SBML (the Systems Biology Markup Language) is an XML-based format for communicating and storing representations of biological processes. Its aim is to be a lingua franca for representing models in biology. SBML is suitable for models commonly found in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others.

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

• UpdatedOct 29, 2025
• Python

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

• UpdatedOct 23, 2025
• Python

memote – the genome-scale metabolic model test suite

• UpdatedAug 14, 2025
• HTML

High-performance sensitivity analysis for large ordinary differential equation models

• UpdatedNov 5, 2025
• C++

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

• UpdatedOct 21, 2025

A web application to visualize and edit pathway models

• UpdatedNov 2, 2025
• JavaScript

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

• UpdatedNov 4, 2025
• Python

LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.

• UpdatedOct 18, 2025
• C++

libRoadRunner: A high-performance SBML simulator

• UpdatedNov 6, 2025
• C++

SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit

• UpdatedAug 2, 2025
• Julia

A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results

• UpdatedNov 2, 2025
• TypeScript

Python utilities for SBML

• UpdatedOct 28, 2025
• HTML

JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.

• UpdatedJul 9, 2025
• Java

The official PySCeS project source code repository.

• UpdatedOct 19, 2025
• Python

Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology

• UpdatedOct 28, 2025
• AMPL

Julia interface to the Systems Biology Markup Language (SBML) library

• UpdatedSep 2, 2025
• Julia

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

• UpdatedNov 5, 2025
• Python

Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML

• UpdatedMar 13, 2023
• Jupyter Notebook

The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package.

• UpdatedAug 7, 2025
• JavaScript

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.

• UpdatedOct 24, 2025
• HTML