Software

We are actively involved in the standardization and reproducibility efforts in Systems Biology and Systems Medicine.

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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

Funding

Title Start End Role Funder Grant Number Project
X-Student Research Group - Digital Twins in Action: Optimizing Direct Oral Anticoagulant Use 10/2025 04/2026 Recipient Bundesministerium für Bildung und Forschung (BMBF) und dem Land Berlin im Rahmen der Exzellenzstrategie von Bund und Ländern
SPP2311 - Startup Funding - SPP-FEMVis: Advancing Open Science with Web-Based FEM Visualization 10/2025 09/2026 Recipient Deutsche Forschungsgemeinschaft (DFG) 465194077 https://www.spp2311.uni-stuttgart.de/en/
AlgoNomy - Algorithmic Regulation Before Medical Liability - Advancing Doctor-Patient Autonomy in AI-Driven Healthcare 2024 2025 Co-Investigator Circle U. - European University Alliance https://algonomy.jus.unipi.it/
Open Science Ambassador 01/2024 06/2026 Recipient BUA - Berlin University Alliance
SPP2311 - SimLivA - SIMulation supported LIVer Assessment for donor organs 10/2025 9/2027 Recipient Deutsche Forschungsgemeinschaft (DFG) 465194077 https://www.spp2311.uni-stuttgart.de/en/
X-Student Research Group - Physiologically based digital twins for the treatment of hypertension with ACE inhibitors and diuretics 04/2023 09/2023 Recipient Bundesministerium für Bildung und Forschung (BMBF) und dem Land Berlin im Rahmen der Exzellenzstrategie von Bund und Ländern
ATLAS - AI and Simulation for Tumor Liver ASessment 03/2023 12/2026 Recipient Bundesministerium für Bildung und Forschung (BMBF) "Computational Life Sciences" 031L0304B
X-Student Research Group - Physiologically based modeling of drugs: ACE inhibitors in the treatment of high blood pressure 10/2022 03/2023 Recipient Bundesministerium für Bildung und Forschung (BMBF) und dem Land Berlin im Rahmen der Exzellenzstrategie von Bund und Ländern
FOR5151 - QuaLiPerF - Quantifying Liver Perfusion-Function Relationship in Complex Resection – A Systems Medicine Approach 07/2021 11/2025 Recipient Deutsche Forschungsgemeinschaft (DFG) 436883643 https://qualiperf.de
SPP2311 - SimLivA - SIMulation supported LIVer Assessment for donor organs 01/2020 12/2023 Co-Investigator Deutsche Forschungsgemeinschaft (DFG) 465194077 https://www.spp2311.uni-stuttgart.de/en/
EOSC-Life - Reproducible simulation studies targeting COVID-19 06/2020 05/2021 Recipient EOSCsecretariat.eu - EU Horizon Program - EOSC-life H2020-INFRAEOSC-05-2018-2019 https://www.ebi.ac.uk/biomodels/covid-19
LiSyM - Systems Medicine of the Liver - Junior group leader - Multi-scale models for the personalized evaluation of liver function 06/2016 05/2022 Recipient Bundesministerium für Bildung und Forschung (BMBF) 031L0054 https://lisym.org/

This work was supported by the BMBF-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.

2020-2025 COMBINE coordinator
The COmputational Modeling in BIology NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models.
2023-2026 PETab editor
PEtab is a data format for specifying parameter estimation problems in systems biology.
2018-2023; 2025-2027 SBML editor
The Systems Biology Markup Language (SBML) is a software data format for describing models in biology.
2017-2022; 2024-2026 SED-ML editor
The Simulation Experiment Description Markup Language (SED-ML) is a format for encoding simulation setups, to ensure exchangeability and reproducibility of simulation experiments.