Full Stack Software Developer
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: 5-6 (monthly salary starting at £2,738 after tax)
Closing Date: 6 October 2020
Reference Number: EBI01697
The use of sequence similarity to electronically transfer annotation is a cornerstone of modern molecular biology. One of the most widely used suite of tools for performing sequence similarity searches, especially for capturing protein family information, is the HMMER suite. EMBL-EBI maintains the HMMER web servers, which provide the research community with web access to these tools, and enables the searching of sequences and profile hidden Markov models (HMMs) against large sequence databases (e.g. UniProtKB, Ensembl and MGnify) and profile HMM libraries (e.g. Pfam). Currently, millions of searches per month are performed on the HMMER web servers. These servers are part of the Microbiome Informatics Team, led by Rob Finn, but notably provide search capabilities to multiple EMBL-EBI resources.

This project will also interface with other EMBL-EBI resources, particularly Ensembl, PDBe, Pfam and UniProtKB, and as such the postholder will be required to liaise with developers in those groups to ensure correct data synchronisation. As well as interacting with teams at EMBL-EBI, the post-holder will also be expected to interact with the HMMER algorithm development team, based in Harvard US. This collaboration allows us to guide HMMER developments and may provide other resources, such as additional compute, as required.

Your role

The successful post-holder will be responsible for maintaining the HMMER search infrastructure and updating the target search databases as new versions become available. Where possible, they will identify areas for increased automation, and opportunities for optimisation to increase scalability. In particular, the postholder will evaluate various approaches to support the delivery of searches for the different resources, particularly for Ensembl as they increase the number of genomes and move to a more continuous update cycle. They will also be responsible for the development of JavaScript components to enable sequence searches and their results to be more easily embedded in third-party websites.

In addition to the growing demand for the HMMER services, the target databases are growing in size, meaning that scaling searches is an active area of development. This includes both hardware solutions, such as increasing search infrastructure, and algorithmic solutions, employing different search strategies. The post-holder will develop and deploy solutions implementing combinations  of these strategies. Finally, the post-holder will help with the migration of components of the HMMER infrastructure from a Perl codebase to a Python codebase.

You have

  • Educated to PhD level in a computational or related discipline or have a demonstrable equivalent level of experience
  • Experience writing robust, high-quality Python code in a production environment, using revision control tools and agile development techniques
  • Experience working with implementation and maintenance of web servers and/or REST APIs
  • Relational databases (MySQL and/or PostgreSQL), programmatic access, schema design and optimisation
  • Experience with NoSQL databases, ideally MongoDB
  • Attention to detail and ability to problem solve when problems arise
  • Knowledge of sequence analysis, ideally related to proteins

You might also have

  • Background in bioinformatics and experience in protein annotation
  • Experience working with other programming language, such as Perl and C
  • The use of containers to enable the deployment of tools, and their orchestration as part of a workflow
  • Use of high-performance computing environments
  • Experience leading small scientific projects

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 27 member states and two associate member states.

We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 850 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.

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 project duration specified.

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.

Applications will close at 23:00 GMT on the date listed above.