Bioinformatics Data Engineer (RNA Resources)

About the Team

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.

Your role 

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.

You have 

• 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

You may also have 

• 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

Other helpful information 

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.

Interviews: 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).

Application instructions: 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.

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.  Watch this video to see how EMBL-EBI makes an impact.

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 - including hybrid working patterns 

• 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 public 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 detailed information please visit our employee benefits page here. 

What else you need to know

• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Please take a look at our International Applicants page for further information.  

• EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here.

• Diversity and inclusion: At EMBL, we believe that diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders, identities, nationalities and/or any other diverse backgrounds.

• How to apply: To apply please submit a cover letter and a CV through our online system. Applications will close at 23:59 CET on the date shown below. We aim to provide a response within two weeks after the closing date.

Closing Date