Bioinformatics Data Engineer (RNA Resources)

Rfam and RNAcentral are key resources for RNA biology, serving tens of thousands of users every year and widely cited in the scientific literature. We are recruiting a Bioinformatics Data Engineer to develop and maintain both the Rfam and RNAcentral databases. They are currently funded by the BBSRC and Wellcome. The RNA Resources team is part of the Sequence Families group led by Alex Bateman. You will be reporting to the Project Leader for RNA Resources, and working closely with an RNA bioinformatician, two full-stack software developers, and an Rfam biocurator.

As a Bioinformatics Data Engineer, you will run, maintain and optimise our data pipelines, ensuring efficient data processing, storage and retrieval for Rfam and RNAcentral. You will work closely with cross-functional teams to analyse requirements, propose new data pipeline architectures, and implement solutions to improve performance and scalability. The tasks will include:

• Analysing existing data curation and data production pipelines and identifying areas for improvement, optimisation, and scalability.
• Modernising and containerising Rfam curation pipelines, and implementing human-in-the-loop, AI-assisted agentic curation.
• Developing and scaling LLM pipelines used in RNAcentral for literature summarisation and curation.
• Developing scalable workflows for ncRNA annotation in genomes.
• Documenting data pipelines, processes, and workflows for internal reference and knowledge sharing.
• Participating in RNAcentral and Rfam data releases.

You will also be responsible for outreach to the scientific community through presentations at major conferences such as the RNA Society Annual Meeting and ISMB. Additionally, you will present at the RNAcentral consortium meetings and Scientific Advisory Board meetings, gathering regular feedback from community members. Finally, you are expected to keep up to date with the latest developments in RNA science to ensure the resources continue to provide our diverse users with valuable data and analysis. You should be passionate about RNA science and want to help the scientific community. RNAcentral and Rfam are widely used resources, and this role offers the opportunity to shape the work of many RNA researchers worldwide.

• Master's level or equivalent qualification in a computational, biological or related scientific discipline
• Proficiency in Python and other relevant languages for bioinformatics tool development.
• Experience with relational databases (PostgreSQL, MySQL) and SQL: knowledge of PostgreSQL and MySQL database architecture, performance tuning, partitioning strategies, indexing techniques, and query optimisation.
• Demonstrated track record of developing and maintaining production bioinformatics pipelines with workflow management systems such as Nextflow or Snakemake
• Experience building applications with LLMs and other AI technologies
• Familiarity with Docker or other containerisation technologies, such as Singularity
• Comfortable using Git/GitHub, Unix, and Bash
• Experience of using AI assisted coding tools
• Ability to apply best-practice software development methodologies
• Strong communication skills

• Knowledge of RNA biology and/or demonstrable practical experience with Rfam, Infernal, R-scape and tools for secondary structure prediction
• Familiarity with gene annotation or genome feature representation
• Experience with high-performance computing environments such as Slurm
• Experience in planning and executing data migration projects, including downtime management, data consistency verification, and rollback strategies
• Experience with AI workflow libraries such as LangChain and LangGraph
• Experience with Kubernetes and cloud infrastructure platforms such as OpenStack.
• Experience with the Rust programming language

Hybrid Working: At EMBL-EBI we are pleased to offer hybrid working options for all our employees. You would be required to work 2 days from the office in Hinxton (currently this is Monday and Tuesday), with the flexibility to come on site more often if preferred.

We plan to hold introductory meetings with selected candidates remotely starting in Early July, following this we plan to hold panel interviews remotely in Mid July.

To apply, please include both a CV and a tailored Cover letter. Applications submitted without both documents will not be considered.

Contract length: 3 years (Grant based contract)

Salary: Grade 5 monthly salary starting at £3,303 per month after tax but excluding pension and insurance contributions. Plus generous benefits.