Senior Software Engineer
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 3 years
Grading: 6 (monthly salary starting at £2,994.54 after tax)
Closing Date: 17 September 2019
Reference Number: EBI01491
We are seeking to recruit an experienced software engineer to join the Sequence Families Team at the European Bioinformatics Institute (EMBL-EBI) located at the Wellcome Genome Campus near Cambridge in the UK. This team is responsible for a number of high profile resources including InterPro, Pfam and MGnify.

InterPro is a resource for classification and analysis of protein sequences, and integrates models and data from various member databases, including Pfam. It includes a tool, InterProScan - usable both as a web service and offline - which allows users to predict function, domains and functionally important sites on novel protein sequences. The web site and API are written in Python using Django, and InterProScan is written in Java with associated technologies such as Spring and Hibernate. Data pipelines are implemented in a mix of scripting languages (such as shell script and Python) and database stored procedures.

The role is primarily concerned with the InterPro resource, and the postholder will be a part of the production sub-team which is responsible for the data workflows that power the InterPro website and internal curation tools, as well as the InterProScan software. The work will involve maintenance of existing software and workflows, as well as development to incorporate new features. It will require interactions both within the wider Sequence Families team (to include web developers and curators) as well as other teams at EMBL-EBI.

Your role

  • Maintenance of InterProScan, adding new features as appropriate while continually seeking to identify potential improvements
  • Taking control of data production pipelines as part of regular data and website releases
  • Identifying poorly performing code, database queries, and other bottlenecks and applying updates in a timely manner in order to keep releases on schedule
  • Taking turns at leading sprints as scrum master
  • Help dealing with user requests submitted via our helpdesk
  • Liaising with and assisting other members of the Sequence Families team
  • Documentation of code, both for internal and external use

You have

You will have a postgraduate degree in computer science, bioinformatics or a related discipline, although equivalent experience will also be considered. You should also have 5 years of experience working in a related professional environment, contributing to software projects as part of a development team.

  • Experience writing production quality code in Java and Python on Unix-like platforms
  • Experience with relational databases such as MySQL and Oracle, along with alternatives such as MongoDB
  • Familiarity with high performance/parallel computing environments
  • Knowledge of fundamental software engineering principles, e.g. OO design, design patterns.
  • Experience with software version control (Git)
  • Knowledge of automated build/continuous delivery
  • Attention to detail and ability to work to tight deadlines
  • Good communication skills
  • Ability to work independently, as well as in a team, using an agile approach

You might also have

  • Experience working with "big data" in the scientific domain
  • Experience using/building data analysis pipelines
  • Familiarity with cloud computing solutions and containerisation (e.g. OpenStack, Docker, Ansible)
  • Background in bioinformatics
  • Familiarity with lower level languages, such as C
  • Awareness of algorithms/tools to align sequences to Hidden Markov Models

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 over 27 member states and two associate member states. 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.

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.

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.