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

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.

memote – the genome-scale metabolic model test suite

High-performance sensitivity analysis for large ordinary differential equation models

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

An integrated visual environment for metabolic modeling 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!

A web application to visualize and edit pathway models

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.

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

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

Python utilities for SBML

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.

The official PySCeS project source code repository.

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

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

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

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

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.

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.

Standalone Python package containing libSBML with support for SBML Level 3 Core and accepted SBML Level 3 packages.

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.

Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.

A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML, and various other formats.

CBMPy is a Python based platform for constraint based modelling and analysis.

Spatial bio-chemical reaction model editor and simulator

COnstraint Based Reconstruction and EXascale Analysis (in Julia)

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

Python package for working with PEtab files

cy3sbml: SBML for Cytoscape 3

Registry of containerized biosimulation tools that support a standard command-line interface