Research Software Engineer Spatial-omics

The Oliver Stegle team and the Bioimage Analysis Support Team at EMBL Heidelberg are looking for a research software engineer to contribute to the development and maintenance of highly-used open-source software for the analysis of spatial omics data. This position is funded by GlaxoSmithKline (GSK) as part of a collaboration between Cellzome a GSK company and EMBL. Cellzome is a center of excellence for Omics technologies of GSK in Heidelberg Germany. The successful candidate will work in close collaboration with computational bioimage analysis groups at GSK.

Your role

The successful applicant will be part of an international highly collaborative team working to advance the field of spatial omics by extending data infrastructures and enabling workflow development. The successful candidate will work in close collaboration with GSK and scverse with the objective of expanding and maintaining the SpatialData frameworka data infrastructure for spatial omics developed at EMBL based on the geospatial Python tech stackand support new use cases within GSK. The team comprises software developers single-cell and spatial omics analysts image analysts and project managers and is embedded in a tight network of collaborators at EMBL GSK and scverse.

Key responsibilities:

• Software development to improve the robustness and scalability of the SpatialData framework and to advance its capabilities for facilitating the creation of data analysis pipelines within GSK.
• Maintain the SpatialData framework with a particular focus on refactoring existing portions of the codebase to aid long-term stability and simplify future maintenance.
• Contribute to the advancement of the Next Generation File Format (NGFF) and OME-Zarr respectively an open specification and a file format for bioimaging data that are used as key components of the SpatialData framework.
• Setup test and ensure the smooth running of continuous integration and automation systems helping to maintain and develop the software infrastructure.
• Improve the documentation example notebooks and training material on the SpatialData framework enabling other developers to adopt the latest versions of the software.

You have

• Masters degree in Computer Science Mathematics Physics Engineering Life Sciences or a related field or a proven equivalent experience.
• Knowledge of the following libraries/technologies in Python (or a willingness to learn quickly). Geospatial: dask xarray geopandas. Bioimaging: zarr ome-zarr napari. Single-cell analysis: AnnData Scanpy SpatialData or other scverse software.
• Curiosity-driven mindset toward new methods and tech.
• Passion for open-source software with a commitment to reducing adoption barriers to support new users.
• Excellent communication and organisational skills with the ability to coordinate and collaborate effectively with other open-source projects.
• Proven ability to work creatively and rigorously in a team environment.
• Fluency in English.

You may also have:

• Experience contributing to open-source projects using git as a version control system and familiar with GitHub operational workflows.
• Background in user support (e.g. software support scientific support).
• Bioinformatics experience especially in single-cell and spatial biology paired with a learning mindset focused on spatial omics best practices.
• Experience in organising and delivering scientific workshops.

Professional development opportunities:

• Several opportunities to collaborate with a multidisciplinary network in a vibrant international environment.
• Support to attend leading workshops and conferences in single-cell and spatial omics (e.g. SCG conference) and Python data science (e.g. PyCon PyData).
• A chance to build deep expertise across the open-source geospatial software stack and stay current with cutting-edge developments

Contract length: 2 years with the possibility of a 1 year extension

Salary: Starting from Grade 5 monthly salary from EUR 4.03102 (after tax and before 12.05% EMBL social security deductions) plus other paid benefits

How to apply

In your online application please submit a cover letter a CV and the contact details of 3 referees. Please elaborate in your cover letter on your (open-source) software development experience or willingness to contribute. Ideally please provide links to git repositories where you made significant contributions.

What else you need to know

GSK is a science-led global healthcare company that researches and develops a broad range of innovative medicines and brands. On the EMBL campus in Heidelberg Cellzome provides a high-quality international research environment with world-class omics capabilities. The candidate will benefit from participation in the GSK formal mentorship and various trainings/seminar series in drug discovery.

Why join us

EMBL is curiosity-driven community-oriented and international. As an inclusive equal opportunity employer we believe that diversity enables us to collaborate more effectively and be innovative in our approaches. We are therefore committed to creating an inclusive and flexible culture - one where everyone can realise their full potential and make a positive contribution to our organisation.

We encourage applications from individuals who can complement our existing team we believe that success is built on having teams whose backgrounds and personal experiences reflect the diversity of the populations that our science serves. We actively encourage applications from all genders and cultures ethnic groups and all demographics to help us avoid perpetuating biases and oversights at this transformational point in our people strategy.

Enjoy lots of benefits:

• Financial incentives:Salary free of income tax 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 insurancefor 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 public holidays

• Relocation packageincluding installation grant (if applicable)

• Campus life:Free shuttle bus (select sites) on-site library subsidised on-site gym and cafeteria casual dress code extensive sports and social club activities (on campus and remotely)

• Family benefits: Kindergarten (Heidelberg) 10 days of child sick leave generous paid maternity/parental leave and monthly family & child allowances

• Benefits for international newcomers: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 detailed information please visit our employee benefits page here

What else you need to know

• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Visit our International Applicants page to find out more.

• EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here.

• Diversity and inclusion: At EMBL we believe that diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders identities nationalities and/or any other diverse backgrounds.

• How to apply: To apply please submit a cover letter and a CV through our online system. Applications will close at 23:59 CET on the date shown below. We aim to provide a response within two weeks after the closing date.

Closing Date