Software

Useful Software

For Boolean Networks:

1. Cyclone: Calculate the dynamics of a discrete dynamical system using exhaustive search.

2. SDDS:  Stochastic simulator for Boolean and multistate networks.

3. SDDS CONTROL: This module computes an optimal policy for a stochastic controllable system.

4. Turing: Different algorithms for modeling and analysis of discrete dynamical systems.

5. Algorun: A Docker-based container template for computational algorithms.

6. GINsim (Gene Interaction Network simulation): is a computer tool for the modeling and simulation of genetic regulatory networks.

7. BooleanNet: Boolean network modeling for life science research.

8. BoolNet: Construction, Simulation and Analysis of Boolean Networks. 

9. The Cell Collective: is a web-based platform for the construction, simulation, and analysis of Boolean-based models.

For ODE:

1. XPPAUT: software for solving differential equations. XPP contains the code for the popular bifurcation program, AUTO.

2. AUTO: software for continuation and bifurcation problems.

For HMM:

1. CpG Educate: a webtool for simulating, decoding, and training HMMs. 

2. The mhsmm package for R.

Other Multipurpose Software:

1. Jupyter: The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. 

2. Macaulay2: is a software system devoted to supporting research in algebraic geometry and commutative algebra. 

3. GNU Octave: a high-level interpreted language, primarily intended for numerical computations. 

4. R: is a free software environment for statistical computing and graphics.

5. 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. 

Old Code:

1. Code for algebraic methods for control of Boolean networks

2. Scripts in Macaulay2 and Matlab can be found here.

3. Code for genetic algorithm for estimating propensity parameters.