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.
sbmlutils
Open & FAIR Digital Twins
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.
SBML4Humans
Open & FAIR Digital Twins
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.
sbmlsim
Open & FAIR Digital Twins Pharmacometrics
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.
cysbml
Open & FAIR Digital Twins
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.
brendapy
Open & FAIR Digital Twins
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.
libsbgnpy
Open & FAIR Digital Twins
Python library for SBGN Developed a Python library for working with Systems Biology Graphical Notation (SBGN), supporting standardized visualization and integration of pathway information.
roadrunner
Open & FAIR Digital Twins
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.
COBRApy
Open & FAIR Digital Twins
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.
tellurium
Open & FAIR Digital Twins
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.
VisFEM
Digital Twins AI Open & FAIR
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.
Funding
X-Student Research Group - Digital Twins in Action: Optimizing Direct Oral Anticoagulant Use
Digital Twins Pharmacometrics Open & FAIR
BMFTR, Recipient, 10/2025–04/2026
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
Open & FAIR Digital Twins
DFG, Recipient, 10/2025–09/2026
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
AI
Circle U., Co-Investigator, 2024–2025
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
Open & FAIR
BMFTR, Recipient, 01/2024–06/2026
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.
DFG, Recipient, 10/2025–09/2027
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
Digital Twins Pharmacometrics
BMFTR, Recipient, 04/2023–09/2023
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 ASessment
Digital Twins AI
BMFTR, Recipient, 03/2023–12/2026
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
Pharmacometrics
BMFTR, Recipient, 10/2022–03/2023
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
Digital Twins AI
DFG, Recipient, 07/2021–11/2025
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.
EOSC-life, Recipient, 06/2020–05/2021
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
Digital Twins AI
BMFTR, Recipient, 06/2016–05/2022
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.
This work was supported by the BMFTR-funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) (031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B).
Editors
We are actively involved in the standardization and reproducibility efforts in Systems Biology and Systems Medicine.
COMBINE coordinator
Open & FAIR
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
Open & FAIR
2023-2026 PEtab is a data format for specifying parameter estimation problems in systems biology.
SBML editor
Open & FAIR
2018-2023; 2025-2027 The Systems Biology Markup Language (SBML) is a software data format for describing models in biology.
SED-ML editor
Open & FAIR
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.
