Bioinformatics Developer

About the team and role

We are seeking an experienced and highly motivated software developer to join the Ensembl team at EMBL-EBI and contribute to the development of the Ensembl Variant Effect Predictor (VEP). 

Ensembl provides open-access, high-quality genome data for a wide range of species. We offer intuitive tools to explore genes, variants, epigenomes and comparative genomics with ease. Ensembl VEP is our most popular tool. It leverages data from Ensembl and other public open sources to create detailed variant annotations, enabling filtering and prioritisation. It is used in a wide range of research projects and genomics resources and in diagnostic pipelines in clinical genomics labs. 

As part of the Ensembl Variation team, you will contribute to the re-implementation and modernisation of Ensembl VEP. This new version is being developed in Python (the current version is in Perl) and will be optimised for the increased data scale and the data types now accessible via modern sequencing technologies. You will work closely with one other developer on code development and review and with the broader team and external collaborators on design and testing. You will also create documentation and interact with the Ensembl VEP user community to aid transition to the updated tool.

Your role

This role offers someone with scientific curiosity and initiative an exciting opportunity to contribute to a highly-used open-source bioinformatics tool and to develop domain knowledge in a fast-moving scientific area. You will see the impact of your work through interactions with collaborators and the broader community.

Main duties and responsibilities

• Developing components of Ensembl VEP functionality including ingestion of genomic data in standard bioinformatics formats; performant identification of overlapping features and calculation of functional sequence change; methods to enable others to integrate new functionality and methods to enable efficient management of large scale genomic data.

• Reviewing the code written by other developers to ensure efficiency and robustness.

• Migrating and extending existing test suites.

• Creating clear documentation and other resources to enable Ensembl VEP users to transition to the new implementation.

• Collaborating with members of the wider Ensembl team and our external collaborators to understand user requirements and data types.

• Contributing to GA4GH efforts to define and implement community standards for variant data representation.

• Supporting our users and presenting our work at internal meetings and scientific conferences

You have 

• Experience in the design and development of user-friendly software, with high proficiency in Python 

• Three or more (3+) years of experience in software development using standard approaches (source control, containerisation, CI/CD)

• Experience of creating tools or methods to manage and process large-scale data, preferably genomics or variation data

• Experience collaborating on development projects and working with colleagues from different disciplines

• Proficiency working in a UNIX/Linux environment

• Excellent attention to detail and the ability to deliver a high-quality product to agreed deadlines

• Good communication and interpersonal skills

• Experience of, or interest in, genomics and variant interpretation

You may also have

• Familiarity with the Ensembl resources, in particular Ensembl VEP

• Experience working in a HPC bioinformatics environment, ideally creating and managing efficient large-scale data analysis pipelines using Nextflow

• Experience with a range of bioinformatics or statistical tools and data formats

• Familiarity with multiple programming languages; Perl, C++, and Rust are particularly relevant

• A higher degree in software development, bioinformatics, computational sciences, or a related field

• Experience working with cloud computing (AWS/GCP)

Other helpful information:

Contract length: 3 years (project based)

Salary: Grade 5 - 6 - monthly salary from £3,303 or 3,695 after tax plus generous benefits (excluding pension and insurance contributions)

Interviews: We plan to hold interviews via VC at the end of March 2026.

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