PK-DB

Pharmacokinetics database
Developed the first FAIR-compliant open database for pharmacokinetics, integrating clinical and pre-clinical trial data. PK-DB enables reproducible PBPK/PD modeling, supports individualized simulations, and has become a key infrastructure for computational pharmacology research.

v0.12.19★ 5317 opentodayPythonMIT

pkpdutils

PK/PD analysis in python
Developed a Python library for the pharmacokinetic and pharmacodynamic analysis of timecourses and parameters, from non-compartmental analysis and curve fitting to bioequivalence and meta-analysis. Formerly pkdb_analysis, the analysis toolbox of PK-DB.

1.4.0★ 62 openyesterdayPythonMIT

pkpdbib

PK/PD literature in python
Developed a Python library for working with pharmacokinetics and pharmacodynamics (PK/PD) literature and bibliographies, from retrieving the PDFs of a Zotero export to programmatic access to Zotero libraries. Supports the literature curation of PK-DB and of the PK/PD models built on it.

0.2.3★ 11 openyesterdayPythonMIT

sbmlutils

Python utilities for SBML
Created a versatile Python library to streamline the use of SBML models, providing robust utilities for model handling, analysis, and integration with libSBML. Widely used in reproducible modeling workflows across systems biology.

0.17.1★ 434 openyesterdayHTMLMIT

SBML4Humans

SBML simulation made easy
Designed an interactive reporting framework that makes SBML models human-readable and accessible, enabling experts and newcomers to explore model content without technical barriers.

0.12.2★ 213 open3 weeks agoPythonMIT

sbmlsim

SBML simulation made easy
Built a lightweight Python package that simplifies simulations of SBML models on top of libRoadRunner, lowering the entry barrier for model testing and teaching.

0.15.0★ 1310 opentodayPythonMIT

sbml2cellml

Conversion between SBML and CellML
Built a bidirectional converter between SBML and CellML 2.0, validating every conversion with libcellml and checking it by simulation against the SBML test suite and the curated BioModels. Lets models move between the two main model description standards instead of being locked into one.

0.4.3★ 21 openyesterdayPythonMIT

sbmlode

Ordinary differential equations of SBML models
Built a Python package that derives the system of ordinary differential equations of an SBML model from its reactions, rules, events and units, and writes it as simulation code for Python, Julia and R, verified against libRoadRunner over the SBML test suite, or as Typst, LaTeX and Markdown documents of the equations. The ODE export of sbmlutils as a package of its own.

0.3.1★ 20 openyesterdayPythonMIT

cysbml

Cytoscape 3 app for the Systems Biology Markup Language
Developed and maintained a widely used Cytoscape app for visualization of SBML models in network contexts. cy3sbml has facilitated intuitive exploration of complex models in systems biology and bioinformatics.

v0.9.1★ 160 openyesterdayJava

brendapy

BRENDA in python
Authored a Python package providing direct programmatic access to BRENDA enzyme information, enabling large-scale, automated enzyme analysis and integration into computational pipelines.

0.5.0★ 2312 open4 years agoPythonLGPL-3.0

libsbgnpy

Python library for SBGN
Developed a Python library for working with Systems Biology Graphical Notation (SBGN), supporting standardized visualization and integration of pathway information.

0.7.2★ 121 opentodayJavaScriptMIT

roadrunner

High-performance simulator for SBML
Contributed to the development of libRoadRunner, a C/C++ library using LLVM for ultra-fast simulation of SBML models, setting a benchmark for performance in computational biology.

v2.11.0★ 6467 open2 days agoC++

COBRApy

COBRA python package
Advanced COBRApy, the leading Python package for constraint-based reconstruction and analysis, widely adopted in genome-scale metabolic modeling. Provides access to key methods such as flux balance and flux variability analysis.

0.32.1★ 595101 open3 weeks agoPythonGPL-2.0

tellurium

systems biology simulation library
Co-developed Tellurium, a Python-based environment for reproducible dynamical modeling of biological networks. Integrated standard formats with powerful simulation libraries, enabling accessible and transparent modeling.

2.2.11.2★ 148135 open2 months agoPythonApache-2.0

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 to lower the barrier to reproducible computational modeling.

0.2.0★ 21 open6 days agoPythonMIT

livermetabolism.com

Source of this website
The complete source of this website, with all research data (publications, people, projects, software, teaching) maintained as open YAML tables and built into a static site.

