Bioinformatician (model organism genomics)
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: Grade 5-6 (Monthly salary starting at £2,729 - £3,064) Plus other paid benefits
Closing Date: 19 November 2020
Reference Number: EBI01717
Surrounded by beautiful South Cambridgeshire countryside, our state-of-the-art Campus provides employees with a relaxed atmosphere where the pursuit of scientific discovery and meaningful work, underpin every role. We are seeking an experienced and motivated bioinformatician to work on model organism genome resources at the EMBL European Bioinformatics Institute (EMBL-EBI).

Model organisms (such as mice, rats, zebrafish, flies, worms and yeast) are studied extensively by scientists around the world to reveal fundamental insights into biology. The Alliance of Genome Resources (AGR) is a major initiative to develop tools and services that facilitate the use of model organism genomes for the understanding human biology, health and disease. Data and tools are made available via an integrated portal (www.alliancegenome.org), as well as a collection of specialist knowledge bases focused on individual species and communities. These include WormBase (www.wormbase.org), which focusses on a nematode worm - Caenorhabditis elegans - that has played a key role in our understanding of development and aging, and was the first animal to have its genome completely sequenced.

You will join a team that acts as the bioinformatics hub for WormBase and AGR, analysing and integrating genomic data for C. elegans and other model organisms. The team constantly strives to provide the user community with the most comprehensive and cutting-edge genomic information and tools. Our recent work has included analysis and integration of nanopore transcriptome data for genome annotation, cloud deployment of community genome annotation tools, and standardised analysis and annotation of genomic variation data across model organisms.

The team is part of a cluster of teams and resources at EMBL-EBI that includes Ensembl (www.ensembl.org), with a culture of collaborative development and shared code, pipelines and processes. Furthermore, AGR is a large consortium of scientists and developers spread across more than ten institutions in Europe and North America. This an outstanding opportunity to work on a dynamic and high-impact international project.  

Your role

You will develop software and pipelines for the annotation, integration and analysis of genomic data for WormBase and the wider AGR. Your work will support diverse activities and areas, including gene-structure annotation, regulatory annotation, gene expression, and comparative genomics. You will work with a codebase and database infrastructure that is well-established and complex (with WormBase), at the same time contributing actively to a new and dynamically evolving genomics database platform (with AGR). Your duties will include:
  • Develop and deploy software and pipelines for genomic data organisation, analysis and integration
  • Collaborate on the development of the WormBase and AGR database platforms and associated infrastructure
  • Help develop and deploy cloud-based tools to support expert curation of genomic data for nematodes and other model species
  • Communicate with an international research community to identify high priority data sets for integration
  • Present work to peers, project partners and collaborators
  • Expand your technical and biological knowledge to support the project

You have

The ideal candidate is an experienced bioinformatician who is well-versed in creating robust, well-designed and well-documented code, pipelines and processes. You should be willing to embrace working in an Agile software development environment and be comfortable switching between different programming languages and database technologies.

You should be able to communicate with with a variety of different stakeholders (from bench biologists to software engineers), and be able to meet deadlines and take responsibility for delivering timely software and data releases.

You have:
  • A post-graduate degree (Masters or PhD) in bioinformatics or a related subject
  • At least two years experience working in a software-oriented bioinformatics role
  • Proficiency in at least two programming languages (in particular Perl, Python, Java)
  • Practical experience working with database systems (in particular NoSQL technologies)
  • Experience developing and deploying software for the cloud (in particular AWS)
  • Experience developing high-throughput analysis pipelines using a workflow management system (such as Snakemake, NextFlow or CWL)

You might also have

You may also have experience in the following areas:
  • Experience working with genome annotation tools
  • Experience working with model organism data and databases
  • Experience working with the Ensembl platform, however not essential 

Why join us

EMBL-EBI is a worldwide leader in bioinformatics. We encourage personal and professional development and are committed to ensuring our employees feel valued, supported and empowered to reach their potential at work. In addition, our employees have access to a wide range of benefits including:
  • 30 days annual leave per year plus 8 bank holidays
  • Flexible work arrangements
  • Unique pension scheme including 17% employer contribution
  • Annual salary review
  • Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
  • Death benefit, long-term care, accident at work and unemployment insurances
  • Relocation package including installation grant (if required)
  • On-site library and subsidised on-site gym and cafeteria
  • Casual dress code
  • Free shuttle bus to and from Campus
  • Extensive sports and social club activities (run on campus and remotely)
  • Family benefits: Onsite nursery, child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
  • Benefits for non UK residents: Visa exemption, education grant for private schooling, financial support to travel back to your home country every second year and a monthly non-resident allowance

What else you need to know

To view a copy of the full job description please click here

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. This position is limited to the Wormbase project which will end at the end of 2023.