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.
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
Advanced Multilanguage Interface to CVODES and IDAS
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
A web application to visualize and edit pathway models
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!
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
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.
ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.