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.
Read more on livermetabolism.comResearch interests
Software is how we do science. These are the five areas the tools serve; the full picture is on livermetabolism.com.
AI
Machine learning combined with mechanistic modeling to extract patterns from complex biomedical data and support predictive, personalized decision-making in medicine.
Read more on livermetabolism.comDigital Pathology
Computational and AI-driven analysis of whole-slide histology images to quantify tissue structure, zonation, and disease patterns at scale.
Read more on livermetabolism.comPharmacometrics
Physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) modeling of drug absorption, distribution, metabolism, and excretion to support precision dosing.
Read more on livermetabolism.comOpen & FAIR
Open, FAIR (Findable, Accessible, Interoperable, Reusable), and reproducible models, data, and software that the research community can build on.
Read more on livermetabolism.comMain projects
Open-source software developed and maintained over many years.
PK-DB
Pharmacokinetics database
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.
- Pharmacometrics
- Digital Twins
- Open & FAIR
- Latest release
- v0.12.19 · 2 Nov 2026
- Language
- Python
- License
- MIT
- Activity
- ★ 53 · ⑂ 13 · updated 2 Nov 2026
sbmlutils
Python utilities for SBML
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.
- Open & FAIR
- Digital Twins
- Latest release
- 0.17.1 · 1 Nov 2026
- Language
- HTML · Python 3.12–3.15
- License
- MIT
- Activity
- ★ 43 · ⑂ 12 · updated 1 Nov 2026
sbmlsim
SBML simulation made easy
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.
- Open & FAIR
- Digital Twins
- Pharmacometrics
- Latest release
- 0.14.1 · 2 Nov 2026
- Language
- Python · Python 3.13–3.15
- License
- MIT
- Activity
- ★ 13 · ⑂ 8 · updated 2 Nov 2026
pymetadata
Metadata and COMBINE archives in Python
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.
- Open & FAIR
- Latest release
- 0.8.3 · 1 Nov 2026
- Language
- Python · Python 3.11–3.15
- License
- MIT
- Activity
- ★ 6 · ⑂ 3 · updated 1 Nov 2026
libsbgnpy
Python library for SBGN
A Python library for the Systems Biology Graphical Notation (SBGN), supporting standardized visualization and exchange of pathway maps.
- Open & FAIR
- Latest release
- 0.7.2 · 2 Nov 2026
- Language
- JavaScript · Python 3.11–3.15
- License
- MIT
- Activity
- ★ 12 · ⑂ 1 · updated 2 Nov 2026
VisFEM
Web visualization of FEM models
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.
- Digital Twins
- AI
- Open & FAIR
- Latest release
- 0.2.0 · 26 Oct 2026
- Language
- Python · Python 3.14
- License
- MIT
- Activity
- ★ 2 · ⑂ 0 · updated 27 Oct 2026
cy3sbml
SBML for Cytoscape 3
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.
- Open & FAIR
- Digital Twins
- Latest release
- v0.9.1 · 1 Nov 2026
- Language
- Java
- License
- MIT
- Activity
- ★ 16 · ⑂ 4 · updated 1 Nov 2026
Contributions
GitHub activity across the repositories listed on this page, refreshed daily.
Primary languages across repositories
- Python · 11
- HTML · 8
- Java · 4
- JavaScript · 2
- C++ · 1
- Matlab · 1
Latest releases
The latest release of every repository on this page that published one in the last two years, newest first, with a summary of its release notes.
Release history
Latest release per repository
- sbmlsim0.14.1
A patch release for petab 0.10.0 and the security updates of the dependencies. sbmlsim 0.14.0 imported SbmlModel from petab.models, which petab 0.10.0 removed, so the PEtab export…
- libsbgnpy0.7.2
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-DBv0.12.19
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…
- sbmlutils0.17.1
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…
- pymetadata0.8.3
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…
- cy3sbmlcy3sbml-v0.9.1
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…
- VisFEM0.2.0
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/roadrunnerv2.11.0
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…
- sbml4humans0.12.2
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/cobrapy0.32.1
fixed import failure when hopsy was not installed
- sys-bio/telluriumv2.2.11.2
Small fix to SED-ML handling of files with paths. SimpleSEDML should now work on Windows.
Repository catalog
Everything else: libraries, apps, models and community projects, grouped by topic.
Most starred
- Python
- C++
- HTML
- Java
- JavaScript
- TeX
All repositories
- matthiaskoenig/pkpdutils★ 6 · Python · 2026
PK/PD pharmacometric analysis utilities in python
SBML4Humans: SBML report for humans
BRENDA parser in python
- matthiaskoenig/dfba★ 13 · HTML · 2020
Encoding Dynamic Flux Balance Analysis in SBML
- matthiaskoenig/tellurium-web★ 1 · JavaScript · 2018
Tellurium Web Tools
- matthiaskoenig/modelmanager★ 0 · HTML · 2017
libRoadRunner: A high-performance SBML simulator
- opencobra/cobrapy★ 595 · Python · 2026
COBRApy is a package for constraint-based modeling of metabolic networks.
Python Environment for Modeling and Simulating Biological Systems
- SED-ML/sed-ml★ 5 · TeX · 2026
Simulation Experiment Description Markup Language (SED-ML)
- matthiaskoenig/cy3sabiork★ 1 · Java · 2018
Cytoscape 3 app to access kinetic information from SABIO-RK
- matthiaskoenig/cy3robundle★ 0 · Java · 2016
Minimal example including taverna robundle
- matthiaskoenig/cy2sabiork★ 0 · HTML · 2016
[DEPRECATED] cy2sabiork: SABIO-RK for Cytoscape 2
- matthiaskoenig/cy3fluxviz★ 0 · Java · 2016
- matthiaskoenig/cy2sbml★ 3 · HTML · 2016
cy2sbml: SBML for Cytoscape 2
- matthiaskoenig/cy2reposition★ 0 · HTML · 2016
- matthiaskoenig/cy2fluxviz★ 1 · HTML · 2015
- dagwa/wholecell-metabolism★ 3 · HTML · 2016
Metabolism module of WholeCell model
- matthiaskoenig/glucose-liver★ 1 · Matlab · 2016
Hepatic glucose model (König2012, König2014): glycolysis, gluconeogenesis and glycogen metabolism of the human liver
- whole-cell-tutors/whole-cell-reduced★ 4 · Python · 2016
the reduced model developed in salt lake city
- matthiaskoenig/hepatonet★ 2 · Python · 2015