Sample Code:
For Boolean Networks:
Cyclone: Calculate the dynamics of a discrete dynamical system using exhaustive search.
SDDS: Stochastic simulator for Boolean and multistate networks.
SDDS CONTROL: This module computes an optimal policy for a stochastic controllable system.
Turing: Different algorithms for modeling and analysis of discrete dynamical systems.
Algorun: A Docker-based container template for computational algorithms.
GINsim (Gene Interaction Network simulation): is a computer tool for the modeling and simulation of genetic regulatory networks.
BooleanNet: Boolean network modeling for life science research.
BoolNet: Construction, Simulation and Analysis of Boolean Networks.
The Cell Collective: is a web-based platform for the construction, simulation, and analysis of Boolean-based models.
For Bioinformatics:
R: is a free software environment for statistical computing and graphics.
Rstudio: free IDE for R and Python
CellChat: Inference and analysis of cell-cell communication with scRNAseq
For ODEs:
XPPAUT: software for solving differential equations. XPP contains the code for the popular bifurcation program, AUTO.
AUTO: software for continuation and bifurcation problems.
Other Software:
MATLAB: programming and numeric computing platform used to analyze data, develop algorithms, and create models.
Anaconda: open ecosystem for sourcing, building, and deploying data science with Python
GRO: language for programming, modeling, specifying and simulating the behavior of cells in growing microcolonies of microorganisms
Macaulay2: is a software system devoted to supporting research in algebraic geometry and commutative algebra.
GNU Octave: a high-level interpreted language, primarily intended for numerical computations.
SAGE: is a free open-source mathematics software system which combines the power of many existing open-source packages into a common Python-based interface.