A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling
☆31Feb 11, 2026Updated 2 weeks ago
Alternatives and similar repositories for Benchmark-Models-PEtab
Users that are interested in Benchmark-Models-PEtab are comparing it to the libraries listed below
Sorting:
- Python package for working with PEtab files☆16Feb 4, 2026Updated 3 weeks ago
- Tool to convert an ODE model specified in the YAML format to SBML.☆12Jun 13, 2023Updated 2 years ago
- PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology☆62Updated this week
- Model selection for PEtab☆13Dec 16, 2025Updated 2 months ago
- Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.☆22Dec 15, 2025Updated 2 months ago
- High-performance sensitivity analysis for large ordinary differential equation models☆132Updated this week
- A simplified python interface to COPASI.☆25Jan 13, 2026Updated last month
- The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in part…☆11May 16, 2023Updated 2 years ago
- python Parameter EStimation TOolbox☆266Updated this week
- The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML suppor…☆26Dec 3, 2025Updated 2 months ago
- MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.☆12Aug 21, 2024Updated last year
- PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.☆27Mar 2, 2020Updated 5 years ago
- Python utilities for SBML☆41Jan 22, 2026Updated last month
- Ontology of algorithms for analyzing biological models, their parameters, and their outputs☆11Dec 2, 2024Updated last year
- Python package for building SBML models without needing to use libSBML.☆11Aug 18, 2021Updated 4 years ago
- A Universal Modeling Language for Metabolic Flux Analysis☆13Mar 6, 2025Updated 11 months ago
- distributed, likelihood-free inference☆216Feb 18, 2026Updated last week
- Encoding Dynamic Flux Balance Analysis in SBML☆12Sep 16, 2020Updated 5 years ago
- ☆17Dec 1, 2022Updated 3 years ago
- GenSSI 2.0 - Generating Series for testing Structural Identifiability☆15Apr 6, 2024Updated last year
- PyCTD is a Python software package to query and analyse data from the CTD database☆12Oct 6, 2022Updated 3 years ago
- Rule-based modeling framework☆66Updated this week
- This is the fully public version of QSP Toolbox. Please check the README file for the current version of MATLAB that is supported.☆25Dec 29, 2025Updated last month
- Create nice documentation for your MatLab project using doxygen☆15Jul 14, 2019Updated 6 years ago
- LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (…☆54Feb 13, 2026Updated 2 weeks ago
- ☆19Feb 19, 2026Updated last week
- Harmonizing pathway databases using Biological Expression Language (BEL)☆20Jul 1, 2024Updated last year
- Create parameter estimation problems for ODE models☆66Feb 9, 2026Updated 2 weeks ago
- 📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology☆32Dec 16, 2019Updated 6 years ago
- Standalone Python package containing libSBML with support for SBML Level 3 Core and accepted SBML Level 3 packages.☆23Jan 9, 2026Updated last month
- Python framework for Systems Biology modeling☆192Updated this week
- A Julia package for consensus-based optimisation☆16Nov 28, 2025Updated 2 months ago
- COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.☆124Feb 18, 2026Updated last week
- PyBioPAX: A python implementation of the BioPAX object model☆26May 10, 2024Updated last year
- LikelihoodProfiler is a Julia package for practical identifiability analysis and confidence intervals estimation.☆36Feb 11, 2026Updated 2 weeks ago
- INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and datab…☆205Updated this week
- XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevi…☆11Jul 25, 2025Updated 7 months ago
- ☆35Oct 30, 2023Updated 2 years ago
- Publications of all kind based on the Open Systems Pharmacology Suite☆17Aug 1, 2022Updated 3 years ago