e.g. CWL). New technologies and approaches will be interweaved into the existing analysis framework largely written in Python and backed by MySQL and NoSQL data stores, to increase the pipeline throughput, robustness and scope of analysis. The candidate will also help establish data exchange procedures between EBI metagenomics and MG-RAST, to deliver a framework for broadcasting and exchange of metagenomics datasets and their associated analysis results, in collaboration with the European Nucleotide Resource. The EBI Metagenomics Portal project is maintained by a four-person sub-team within the larger Sequence Families team lead by Rob Finn (organised into biocurators, production software developers and web developers each with a sub-team lead). The post-holder will report to Simon Potter, participate in daily scrum meetings with the production software and web developers, attend EMG team meetings and gather requirements from key stakeholders for sprint planning meetings. The collaborative nature of EBI requires the post-holder to interact with other EBI teams, particularly the Technical Services teams and maintain and foster external collaborations, particularly with the MG-RAST team.

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 22 member states and two associate member states and proud to be an equal-opportunity employer. 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.

Qualifications and Experience

The ideal candidate will have a postgraduate degree in computer science, bioinformatics or a related discipline, although candidates with equivalent experience will also be considered.

Essential skills:

  • Strong programming background, preferably in Python (minimum 3 years);

  • Cloud computing platforms (e.g. AWS);

  • Application deployment frameworks (e.g. OpenStack, Docker, Ansible);

  • High performance/parallel computing;

  • Complex workflow/pipeline design and description;

  • Expertise with relational databases including schema design and programmatic access (ideally MySQL, minimum 3 years);

  • NoSQL solutions (e.g. Solr, MongoDB, Cassandra);

  • Software version control;

  • Unix/Linux.

Desirable experience:

  • Data analysis pipelines;

  • Handling/manipulation of big data;

  • Lower-level languages, such as C/C++;

  • Software development cycle;

  • Containerisation;

  • Knowledge of sequencing technologies;

  • Understanding of metagenomics analysis.

The candidate will need to be able to work independently, as well as interact with the rest of the development team. Good communication skills and attention to detail are essential, as is the ability to work to deadlines.

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.

Application Instructions

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

Additional Information

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.

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