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Software Developer (Classifications)

European Molecular Biology Laboratory (EMBL)

About the team/job

We are seeking a Java Software Engineer with a preferably a background in bioinformatics or life sciences to join the Data Coordination and Archiving (DCA) Team at the EMBL-European Bioinformatics Institute (EMBL-EBI). The DCA team provides data coordination services for partners around the world for a portfolio of sequencing-based studies, with underlying infrastructure for these services based around the European Nucleotide Archive, one of life science’s largest and longest standing data resources. 

You will be joining a sub-team which currently consists of 6 developers from various backgrounds, with an informal and supportive culture. This is an opportunity to work with a global consortium of scientists and developers and make contributions that advance the reach and utility of sequence data. 

Your role

You will play a key role in developing classifications systems (both hierarchical and tag-based) across multiple data types in the ENA as well as other EMBL-EBI data resources. 

Examples might be:

  • Taxonomy based classification and cross referencing, relating to the UniEuk project
  • Labelling of pathogens data, relating to the European COVID-19 Data Platform
  • Identifying records (or organisms) from terrestrial vs marine environments, relating to the Blue-Cloud project

The goal will be to implement search/discovery functionality that would leverage these classifications, integrating with or feeding into other indexing and search services. 

You will have the opportunity to work on: 

  • Analysis of content from Bioinformatics data sources, mapping data to taxonomic and other classes, tagging of metadata, and defining data flow routes
  • Developing parallel backend processing pipelines for large volumes of data
  • Enhancement/development of RESTful APIs
  • Relational and noSQL databases and search engines (e.g. Oracle/MongoDB/Elasticsearch)
  • Other tools and technologies that support the flow of data including distributed computing 

You have

  • A university degree in the computer sciences or life sciences. 
  • Several years’ experience in a bioinformatics or software developer capacity. 
  • A Strong command of Java, including Spring/Spring Boot framework
  • Proficiency with database operations (Relational and noSQL)
  • RESTful API development experience
  • Experience in the full software development cycle including design, implementation, testing, version control, and deployment
  • Willingness to learn new skills as the project requires
  • Ability to understand, enhance, or transform existing code (including legacy)
  • Self-motivation and ability to work both independently and as part of a team
  • Experience with Batch / Shell programming and scripting 
  • Excellent communication, interpersonal, and English language skills 

You might also have

  • Prior experience working in a multidisciplinary scientific environment.
  • Experience with creating and managing complex data processing pipelines
  • Experience with microservices architecture
  • Experience with viral sequence data and/or ‘omics sequencing
  • Experience with CI/CD pipelines (e.g. gitlab)
  • Experience with software packaging and distribution 

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. 

Enjoy lots of benefits:

  • Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme, 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

What else you need to know

  • Contract duration: This position is a 2 year fixed-term contract to work on the Blue-Cloud and UniEuk projects. Ideally successful candidate must be able to commence immediately.  
  • 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, near Cambridge, UK. You will be required to relocate if you are based overseas and you will receive a generous relocation package to support you.
  • How to apply: 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.
Location: Hinxton
Salary: Monthly salary starting at £2,882 or £3,224 per month after tax plus benefits (Grade 5 or 6)
Hours: Full Time
Contract Type: Fixed-Term/Contract
Placed On: 23rd September 2022
Closes: 23rd October 2022
Job Ref: EBI02070
 
   
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