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BioImaging Data Resources Research Software Engineer
2 months ago
About the team/job
The revolution in imaging technologies has led to the need to share, integrate and reuse image data in a comprehensive way. EMBL-EBI is a world-leader in archival and dissemination of biological image data, operating the BioImage Archive and EMPIAR (the Electron Microscopy Public Image Archive), which together provide the means to store and search life science datasets from all imaging technologies at all scales and across all modalities.
These data resources are growing rapidly, and provide critical services to tens of thousands of scientists worldwide. We are looking for a talented research software engineer to support the next phases of their development, extending services to support the growing biosciences AI community and accommodate new imaging modalities such as cryoET.
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 via 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 systemsPersonal 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 teamYou 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 environmentWhy 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 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 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 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 to eight bank 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 more details please see our employee benefits page.
What else you need to know
What else you need to know
Contract duration: This position is a 2 year contract. International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants. Diversity and inclusion: At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ and individuals from all nationalities. Job location: This role is based in Hinxton, UK and you will be required to relocate once it is safe to do so, if you are currently based abroad. Read more about how we are recruiting during the pandemic. How to apply: To apply please submit a cover letter and a CV through our online system before the 30th September 2024.