0.12.7★ 52 opentodayTypeScript

AI-Ready PK-DB: From Pharmacokinetic Data to Executable PBPK Models with Claude

Anthropic, Recipient, 09/2026–03/2027
$50,000
Developing an MCP server that lets AI agents navigate the pharmacokinetics database PK-DB from study to concentration-time profile and on to an executable PBPK model, making the database accessible to agents well beyond our own group. Awarded as usage credits for Claude.

X-Student Research Group - Digital Twins in Action: Optimizing Direct Oral Anticoagulant Use

BMFTR, Recipient, 10/2025–04/2026
€1,500
Project-based teaching initiative on digital twins in medicine, focusing on physiologically based pharmacokinetic (PBPK) modeling to optimize the use of direct oral anticoagulants.

SPP2311 - Startup Funding - SPP-FEMVis: Advancing Open Science with Web-Based FEM Visualization

DFG, Recipient, 10/2025–09/2026
€15,000
Startup funding to develop an open science platform for interactive, web-based visualization of finite element method (FEM) simulations.

AlgoNomy - Algorithmic Regulation Before Medical Liability - Advancing Doctor-Patient Autonomy in AI-Driven Healthcare

Circle U., Co-Investigator, 2024–2025
€10,000
Building an international academic network to investigate the role of algorithms and AI in medical decision support systems, with a focus on legal, ethical, and patient autonomy implications.

Open Science Ambassador

BMFTR, Recipient, 01/2024–06/2026
€4,000
Supporting the promotion and implementation of open science practices across research communities at Berlin Universities, with a focus on reproducibility, FAIR data, and fostering collaborative exchange.

SPP2311 - SimLivA - SIMulation supported LIVer Assessment for donor organs

DFG, Recipient, 10/2025–09/2027
€895,500 (group share: €219,000)
Developing computational models and simulation workflows to assess liver function in donor organs, advancing predictive tools for transplantation and improving clinical decision-making.

X-Student Research Group - Physiologically based digital twins for the treatment of hypertension with ACE inhibitors and diuretics

BMFTR, Recipient, 04/2023–09/2023
€1,500
Project-based teaching initiative on digital twins in pharmacology, focusing on physiologically based pharmacokinetic (PBPK) modeling to optimize hypertension therapy with ACE inhibitors and diuretics.

ATLAS - AI and Simulation for Tumor Liver ASsessment

BMFTR, Recipient, 03/2023–12/2026
€1,530,550 (group share: €311,000)
Developing AI-driven and simulation-based methods to improve the assessment of liver tumors, integrating computational modeling with clinical data to support personalized diagnosis and treatment planning.

X-Student Research Group - Physiologically based modeling of drugs: ACE inhibitors in the treatment of high blood pressure

BMFTR, Recipient, 10/2022–03/2023
€1,500
Project-based teaching initiative on physiologically based pharmacokinetic (PBPK) modeling, focusing on optimizing the use of ACE inhibitors in hypertension therapy.

FOR5151 - QuaLiPerF - Quantifying Liver Perfusion-Function Relationship in Complex Resection – A Systems Medicine Approach

DFG, Recipient, 07/2021–11/2025
€3,825,000 (group share: €425,000)
Advancing systems medicine by developing computational models to quantify the relationship between liver perfusion and function in complex surgical resections, supporting risk assessment and personalized treatment planning.

SPP2311 - SimLivA - SIMulation supported LIVer Assessment for donor organs

DFG, Co-Investigator, 01/2020–12/2023
€658,942
Collaborative project developing simulation approaches to assess donor liver function, aiming to improve transplantation outcomes through predictive computational modeling.

EOSC-Life - Reproducible simulation studies targeting COVID-19

EOSC-life, Recipient, 06/2020–05/2021
€25,000 (group share: €5,000)
Developed reproducible computational simulation studies to investigate COVID-19 dynamics, integrating standardized workflows and open science practices for rapid and transparent research dissemination.

LiSyM - Systems Medicine of the Liver - Junior group leader - Multi-scale models for the personalized evaluation of liver function

BMFTR, Recipient, 06/2016–05/2022
€723,000
Led a junior research group developing multi-scale computational models to assess and predict liver function, advancing personalized medicine approaches and translational applications in hepatology.

COMBINE coordinator

2020-2025
The COmputational Modeling in BIology NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models.

PETab editor

2023-2026
PEtab is a data format for specifying parameter estimation problems in systems biology.

SBML editor

2018-2023; 2025-2027
The Systems Biology Markup Language (SBML) is a software data format for describing models in biology.

SED-ML editor

2017-2022; 2024-2026
The Simulation Experiment Description Markup Language (SED-ML) is a format for encoding simulation setups, to ensure exchangeability and reproducibility of simulation experiments.