Software Engineer - Natural Language Search and AI Integration

EMBL-EBI - European Bioinformatics Institute

Hinxton, United Kingdom

The European Bioinformatics Institute (EMBL-EBI) is seeking a talented and motivated Software Engineer to join our SearchBot project. This new initiative will pilot natural language query (NLQ) capabilities across EBI Search, which indexes more than 6.6 billion records from EMBL-EBI’s world-leading 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:

You will be responsible for designing, developing, and deploying prototype services that enable natural language queries across EBI metadata and selected data type specific searches.

You will:

Implement MCP-based services to expose search endpoints to AI agents.
Develop a central NLQ entry point integrating metadata search and specialised search modalities.
Support multilingual search and text summarisation.
Work closely with the user community, organising workshops, surveys, and UX testing to capture evolving requirements in a rapidly changing technical environment.
Collaborate with EMBL-EBI technical teams and external partners to ensure interoperability, scalability, and sustainability of the developed services.

You have:

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.