The Sequence Families team, led by Rob Finn, is responsible for the delivery of world leading databases and services, including EMBL-EBI’s microbiome analysis platform MGnify. This project will also interface with other EMBL-EBI resources, such as Ensembl and BioSamples.
MGnify is EMBL-EBI’s microbiome analysis platform, which performs the archiving, assembly and analysis of amplicon, metagenomics and metatranscriptomics data. We are participants in the recently funded EU project, HoloFood. This project aims to develop a holistic solution to improve animal food production through deconstructing the biomolecular interactions between animal feed, gut microorganisms and animals (salmon and chicken). Our role in this project will be to help perform the analysis of the gut microbiomes, using our own in-house compute cluster and cloud platforms. We will also be responsible for the integration of different data, allowing their discovery and contextualisation with respect to each other.
Analysis and assembly of data produced within the project and related datasets
Deal with consortium user queries about metagenomics analysis
Development of additional metagenomics analysis components, such as biochemical pathway and feed cross-talk
Maintain analysis and assembly pipelines to incorporate updates to software and reference databases and ensure that it continues to be deployable on the cloud
Attend regular consortium meetings, to enable consistent and clear communication to the MGnify team and consortium
Interact with teams at EMBL-EBI, to allow appropriate data to be extracted from their resources (e.g. API) and using these to help construct the HoloFood workbench
Degree level or equivalent qualification/experience in computational, biological or related scientific discipline
The ideal candidate would have worked within a professional environment for two or more years, running analysis pipelines and contributing to their development as part of a team effort.
Strong scripting skills in Python, although other languages would be considered for the right candidate
Software version control (e.g. GitHub)
Relational database querying, basic schema design and optimization (e.g. MySQL, Postgresql)
Experience running bioinformatics pipelines
Knowledge of metagenomics analysis and tools
Attention to detail and ability to problem solve when problems arise
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.
You might also have
Workflow languages (e.g. Common Workflow Language, SnakeMake)
Use of compute cluster job schedulers (e.g. LSF, Oracle grid engine)
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.
The successful candidate will be expected to bridge between MGnify staff and the wider HoloFoods consortium. This will be achieved via regular meetings and videoconferencing. The primary direction for the pipeline development and data analysis will come from team leader and line manager. Other requirements may also come from other team members and the consortium. The postholder will also be required to interact with members of other teams at EMBL-EBI. 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.
Applications will close at 23:00 GMT on the date listed above.