MGnify 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 collaboration between these platforms and the European Nucleotide Archive (ENA), aiming to promote data exchange, discovery and cross talk between the resources and their analysis pipelines. Metagenomics analysis is challenging in terms of scale, diversity of data and the different approaches used to analyse them. This project aims at enabling data exchange via the MGnify and Metagenomics Exchange programmatic interfaces.
Your role
- Maintain exisiting MGnify RESTful API, incorporating and exposing new data types where necessary
- Evaluate different NoSQL solutions to ensure continued scaling of the resources with ever increasing data volumes, and to ensure that all data are accessible via the API
- Develop high level functional end-to-end testing to ensure quality of service
- Ensure that the infrastructure is monitored for performance
- Produce a client library for performing a range of different queries on the API, driven by commonly posed questions and stakeholder's needs
- Help deal with user reqests that concern accessing the API
- Periodically participate in training workshops
- Documentation of API, both for internal and external use
You have
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. They will have 5 years of experience working in a related professional environment, contributing to software projects as part of a development team.
- Demonstrable, hands-on experience creating tools and services using Python and JavaScript, ideally with frameworks such as Django, Flask and Backbone or React.js.
- Experience with relational databases such as MySQL (including schema design) and NoSQL technologies such as MongoDB, Solr, Cassandra and handling/manipulation of big data.
- Familiarity with RESTful web service APIs and JSON standards.
- Knowledge of fundamental software engineering principles, e.g. OO design, design patterns.
- Development of API client libraries for use by the community
- Software version control;
- Unix/Linux.
You might also have
- Experience working with "big data" in scientific domain
- Data analysis pipelines
- Cloud computing solutions and containerisation (e.g. OpenStack, Docker, Ansible)
- High performance/parallel computing
- Software development cycle
- Knowledge of sequencing technologies
- Understanding of metagenomics analysis
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 22 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 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 do I need to know
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.
Applications will close at 23:00 GMT on the date listed above.
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