Bioinformatics Data Engineer (RNA Resources)The RNA Society • Indiana, Pennsylvania, United States
Bioinformatics Data Engineer (RNA Resources)
The RNA Society
- Indiana, Pennsylvania, United States
- Indiana, Pennsylvania, United States
À propos
Rfam and RNAcentral are key resources for RNA biology, serving tens of thousands of users every year and widely cited in the scientific literature. Rfam and RNAcentral are funded by the BBSRC and Wellcome. The RNA Resources team is part of the Sequence Families group led by Alex Bateman. You will report to the Project Leader for RNA Resources and work 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 analyse requirements, propose new data pipeline architectures, and implement solutions to improve performance and scalability. The Tasks Will Include
Analyzing existing data curation and 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. Outreach and Community Engagement
You will be responsible for outreach to the scientific community through presentations at major conferences such as the RNA Society Annual Meeting and ISMB, as well as at RNAcentral consortium meetings and Scientific Advisory Board meetings, gathering regular feedback from community members and keeping up to date with the latest developments in RNA science. Required Qualifications
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, including 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 using AI assisted coding tools. Ability to apply best‑practice software development methodologies. Strong communication skills. Preferred Qualifications
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 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. Location & Working Arrangement
Hybrid Working: At EMBL‑EBI we offer hybrid working options. You would be required to work 2 days from the office in Hinxton (Monday and Tuesday) with flexibility to come on site more often if preferred. Compensation and Contract
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. Benefits
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). 30 days annual leave per year, in addition to 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. Equal Opportunity Statement
International applicants are recruited and successful candidates are offered visa exemptions. EMBL is a signatory of DORA. We believe that diverse teams drive innovation and scientific excellence and encourage applications from candidates of all genders, identities, nationalities and other diverse backgrounds. All qualified applicants will receive appropriate consideration for employment.
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Compétences linguistiques
- English
Avis aux utilisateurs
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