Bioinformatics Developer

Bioinformatics Developer

EMBL-EBI - European Bioinformatics Institute

Hinxton, United Kingdom

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).