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Bioinformatician - Metagenomics

European Molecular Biology Laboratory (EMBL)

Location: Cambridge, Hinxton
Salary: £2,632 to £2,945 monthly starting salary after tax (Grade 5 or 6)
Hours: Full Time
Contract Type: Fixed-Term/Contract
Placed On: 15th January 2019
Closes: 25th February 2019
Job Ref: EBI01330

Contract Duration: 3 years

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.

Your role

  • 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

You have

Degree level or equivalent qualification/experience in computational, biological or related scientific discipline.

The ideal candidate would have worked within a professional environment for ideally 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
  • Unix/Linux

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

For more information about pay and benefits click here

What else do I need to know

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. 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.

This position is limited to the project duration specified. 

   
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