28 repositories · 983 stars · 1142 commits and 123 pull requests in the last year · primary language Python in 9 repositories (details)
Research software engineering for systems medicine: open-source tools, standards and reproducible workflows for digital twins of the liver and human physiology. Professor of Metabolic Inflammation and Carcinogenesis of the Liver at the University of Lübeck (UKSH, Campus Lübeck) and head of the König Lab at Humboldt-Universität zu Berlin.
🔗 matthiaskoenig.github.io (this page with interactive charts) · livermetabolism.com · ORCID · CV
Digital Twins — Mechanistic, patient-specific models spanning molecule to whole body that mirror an individual's physiology, enabling simulation-based prediction of disease progression and treatment response.
AI — Machine learning combined with mechanistic modeling to extract patterns from complex biomedical data and support predictive, personalized decision-making in medicine.
Digital Pathology — Computational and AI-driven analysis of whole-slide histology images to quantify tissue structure, zonation, and disease patterns at scale.
Pharmacometrics — Physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) modeling of drug absorption, distribution, metabolism, and excretion to support precision dosing.
Open & FAIR — Open, FAIR (Findable, Accessible, Interoperable, Reusable), and reproducible models, data, and software that the research community can build on.
| Project | Latest release | Language | License | Links | |
|---|---|---|---|---|---|
 |
PK-DB Pharmacokinetics database |
v0.9.8 6 Oct 2025 |
Python | MIT | Website · Zenodo · Paper |
 |
sbmlutils Python utilities for SBML |
0.10.2 8 Sept 2026 |
HTML Python 3.11–3.14 |
MIT | Docs · Zenodo |
 |
sbmlsim SBML simulation made easy |
0.7.1 14 Sept 2026 |
Python Python 3.13–3.14 |
MIT | Docs · Zenodo |
 |
pymetadata Metadata and COMBINE archives in Python |
0.6.2 8 Sept 2026 |
Python Python 3.11–3.14 |
MIT | Docs · Zenodo |
 |
libsbgnpy Python library for SBGN |
0.6.2 13 Sept 2026 |
JavaScript Python 3.11–3.14 |
MIT | Docs · Zenodo |
 |
VisFEM Web visualization of FEM models |
0.1.0 5 May 2026 |
Python Python 3.13–3.14 |
MIT | Docs · Zenodo |
 |
cy3sbml SBML for Cytoscape 3 |
v0.5.0 21 Oct 2025 |
Java | — | Zenodo |
- PK-DB — The first FAIR-compliant open database for pharmacokinetics, integrating clinical and pre-clinical trial data. PK-DB enables reproducible PBPK/PD modeling and individualized simulations and has become a key infrastructure for computational pharmacology research.
- sbmlutils — A versatile Python library that streamlines working with SBML models: model creation, annotation, reports, and integration with libSBML. Widely used in reproducible modeling workflows across systems biology.
- sbmlsim — A lightweight Python package that simplifies simulations of SBML models on top of libRoadRunner: timecourses, scans, parameter fitting and reports, lowering the entry barrier for model testing and teaching.
- pymetadata — Python utilities for working with metadata, ontologies and identifiers, and for reading and writing COMBINE archives, so that models and data carry the annotations that make them FAIR.
- libsbgnpy — A Python library for the Systems Biology Graphical Notation (SBGN), supporting standardized visualization and exchange of pathway maps.
- VisFEM — A browser-based visualization tool for finite element method (FEM) simulation results, making FEM-based digital twin models interactively explorable and shareable directly from the web.
- cy3sbml — A widely used Cytoscape app for the visualization of SBML models in network contexts, enabling intuitive exploration of complex models in systems biology and bioinformatics.
Latest release of every repository on the site that published one in the last two years:
- sbmlsim 0.7.1 · 14 Sept 2026 — A patch release of the fixes which 0.7.0 surfaced: the page of the SBML Test Suite in the documentation was replaced by the report it links, the release workflow could not build…
- libsbgnpy 0.6.2 · 13 Sept 2026 — every change goes into develop through a pull request; the tests, ruff, ty and the documentation build have to pass before a merge is possible · the master branch is renamed to…
- sbmlutils 0.10.2 · 8 Sept 2026 — antimony 3.2.0 is excluded on Windows: its wheel raises OSError: [WinError -529697949] Windows Error 0xe06d7363 in loadAntimonyString when parsing the antimony of the…
- pymetadata 0.6.2 · 8 Sept 2026 — EntryFormat.ANTIMONY for Antimony model files in COMBINE archives (text/plain) · every change goes into develop through a pull request; the tests, ruff, ty and the documentation…
sbml4humans 0.2.0 · 7 Sept 2026 — The first release of sbml4humans from its own repository. Until sbmlutils 0.10.0 the application lived in the sbmlutils repository, the backend api was sbmlutils.report.api with…- opencobra/cobrapy 0.32.1 · 11 Aug 2026 — fixed import failure when hopsy was not installed
sys-bio/roadrunner v2.10.0 · 5 Aug 2026 — Major new capability: variable stoichiometries. · Support for variable stoichiometries is now present and should be complete: all the SBML Test Suite cases with variable and named…- VisFEM 0.1.0 · 5 May 2026 — first working prototype
sys-bio/tellurium v2.2.11.2 · 5 Dec 2025 — Small fix to SED-ML handling of files with paths. SimpleSEDML should now work on Windows.- cy3sbml cy3sbml-v0.5.0 · 21 Oct 2025 — fixed deprecation issues with HTML escape · release documentation added to repository · Fix ':' in network names · Update OLS to OLS4, #353 (@kyxhik) · fixing url patterns and…
- pkdb_analysis 0.3.1 · 20 Oct 2025 — warnings to info on pharmacokinetics calculation · support python 3.10, 3.11, 3.12, 3.13 · updated build system with uv and ruff · fixed tests
- PK-DB pkdb-v0.9.8 · 6 Oct 2025 — updated code licensing to MIT · removed travis · uv installation · updated postgres to version 18 · python update to py3.9 and pinned versions for stability
The full catalog with search and sorting, the interactive charts and the zoomable release history are on matthiaskoenig.github.io.
Publications, projects, team and teaching of the König Lab: livermetabolism.com (publications, projects). Interested in collaborating? Get in touch via the lab website.
Generated from GitHub data fetched on 2026-09-14; refreshed weekly by the Update profile README workflow. This repository also holds the source of the site under site/ (see site/README.md).