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
- v0.9.8 · 6 Oct 2025
- Language
- Python
- License
- MIT
- Activity
- ★ 49 · ⑂ 12 · updated 5 Nov 2025
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
- 0.10.2 · 8 Sept 2026
- Language
- HTML · Python 3.11–3.14
- License
- MIT
- Activity
- ★ 41 · ⑂ 12 · updated 8 Sept 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
- 0.6.1 · 10 Sept 2026
- Language
- Python · Python 3.13–3.14
- License
- MIT
- Activity
- ★ 8 · ⑂ 8 · updated 10 Sept 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
- 0.6.2 · 8 Sept 2026
- Language
- Python · Python 3.11–3.14
- License
- MIT
- Activity
- ★ 6 · ⑂ 3 · updated 8 Sept 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
- 0.6.1 · 7 Sept 2026
- Language
- JavaScript · Python 3.11–3.14
- License
- MIT
- Activity
- ★ 12 · ⑂ 0 · updated 8 Sept 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
- 0.1.0 · 5 May 2026
- Language
- Python · Python 3.13–3.14
- License
- MIT
- Activity
- ★ 1 · ⑂ 0 · updated 4 Sept 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
- v0.5.0 · 21 Oct 2025
- Language
- Java
- License
- —
- Activity
- ★ 15 · ⑂ 4 · updated 22 Jan 2026
Contributions
GitHub activity across the repositories listed on this page, refreshed weekly.
Primary languages across repositories
- Python · 9
- HTML · 8
- Java · 4
- JavaScript · 2
- C++ · 1
- Jupyter Notebook · 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
- sbmlsim0.6.1
library code does not show figures. sbmlsim.sensitivity.plots.heatmap and S1_ST_barplot return the matplotlib.figure.Figure they create and close it instead of calling plt.show()…
- sbmlutils0.10.2
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…
- pymetadata0.6.2
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…
- sbml4humans0.2.0
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…
- libsbgnpy0.6.1
the validation documentation walks through an invalid document: examples/sbgn/invalid.sbgn breaks the schema in three ways, one per kind of error the validation reports, and the…
- opencobra/cobrapy0.32.1
fixed import failure when hopsy was not installed
- sys-bio/roadrunnerv2.10.0
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…
- VisFEM0.1.0
first working prototype
- sys-bio/telluriumv2.2.11.2
Small fix to SED-ML handling of files with paths. SimpleSEDML should now work on Windows.
- cy3sbmlcy3sbml-v0.5.0
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_analysis0.3.1
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-DBpkdb-v0.9.8
updated code licensing to MIT · removed travis · uv installation · updated postgres to version 18 · python update to py3.9 and pinned versions for stability
Repository catalog
Everything else: libraries, apps, models and community projects, grouped by topic.
Most starred
- Python
- C++
- HTML
- Java
- JavaScript
- TeX
All repositories
- matthiaskoenig/pkdb_analysis★ 2 · Jupyter Notebook · 2026
PKDB python library
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★ 586 · 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-model★ 1 · Matlab · 2016
Hepatic glucose model
- whole-cell-tutors/whole-cell-reduced★ 4 · Python · 2016
the reduced model developed in salt lake city
- matthiaskoenig/hepatonet★ 2 · Python · 2015