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For Companies At a Glance
- Tasks: Develop and maintain tools for genomic data analysis and visualisation.
- Company: Join EMBL-EBI, a leader in bioinformatics and genome data services.
- Benefits: Enjoy hybrid working, generous leave, and private medical insurance.
- Why this job: Contribute to impactful open-source projects in a collaborative environment.
- Qualifications: Proficiency in Python and experience with large-scale genomics data required.
- Other info: Contract length is 3 years with opportunities for international applicants.
Overview
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. Ensembl VEP is our most popular tool, leveraging data from Ensembl and other public sources to create detailed variant annotations for filtering and prioritisation. The project involves re-implementation and modernisation of Ensembl VEP in Python (current version is in Perl) to cope with increased data scale and new data types from modern sequencing technologies. You will work closely with one other developer on code development and review, plus the broader team and external collaborators on design and testing, and you will 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 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)
Working hours: 39 per week full time. We are also open to applications from candidates looking for part time hours and could accommodate 0.8 FTE or 0.9 FTE too.
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 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
14/02/2026
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Bioinformatics Developer employer: European Bioinformatics Institute | EMBL-EBI
Contact Detail:
European Bioinformatics Institute | EMBL-EBI Recruiting Team
StudySmarter Expert Advice 🤫
We think this is how you could land Bioinformatics Developer
✨Tip Number 1
Familiarise yourself with the Ensembl resources, especially the Ensembl Variant Effect Predictor (VEP). Understanding how these tools work and their applications will give you a significant edge during discussions with the team.
✨Tip Number 2
Engage with the bioinformatics community by attending relevant conferences or webinars. Networking with professionals in the field can provide insights into current trends and challenges, which you can discuss during your interview.
✨Tip Number 3
Brush up on your Python skills and ensure you're comfortable with managing large-scale genomic data. Consider working on personal projects or contributing to open-source bioinformatics tools to showcase your abilities.
✨Tip Number 4
Prepare to discuss your experience with version control systems like GitHub. Being able to articulate your collaborative projects and how you've used these tools effectively will demonstrate your readiness for teamwork in this role.
We think you need these skills to ace Bioinformatics Developer
Some tips for your application 🫡
Tailor Your CV: Make sure your CV highlights relevant experience in bioinformatics, software development, and any specific tools or languages mentioned in the job description, such as Python and MySQL.
Craft a Compelling Cover Letter: In your cover letter, express your enthusiasm for the role and the Ensembl Project. Mention specific projects or experiences that demonstrate your skills in managing large-scale genomic data and your ability to collaborate with diverse teams.
Showcase Your Technical Skills: Clearly outline your technical skills related to bioinformatics, including any experience with REST or GraphQL APIs, version control systems like GitHub, and familiarity with UNIX/Linux environments.
Highlight Collaborative Experience: Emphasise any previous collaborative projects you've worked on, especially those involving cross-disciplinary teams. This will show your ability to work effectively within the Ensembl team and with external collaborators.
How to prepare for a job interview at European Bioinformatics Institute | EMBL-EBI
✨Showcase Your Technical Skills
Make sure to highlight your proficiency in Python and experience with large-scale genomics data during the interview. Be prepared to discuss specific projects where you've applied these skills, especially if they relate to functional annotation or variant prioritisation.
✨Demonstrate Collaboration Experience
Since the role involves working closely with bioinformaticians and developers, share examples of past collaborations. Discuss how you’ve worked with colleagues from different disciplines and how you’ve contributed to team projects, particularly in a version control environment like GitHub.
✨Familiarise Yourself with Ensembl Resources
Research the Ensembl project and its tools, especially the Ensembl Variant Effect Predictor (VEP). Understanding their functionalities and recent developments will show your genuine interest in the role and help you engage in meaningful discussions during the interview.
✨Prepare for Problem-Solving Questions
Expect questions that assess your problem-solving abilities, particularly in managing and analysing large datasets. Think of scenarios where you had to troubleshoot issues or optimise workflows, and be ready to explain your thought process clearly.
