Releases
Latest releases
- pkdbv0.12.13
pkdb 0.12.13 closes the last gap of the conversion of study format 1 folders: pkdb migrate refuses a study when a row that it converts holds a number in a column that study.json does not map, as it already did for rows that it drops, so no number of a converted row is lost without notice, and the…
- sbmlsim0.9.7
A performance release: the constant parameters and the species of a model are read once per instance of roadrunner instead of on every call of sampling.parameters_of. The simulations are unchanged. The faster JIT of roadrunner, LLJIT, was measured and is not used, roadrunner 2.10 crashes with it…
- livermetabolism-site0.12.6
A patch release that announces the Open Science Award 2026 of the University of Lübeck, updates two publications, and makes continuous integration lighter and faster.
- sbmlode0.3.0
sbmlode 0.3.0 writes the ODE system of an SBML model as python code of JAX, which diffrax simulates: jax.jit compiles the simulation, jax.vmap batches it over constants and initial states, and jax.grad and jax.jacfwd differentiate it, a model with events included. It passes every case of the SBML…
- sbmlutils0.16.0
Interpolation.drive drives a parameter, species or compartment of an existing model with the interpolated data, in place; x is the time or a quantity of the model, targets maps a column to the element it drives (#16, #500) · Interpolation.drive_comp drives a model through a comp model which…
- sbml4humans0.12.2
The python package supports Python 3.12, 3.13, 3.14 and 3.15.
- cy3sbmlv0.9.0
This release opens the model of a network in sbml4humans with one click, and reviews the code base: fixes, security hardening, cleanups, performance and documentation.
- pkpdbib0.2.1
The code is now licensed under the MIT license instead of the LGPLv3, as the other packages of the group (sbmlutils, sbmlsim, pymetadata). · pyzotero and polars are standard dependencies, the optional zotero extra was removed; pip install pkpdbib installs everything needed for pkpdbib.zotero_tools.
- libsbgnpy0.7.0
This release follows the latest SBGN specifications (PD L1V2.1, ER L1V2.0, AF L1V1.2) and validates documents against the rules of the specifications: the rules the schema cannot express, and the schematron rules of the SBGN languages, as the Java library libSBGN does.
- sbml2cellml0.4.2
libopencor is installed from PyPI with the simulate extra (#54).
- pkpdutils1.3.0
Minor release of pkpdutils which compares the non-compartmental analysis against the public benchmark suite of the NonCompart validation report (#103): all eight scenarios (theophylline and indomethacin, intravenous bolus, 0.25 h infusion and extravascular dose, linear and linear-up / log-down…
- cobrapy0.32.1
fixed import failure when hopsy was not installed
- roadrunnerv2.10.0
Major new capability: variable stoichiometries.
- visfem0.1.0
first working prototype
- tellurium2.2.11.2
Small fix to SED-ML handling of files with paths. SimpleSEDML should now work on Windows.
Release history
Activity
Commit activity
Stars
- Python
- C++
- HTML
- Java
- JavaScript
- TypeScript
Software
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.
v0.12.13★ 519 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.
1.3.0★ 52 open6 days agoPythonMIT
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.
0.2.1★ 10 open6 days agoPythonMIT
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 open6 days agoPythonMIT
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.
0.4.2★ 10 open6 days agoPythonMIT
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.
0.3.0★ 21 open6 days agoPythonMIT
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.
v0.9.0★ 160 open6 days agoJava
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.
v2.10.0★ 6484 opentodayC++
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★ 146135 open1 month 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.
0.1.0★ 10 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.
0.12.6★ 52 opentodayTypeScript
Nothing in this research area yet.
Data from GitHub, updated .
Funding
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.
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.
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.
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.
Nothing in this research area yet.
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.
Nothing in this research area yet.