EMBL - EBI - European Bioinformatics Institute

Hinxton near Cambridge, United Kingdom

The Ensembl Genomes team is looking to appoint a skilled and highly motivated bioinformatician to join the team at the European Bioinformatics Institute (EMBL-EBI), which is located on the Wellcome Trust Campus near Cambridge in the UK. Ensembl Genomes is a leading genomic database for non-vertebrate species (and a sister project of the Ensembl database), and you will work on the production and development of this resource by contributing to the Ensembl Genomes extension project. The different components of the project will bring you into contact with scientific communities facing particular problems, and your role will be to apply the Ensembl platform to develop solutions to their needs.

One major responsibility will be to work on the INFRAVEC2, funded by the Horizon 20-20 program of the European Union. This grant is designed to construct and operate technical infrastructure to support research into insect vectors of human disease (such as mosquitoes and midges). Our role in the project as follows:

  • Integrate and analyse data generated in the project within Ensembl Genomes;
  • Link these data with other data types (phenotypic data, information about publically available stocks, etc.) relevant to the project, and to other resources (including VectorBase);
  • Developing data standards and a data management policy for INFRAVEC.

The other components of this project which you will also contribute to include our work on the annotation of the genomes of the whitefly (Bemisia tabaci) and the biting midge (Culicoides spp.), and to the development of the pan-European data infrastructure, ELIXIR.

Specific day-to-day duties will include:

  • Analysis of genomic and transcriptomic data (including genome assembly, annotation and variant calling);
  • Integration and dissemination of data through the Ensembl Genomes platform;
  • Working with collaborators to develop appropriate data standards and policies on data publication;
  • Attendance at remote and in-person meetings with collaborators.

The successful candidate will work in the Ensembl Genomes team alongside staff addressing similar challenges in other species, and will report to the Ensembl Metazoa Project Leader.

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 successful candidate must hold a degree in computer science or bioinformatics or a degree in biological sciences and a post-graduate qualification in computer science or bioinformatics. Experience working in genomic biology, vector biology or bioinformatics is highly desirable, but not essential.

You should have one of the following: a minimum of two years professional programming experience, a bioinformatics based PhD; or research experience with next generation sequencing data. Experience of working in a dynamic, team-based environment, of working in large collaborative projects, and of contributing to a shared code-base is desirable.

The post holder must be highly self-motivated, interested in vector biology, and be able to work independently. They must be open to working in a production team (willing to conform and contribute to standard working practices); and are expected to have good communication skills, written and verbal, both to facilitate effective communications with other team members and to communicate with external collaborators and users.

You must have knowledge of Perl, though experience in a related scripting language (e.g. Python, Ruby) or compiled programming language (e.g. Java) is relevant. Knowledge of relational database management systems (e.g. mySQL), writing SQL statements and designing database schemas is essential. Additionally, strong candidates will have experience in many of the following: genome annotation; handling large data sets; workflow management systems for distributed computing (e.g. LSF, SGE); RDF; alternative database technologies (i.e. NoSQL and traditional RDBMS); biological ontologies for data annotation.

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