Scientific Software Developer
Location: Heidelberg, Germany
Staff Category: Staff Member
Contract Duration: 3 years
Grading: commensurate, depending on qualifications and experience
Closing Date: 3 September 2020
Reference Number: HD01807
The European Molecular Biology Laboratory (EMBL,, one of the highest ranked scientific research organizations in the world, is looking for a Scientific Software Developer who will actively contribute to data analysis, methods development, and software development in the Alexandrov team in the field of single-cell metabolomics.

The Alexandrov team at EMBL (, unites 10 scientists and 4 software developers with the aim to develop novel methods and software for life sciences. We have a proven track record creating software which becomes widely adopted in the field, e.g. see our main software platform METASPACE (;

The main project to contribute to will be SpaceM, a method and software for single-cell metabolomics, an emerging field of biological, medical and pharmacological importance. For more information about SpaceM, check out our preprint ( and the GitHub repository of the early scientific prototype ( This project is funded by the European Research Council supporting visionary research projects in Europe. By working on this project, you will have a chance to contribute to creating an important scientific technology right at the beginning of its evolution.

The responsibilities will cover the whole workflow from data to software: data analysis, method development (image analysis, deep learning, single-cell analysis), and software development.

Your role

  • Analysis of data collected by scientists using Python and existing prototype software
  • Work together with scientists to improve existing methods and develop new methods (including image analysis in particular using deep learning frameworks and available models, statistical analysis, and single-cell analysis in particular using scanpy)
  • Implement methods into the prototype software
  • Design and implement the next version of the software together with other software developers

You have

  • Experience in data analysis in particular using Python, Pandas and NumPy
  • 3+ years of experience of programming in Python
  • Experience in implementing custom data analysis workflows
  • Interest in science

You might also have

  • Knowledge of image analysis, machine learning, single-cell analysis
  • Experience in web software development (both backend and frontend)
  • Experience in scientific visualization and using visualization libraries (e.g. Matplotlib or D3.js)

Why join us

You will be a critical part of a dynamic, interdisciplinary, international and cross-cultural team where we work at the intersection of biology, chemistry, and computer science (, Our team includes 10 scientists and 4 software developers. We develop integrative computational and experimental methods for spatial metabolomics to detect metabolites in tissues and cells and interpret this molecular data in light of the spatial context. Some of our software packages became de facto standards in the field, have a growing community of users and are generously supported by public funding ( We strive to provide a healthy work environment with a flat hierarchy supporting a diversity of opinions, with freedom to make decisions and with funded opportunities to grow professionally.

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits. Excellent child care facility is available on campus.

What else you need to know

We are Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1700 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome.

Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research.

The working language of the institute is English.