28 repositories · 1017 stars · 1950 commits and 960 pull requests in the last year · primary language Python in 11 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 |
v0.12.19 2 Nov 2026 |
Python | MIT | Website · Zenodo · Paper |
 |
sbmlutils Python utilities for SBML |
0.17.1 1 Nov 2026 |
HTML Python 3.12–3.15 |
MIT | Docs · Zenodo |
 |
sbmlsim SBML simulation made easy |
0.15.0 2 Nov 2026 |
Python Python 3.13–3.15 |
MIT | Docs · Zenodo |
 |
pymetadata Metadata and COMBINE archives in Python |
0.8.3 1 Nov 2026 |
Python Python 3.11–3.15 |
MIT | Docs · Zenodo |
 |
libsbgnpy Python library for SBGN |
0.7.2 2 Nov 2026 |
JavaScript Python 3.11–3.15 |
MIT | Docs · Zenodo |
 |
VisFEM Web visualization of FEM models |
0.2.0 26 Oct 2026 |
Python Python 3.14 |
MIT | Docs · Zenodo |
 |
cy3sbml SBML for Cytoscape 3 |
v0.9.1 1 Nov 2026 |
Java | MIT | 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 0.15.0 · 2 Nov 2026 — A release of the likelihood and of PEtab v2. A fit minimizes the negative log-likelihood of the noise models of PEtab or the log posterior with the priors, so the standard…
- libsbgnpy 0.7.2 · 2 Nov 2026 — This is a maintenance release: the dependencies are updated, the package itself is unchanged. · The lock of the development environment uses filelock 4.2.1 instead of 3.32.5…
- PK-DB v0.12.19 · 2 Nov 2026 — pkdb 0.12.19 is a security release: the pkdb package and the backend require Pillow 13.0.0, which fixes 41 advisories of the earlier releases, five of them critical, and the…
- sbmlutils 0.17.1 · 1 Nov 2026 — pillow>=13.0.0 is a dependency of the examples extra: matplotlib writes its images with pillow, which reaches a user of sbmlutils[examples], and pillow 13.0.0 fixes the advisories…
- pymetadata 0.8.3 · 1 Nov 2026 — The lock of the development environment, uv.lock, has filelock 4.2.6 instead of 4.1.0 (#111), which fixes the advisories of filelock before 4.2.1 (GHSA-2g95-wg33-c5x2…
- cy3sbml cy3sbml-v0.9.1 · 1 Nov 2026 — A dependency maintenance release for Cytoscape 3.10 and Java 17, with updated runtime libraries, build tools, Python helpers and documentation tooling. · Jackson Databind is…
- VisFEM 0.2.0 · 26 Oct 2026 — In this release, datasets are described by JSON files and drawn by built-in renderers. It adds two public example datasets, LS-DYNA and FEBio support, documentation at…
sys-bio/roadrunner v2.11.0 · 21 Oct 2026 — Updates: · Now released for python 3.15 (and three previous python versions, through 3.12) · Use latest SWIG for python bindings. · Update Sundials library · The absolute…
sbml4humans 0.12.2 · 6 Oct 2026 — The python package supports Python 3.12, 3.13, 3.14 and 3.15. · pip install sbml4humans installs on Python 3.12 to 3.15, formerly 3.14 only: the forward references of the report…- opencobra/cobrapy 0.32.1 · 11 Aug 2026 — fixed import failure when hopsy was not installed
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.
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 2026-11-02; refreshed daily by the Update profile README workflow. This repository also holds the source of the site under site/ (see site/README.md).