Bioimaging Data Resources Research Software Engineer

EMBL-EBI - European Bioinformatics Institute

Hinxton, United Kingdom

Your role

The role will work across the technical stack to support scaling and automation of deposition and presentation systems for high volumes of biological image data. You will extend and build on the EMBL-EBI imaging resources’ to enable better automation, integrate with high performance computing and storage resources and develop/implement new functionality, such as extraction of structured metadata from freeform text through LLMs.

A key focus of the role will be developing and integrating systems for interactive visualisation of biological images: we aim to make biology beautiful!

Specific responsibilities:

Design and implement systems to support rapid deposition, curation and archival of biological image data, including back-end, front-end and supporting infrastructure;
Develop systems for interactive online exploration of biological image data, working with existing tools, extending these, and developing new solutions as appropriate;
Act as liaison between the BioImage Archive/EMPIAR and EMBL-EBI's compute/storage infrastructure teams to deploy and manage these systems;
Coordinate with other service teams on shared development and process implementation;
Contribute to the broader team activities, including helpdesk support, planning, design review and improvement of the team's software development processes.

You have

You should have a university degree in computer science, life sciences or a related discipline and have several years' experience in a software development capacity.

Specific experience:

Substantial experience developing full stack applications;
Extensive hands-on experience with Javascript and Python;
Working with relational databases such as PostGres or MySQL;
Software development lifecycle, including design, implementation, testing, continuous integration, deployment and version control;
Working with Linux systems.

Personal attributes:

A strong affinity with, and enthusiasm for, the goal of EMBL-EBI to provide world-class open data and services to the global community;
A strong desire to learn new skills and technologies;
Excellent communication and interpersonal skills;
The ability to work both independently and as part of a team.

You might also have

Experience working with BioImaging data from one or more modalities;
Experience developing or integrating image visualisation systems;
Experience with NoSQL databases, such as MongoDB;
Experience with batch scheduling systems such as SLURM;
Experience with containerisation (e.g. Docker) and container orchestration (e.g. Kubernetes);
Infrastructure-as-code deployment tools such as Ansible or Terraform;
Experience working in an academic environment.

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