Bioinformatics Developer Ensembl Compara

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. There are a growing number of global biodiversity initiatives, such as Darwin Tree of Life, the Vertebrate Genomes Project, the European Reference Genome Atlas and the Human pangenome reference graph consortium, providing high-quality reference genomes and pangenomes for eukaryotic species. Ensembl provides a platform for the annotation and comparison of these genomes, from the single-species pangenome level right up to annotating and modelling the evolutionary relationships across all eukaryotes.

You will join the Ensembl Comparative Genomics team, whose work spans computational biology, software development, large-scale computing, big data, workflow management and automation. The Comparative Genomics team provides resources to help researchers understand the relationships between species. The team generates data on orthologues, gene trees, large scale syntenies, whole genome alignments and a variety of other analyses. A primary objective is to ensure these analyses remain scalable with the growing influx of high-quality genomes being added each year.

As part of the Comparative Genomics team you will work with the Eukaryotic Annotation team and several other teams in the Ensembl project, as well as research consortia and communities from across the globe. On joining the team, you will play a key role in developing software and workflows to compare thousands of genomes, directly contributing to making Ensembl a world leading resource for the comparative analysis of genomic diversity.

Your primary tasks will be to maintain, run and develop our Comparative Genomics pipelines. This will include working closely with collaborators and gaining in-depth knowledge of gene and species tree inference, multiple genome alignment, workflow managers and Python-based technologies.

Your Key Responsibilities Will Include:

• Maintaining, running, and developing the Ensembl Comparative Genomics pipelines, databases and API.
• Assisting the project leader in making technical decisions for the project.
• Helping with the coordination of the Ensembl comparative genomics release process.
• Supporting external users in their use of the comparative genomics pipelines.
• Applying scientific expertise to advance resource development.
• Participation in collaborations between Ensembl and other research groups and scientific consortia and representing the project and the institute at conferences.

You have a 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 on 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.

You may also have:

• 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.

Other Helpful Information:

• Contract length: 3 years (grant based)
• Salary: 5 or 6 depending on qualifications and experience, monthly salary at £3,303 or £3,695 after tax but excluding pension and insurance contributions.
• Plus generous benefits

Why join us:

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.

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.

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).