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Bioinformatician (Protein Data Bank in Europe Team)

Organization

EMBL EBI

Job Location

EMBL-EBI, Wellcome Genome Campus, Hinxton
Cambridge
CB10 1SD
United Kingdom

Salary

Grade 5 or 6 (monthly salary starting at £2,738 or £3,063 per month after tax) + other paid benefits

Benefits

Enjoy lots of benefits:

  • Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme including 17% employer contribution, death benefit, long-term care, accident-at-work and unemployment insurances
  • Flexible working arrangements
  • Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
  • Generous time off: 30 days annual leave per year, in addition to eight bank holidays
  • Relocation package including installation grant (if required
  • Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely)
  • Family benefits: On-site nursery, 10 days of 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.

For more details please see our employee benefits page.

Job Description

The Protein Data Bank in Europe Team (PDBe; pdbe.org) is part of the worldwide Protein Data Bank organisation (wwPDB; wwpdb.org), which maintains the global archive of structural data on biomacromolecules - the PDB. The PDBe Team also maintains a number of databases that support deposition and advanced search services for structural biologists and the wider scientific community. Recently PDBe launched a new community-driven data resource – the Protein Data Bank in Europe Knowledge Base (PDBe-KB; pdbe-kb.org), which enriches the structures in the PDB with added value annotations. The Team consists of an international and inter-disciplinary mix of professionals: bioinformaticians, structural biologists, data scientists and software developers. The PDBe and CS3DB teams form the Molecular and Cellular Structure cluster within the EBI.

We are looking for a bioinformatician/scientific programmer to work on a research project exploring the utility of residue covariation data in predicting protein quaternary structure. The project is a collaboration between PDBe, the Orengo group at UCL and the Baker group at the University of Washington (USA). 

Your role

The successful candidate will report to the project manager for the PDBe-KB resource. This is an opportunity for the right person to develop an excellent understanding of complex biological data (structure, sequence and genetic variation), how it relates to each other and how it can be standardised, and then develop robust mechanisms for data integration, visualisation and access.

The tasks for this post include:

  • In collaboration with the other partners, to identify the residue covariation data that can be integrated into the PDBe-KB infrastructure, define formats and ontologies for its standardisation;
  • to design and develop a process for data integration;
  • to design and develop reusable web components to display this data on the PDBe website;
  • to integrate the data in the PDBe/PDBe-KB search system;
  • to extend the existing PDBe REST and/or Graph API by developing new calls to export this data;
  • to perform exploratory analysis to validate the reliability of the covariation data by comparing it with known quaternary structures;
  • to update the PISA webservice to take into account residue covariation when predicting quaternary structures;
  • to evaluate visualisation approaches that would allow intuitive distinction between experimentally determined structures and predicted models;
  • to contribute to the biocuration work at PDBe (10%).

Requirements

You have

  • Strong software engineering skills
  • A background in bioinformatics
  • Experience working both independently and in close collaboration with a team
  • Excellent communication and interpersonal skills
  • Excellent knowledge of English
  • A Master’s degree or Bachelor’s degree and a minimum of 2 years’ work experience in Bioinformatics, Computer Science or related subjects
  • Strong knowledge of structural biology, protein sequencing or enzyme chemistry
  • Excellent knowledge of C++
  • Some experience with Python (scripting, data integration, REST API development)
  • Basic understanding of SQL (querying). 

You might also have

Ideally, you will have experience in Web technologies:

  • JavaScript
  • Web component development with Polymer and Angular 2
  • Front end development - Responsive design templates
  • Apache Solr
  • The ideal candidate would have a PhD in Bioinformatics or related fields

How to Apply

What else you need to know

  • Contract duration: This position is a grant/project-limited fixed-term contract estimated for a duration of 1 year or until grant end-date on 30/09/2022.
  • International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants.
  • Diversity and inclusion: At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ and individuals from all nationalities.
  • Job location: This role is based in Hinxton, UK and you will be required to relocate once it is safe to do so, if you are currently based abroad. Read more about how we are recruiting during the pandemic.
  • Your application: To apply please submit a cover letter and a CV through our online system. We aim to provide a response within two weeks after the closing date: 28th July 2021

About Our Organization

Why join us

Do something meaningful
At EMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity.

Join a culture of innovation
We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential. 

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