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

• UpdatedMar 15, 2025
• Python

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

• UpdatedMar 28, 2025

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.

• UpdatedApr 14, 2025
• HTML

Spatial bio-chemical reaction model editor and simulator

• UpdatedApr 14, 2025
• C++

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

• UpdatedMar 20, 2024
• Jupyter Notebook

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.

• UpdatedMar 7, 2022
• Python

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

• UpdatedOct 11, 2024
• Python

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

• UpdatedNov 9, 2022
• Python

Interface between the Systems Biology Markup Language and Julia

• UpdatedSep 1, 2021
• Julia

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

• UpdatedNov 21, 2023
• Shell

Python package for managing systems and subsystems of SBML models

• UpdatedOct 23, 2020
• Jupyter Notebook

A graphical editor for systems biology models.

• UpdatedMay 9, 2018
• Java

This repository contains all changes made to the strain specific models of Corynebacterium striatum.

• UpdatedMay 22, 2024
• HTML

• UpdatedApr 2, 2025
• JavaScript

Physiologically based pharmacokinetics (PBPK) model of tirzapetide

• UpdatedMar 6, 2025
• HTML

Python utilities for SBML extended for cpp

• UpdatedJul 12, 2023
• HTML

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

• UpdatedAug 17, 2024
• Nextflow

Final Infobiotics Workbench implementation of SBOL and SBML conversion functionality, UI updates, and sequence fetching

• UpdatedSep 20, 2018
• Java

Hepatocyte model of ischemia reperfusion injury (IRI)

• UpdatedMar 12, 2024