Helmholtz Zentrum München is a research center with the mission to discover personalized medical solutions for the prevention and therapy of environmentally triggered diseases and promote a healthier society in a rapidly changing world.

The Institute of Computational Biology is globally recognised for innovations in data analysis and modelling of biological systems and diseases, anchored at the Helmholtz Munich and the Technical University Munich.

Scanpy is the leading toolkit for the analysis of single-cell gene expression data in Python (> 300k downloads, > 900 stars on github). Scanpy is scalable and memory efficient, and allows the analysis of large single cell analysis datasets. Scanpy relies on the data structure package Anndata, a scalable way to store molecular data and annotations. Scanpy provides functions for the full analysis workflow, such as preprocessing, normalisation, batch effect correction, visualisation, clustering, trajectory inference and differential expression testing.

As a software developer you will:

The Theis lab is looking for a highly motivated

Software Developer (f/m/x) - Scanpy 101376

Image Part time, Full time
Image Neuherberg near Munich
Image Graduates & Entry-level Professionals, Professionals

Your responsibilities

  • Create the infrastructure to run a benchmark suite for Scanpy, Anndata, and associated projects using tools like AirSpeedVelocity, to ensure that Scanpy stays fast and memory efficient
  • Improve Scanpy integration to state of the art ML/DL frameworks in Python
  • Organize and overhaul test suites and increase test coverage for Scanpy
  • Improve documentation by creating infrastructure that enables rendering and testing of tutorials (Jupyter notebooks) in the continuous integration pipeline
  • Develop and maintain Scanpy websiteand keep it up to date

Your qualifications

  • Bachelor or Master's degree in Computer Science, Software Engineering or related fields
  • Extensive knowledge of the scientific computing and machine learning ecosystem in Python (numpy, numba, scikit-learn, pandas, dask, matplotlib etc.)
  • Extensive knowledge of continuous integration and testing suite maintenance (github actions, tox, readthedocs etc.)

Desired qualifications

  • Web design experience (required only for the Website task)

What we offer you

work-life balance
flexible working hours & working-time models
continuous education and training
30 days annual leave
on-site health management service
Image home office options
Image on-site nursery & holiday care
Image elder care
Image company pension scheme
Image discounted public transport ticket

Munich, with its numerous lakes and its vicinity to the Alps, is considered to be one of the cities with the best quality of life worldwide. With its first-class universities and world-leading research institutions it offers an intellectually stimulating environment.

Provided that the prerequisites are fulfilled, a salary level up to E 13 is possible. Social benefits are based on the collective agreement for the federal public service (TVöD). The position is (initially) limited to 2 Jahre, under certain circumstances an extension can be arranged.

To promote diversity, we welcome applications from talented people regardless of gender, cultural background, nationality, ethnicity, sexual identity, physical abilities, religion and age. Qualified applicants with physical disabilities will be given preference.
If you have obtained a university degree abroad, we require further documents from you regarding the recognition of the degree. Please request the recognition as early as possible.

If you have further questions, simply contact Dr. Anna Sacher,, Tel.: +49 89 3187-2926, who will be happy to be of assistance.
Helmholtz Zentrum München
Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
Institute of Computational Biology
Ingolstädter Landstraße 1

85764 Neuherberg

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