Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.

A Python Framework for Modeling and Analysis of Signaling Systems

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.

Patient-Specific Modeling in Python

LibSBMLSim: A library for simulating SBML models

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

Ecosystem of Machine-maintained Models with Automated Analysis

A text-based computational framework for patient -specific modeling for classification of cancers. iScience (2022).

Metabolic Network Toolbox for MATLAB

Spatial Model Simulator with SBML Model

LibSBMLSim: A library for simulating SBML models (Version 2)

DMS1401ZB Mathematical Systems Biology

An efficient Java™ solver implementation for SBML

Matlab code and data for Enzyme Cost Minimisation

Parinsula is an interactive visual simulator of relatively isolated systems, which are a particular type of complex system.

Code and models for Flux-balance Enzyme Cost Minimization (fECM)

Simulator for SBML Models

A package for researchers working with biological oscillations

This package simplifies evolutionary algorithms for applications in systems biology. It can be used to generate oscillating reaction networks, networks that match input timeseries data, or fit parameters (rateconstants).

Matlab code for Metabolic Economics calculations