COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
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.
Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.
Spatial bio-chemical reaction model editor and simulator
SPARCED model creation and simulation package.
System Dynamics script utilities
Design Explorer and Viewer for Iterative SBML Enhancement of Representations
Spatial Model Simulator with SBML Model
An organism simulation framework based on cell growth and resultant emergent phenomena.
To show how to use odeint for biochemical simulation
In silico research group's bioinformatics toolbox for network and machine learning analysis
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