Bioinformatics Developer Ensembl Compara

EMBL EBI; Newcastle upon Tyne; On-site; GBP 60,000 - 80,000; Full time

Job summary

A leading genomics research institute in the UK is seeking an experienced bioinformatics developer to enhance comparative genomics resources within Ensembl. The role involves maintaining and developing data pipelines, collaborating on projects, and applying scientific expertise in comparative analysis. The ideal candidate should have a Master's or PhD, strong knowledge of comparative genomics, and experience in software development, including proficiency in Python and workflow systems. Competitive salary and benefits are offered for this 3-year contract position.

Benefits

Generous pension scheme

Private medical insurance

Qualifications

• Master/PhD in bioinformatics or molecular biology or equivalent experience.
• Strong knowledge of comparative genomics including whole-genome alignment.
• Experience in driving and leading software development projects.

Responsibilities

• Maintain, run and develop the Ensembl Comparative Genomics pipelines.
• Collaborate on the coordination of the Ensembl comparative genomics release process.
• Support external users in their use of the comparative genomics pipelines.

Skills

Comparative genomics knowledge

Algorithm development

Bioinformatics experience

Python programming

UNIX/Linux environment

Relational databases and SQL

Workflow systems experience

Containerisation (Docker/Singularity)

Organizational skills

Communication skills

Education

Master/PhD in bioinformatics or related field

Tools

Nextflow

Snakemake

MongoDB

GraphQL APIs

Job description

Overview

We are seeking a highly motivated and experienced bioinformatics developer to help expand the Comparative Genomics resources in Ensembl, a world-leading provider of genomics data, infrastructure, and tools. Ensembl provides a platform for the annotation and comparison of genomes, from single-species to annotating and modelling evolutionary relationships across all eukaryotes. You will join the Ensembl Comparative Genomics team, which works across computational biology, software development, large-scale computing, big data, workflow management and automation. The team generates data on orthologues, gene trees, large-scale syntenies, whole genome alignments and other analyses, with a primary objective to keep these analyses scalable as more high-quality genomes are added each year. You will work with the Eukaryotic Annotation team and other Ensembl teams, as well as research consortia and global communities, contributing to software and workflows to compare thousands of genomes and to make Ensembl a leading resource for comparative genomic analysis. Ensembl Compara is part of the Genome Analysis Team and operates within the broader Ensembl infrastructure. You will report to the Comparative Genomics Project Lead.

Responsibilities

• Maintain, run and develop the Ensembl Comparative Genomics pipelines, databases and API.
• Assist the project leader in making technical decisions for the project.
• Collaborate on the coordination of the Ensembl comparative genomics release process.
• Support external users in their use of the comparative genomics pipelines.
• Apply scientific expertise to advance resource development.
• Participate in collaborations between Ensembl and other research groups and scientific consortia, and represent the project and the institute at conferences.

Qualifications & Skills

• Master/PhD in bioinformatics or molecular biology, bioinformatics, data sciences or a related field (or equivalent practical experience).
• Strong knowledge of comparative genomics, including whole-genome alignment, gene and species-tree reconstruction, sources of bias/error and associated software and tools.
• Excellent understanding of algorithm development and performance optimisation for large-scale data.
• Experience in bioinformatics and the management of genomics data.
• Proficiency in at least one programming language (e.g., Python).
• Excellent proficiency working in a UNIX/Linux environment, using command-line tools and version control.
• Proficiency with relational databases and SQL.
• Hands-on experience with workflow systems Nextflow/Snakemake or similar.
• Experience with Singularity/Docker to run containers on a shared compute environment and workflow optimisation.
• Excellent organisational and communication skills.
• Experience working on high-performance clusters and cloud computing or GPU-based acceleration.
• Working within a release cycle for software or data.
• Experience with MongoDB and building GraphQL APIs.
• Experience in driving and leading software development projects.
• Working knowledge of machine learning concepts.
• Experience working on scientific projects in the field of comparative genome analysis.

Contract & Benefits

• Contract length: 3 years (grant based).
• Salary: £3,303–£3,695 per month (after tax, excluding pension and insurance contributions), with 5 or 6 depending on qualifications and experience.
• Benefits include generous pension scheme, private medical insurance, and other allowances as described by EMBL-EBI.

Why join us

• We provide the global research community with access to publicly available databases and tools essential for healthcare, food security, and biodiversity.
• Work on a collaborative, inclusive culture on the Wellcome Genome Campus in Cambridgeshire.
• We support employees to reach their professional potential with a focus on innovation and impact.