Open source contributions

We often rely on open-source libraries to make your scientific software work. The SSC strives to give back to the open-source community by publishing open source.

Often during development work we find ourselves implementing functionality that could be reused in other projects if it was packaged as an independent library, or adding a feature or extension to some existing open source software that other people could also find useful.
When feasible we try to make this work available and usable by others as open source software, and in this way contribute to the open source community that indirectly supports so much of our work by providing and maintaining the open source tools and libraries that our projects depend on.

We have a diverse set of completed and ongoing software development projects. On this page we only list the following project type:

  • Open source contributions
    Our open source projects and contributions to the open source community

Projects

Table

Alignment Workflow for Deformed EM images

Alignment workflow for deformed electron microscopy images of entire planktonic animals
Biosciences
Open Call Project
2025
Bio-Structure Hub

Bio-Structure Hub provides scripts, documentation and training, to run simulations, validate and interpret results.
Biosciences
Funded Project
2025
Photobodies

Evaluating PPI in Photobodies
Biosciences
Small Scale Project
2025
Quanty

Consultation on updating a legacy code base to new coding standards, initializing a cmake build system, improving CI pipeline
Physics
Small Scale Project
2025
REP

Evaluating interactions of REP proteins
Biosciences
Small Scale Project
2025
X-Ray machine for the teddy bear clinic

A generative AI 'X-ray machine' for teddy bears - used by medical students in the teddy bear clinic, an outreach initiative for children.
Medicine
Software Practical
2025
yTubulin

Evaluating PPI in yTubulin Complexe
Biosciences
Small Scale Project
2025
Kinetic Data Fitting

Improve algorithm for kinetic data fitting to achieve higher accuracy and provide more descriptors of the quality of the fit.
Biosciences, Chemistry
Small Scale Project
2024
parzivAI

Chatbot for German medieval language and history interaction.
Modern Languages
Small Scale Project
2024
sci-rocket

Genome processing pipeline and dashboard
Biosciences
Small Scale Project
2024
ShinyLipids bugfixing

Fixing some bugs in an established lab code for lipidomics, developed as an R Shiny app.
Biosciences
Small Scale Project
2024 - 2025
CebraEM

Quantifying organelle geometry and morphology based on volume electron microscopy data.
Biosciences
Open Call Project
2023
Oxygen video linking of xml annotations

Link videos as xml annotations in the Oxygen XML editor
Modern Languages
Small Scale Project
2022
Parafields

Development of an MPI-parallel Python library for the generation of stationary Gaussian fields based on an existing C++ library
Scientific Computing
Open Call Project
2022
Predictive modeling in TB screening

Develop a machine learning model to predict TB disease
Medicine
Open Call Project
2022
Advice on math

Consultation on solving partial differential equations.
Medicine
Small Scale Project
2021