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
- 0.12.1 · 21 Sept 2026
- Language
- HTML · Python 3.11–3.14
- License
- MIT
- Activity
- ★ 42 · ⑂ 12 · updated 21 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
- 0.7.2 · 14 Sept 2026
- Language
- Python · Python 3.13–3.14
- License
- MIT
- Activity
- ★ 10 · ⑂ 8 · updated 18 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
- 0.6.4 · 20 Sept 2026
- Language
- Python · Python 3.11–3.15
- License
- MIT
- Activity
- ★ 6 · ⑂ 3 · updated 21 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
- 0.6.2 · 13 Sept 2026
- Language
- JavaScript · Python 3.11–3.14
- License
- MIT
- Activity
- ★ 12 · ⑂ 1 · updated 20 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 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
- sbml4humans0.8.0
A report can be read on a phone: below 768 px the report shows the tables or the inspector, one at a time, and no page scrolls sideways any more. · a window narrower than 768 px…
- sbmlutils0.12.1
an annotation resource of a collection the identifiers.org registry does not know is normalized like every other resource: http://identifiers.org/sabiork/1406 is written as…
- pymetadata0.6.4
Omex.from_directory, and with it Omex.from_omex and Omex.from_url, add the entries in the order of the manifest, followed by the files which the manifest does not list, sorted by…
- sbmlsim0.7.2
A patch release of the plotting: the axis labels of a figure, an inspection of the figure model and of its matplotlib rendering, and the citation. · the axis label follows the…
- libsbgnpy0.6.2
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…
- 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…
- 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
SBML4Humans: SBML report for humans
- matthiaskoenig/pkpdutils★ 3 · Python · 2026
PK/PD pharmacometric analysis utilities in python
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
- opencobra/cobrapy★ 587 · Python · 2026
COBRApy is a package for constraint-based modeling of metabolic networks.
libRoadRunner: A high-performance SBML simulator
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