Software Engineer – Natural Language Search and AI Integration

The European Bioinformatics Institute (EMBL-EBI) is seeking a talented and motivated Software Engineer to join our SearchBot project. This initiative will pilot natural language query (NLQ) capabilities across EBI Search, which indexes more than 6.6 billion records from EMBL-EBI’s life science resources. The project will also explore frameworks for integrating specialised search services, such as sequence and chemical searches, with modern AI agents using emerging standards like the Model Context Protocol (MCP).

Your role includes:

• Designing, developing, and deploying prototype services that enable natural language queries across EBI metadata and selected data type specific searches.
• Implementing MCP-based services to expose search endpoints to AI agents.
• Developing a central NLQ entry point integrating metadata search and specialised search modalities.
• Supporting multilingual search and text summarisation.
• Working closely with the user community, organising workshops, surveys, and UX testing to capture evolving requirements in a rapidly changing technical environment.
• Collaborating with EMBL-EBI technical teams and external partners to ensure interoperability, scalability, and sustainability of the developed services.

Qualifications:

• University degree in computer science, bioinformatics, or a related field.
• Experience with emerging AI agent standards like MCP.
• Strong experience in software development (Python, Java, or similar) and working with search technologies (e.g. Lucene/SOLR, Elasticsearch).
• Familiarity with natural language processing, large language models, or conversational AI frameworks.
• Proven ability to engage with scientific communities and translate user requirements into technical solutions.
• Excellent communication skills and ability to work in a highly collaborative environment.

You may also have:

• Knowledge of biological data resources and their use in research.
• Experience with user experience testing and workshop facilitation.

Contract length: 3 year project limited contract. Salary: Grade 5 or 6 depending on experience. Monthly salary starting at £3,303 or £3,695 per month after tax but excluding pension and insurance contributions. Plus, generous benefits.

This vacancy will run from 27th April with a scheduled closing date of Sunday 17th May. Please submit your application as soon as possible, including both an up-to-date CV and a cover letter for consideration.

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.

We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by Cambridgeshire countryside. This is a collaborative and inclusive community where our employees feel valued, supported and empowered to reach their professional potential.

Benefits include financial incentives such as 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 including hybrid working patterns, and private medical insurance for you and your immediate family (including all prescriptions and generous dental).