sbml-model

COBRApy is a package for constraint-based modeling of metabolic networks.

PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.

A Python package for "classic" Constraint-Based Reconstruction and Analysis (COBRA) and the new COBRA with kinetics (COBRA-k). Link to documentation and tutorials:

Spatial bio-chemical reaction model editor and simulator

pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.

sbml2hyb is a tool for SBML compatible hybrid modelling of biological systems

Python package and workflow for EFM calculation via (mp)lrs and efmtool

Interface between the Systems Biology Markup Language and Julia

A tool to for optimizing parameters of ordinary differential equation (ODE) models. SBML2Julia translates a model from SBML/PEtab format into Julia for Mathematical Programming (JuMP), performs the optimization task and returns the results.

Easily use the memote command line interface from a docker container.

Test and grade genome-scale metabolic models (GEMs).

An AI agent to build and curate genome scale metabolic network models

This project provides a simulation framework for synthetic biology and metabolic engineering, with a focus on the analysis of metabolic models for the production of novel compounds.

Physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of canagliflozin

Physiologically based pharmacokinetics/pharmacodynamics (PBPK/PD) model of dulaglutide

Python package for managing systems and subsystems of SBML models

Glimepiride Web Application

Physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of empagliflozin

A graphical editor for systems biology models.