# Software

Our workgroup produces software written in several programming languages. There is a set of legacy programs created in Fortran and in C++. Newer versions of the software are assembled in more productive environments such as Python or MATLAB. Some of this software is available upon request. However the workgroup also publishes a software package detailed below.

## INTERACT Toolbox

The INTERACT Toolbox is a MATLAB toolbox for analysis of interactions in time series with focus on phase dynamics. Using the toolkit common tasks can be performed with a call of a function. Specifically, the toolkit allows the user to:

- extract phase from time series,
- compute various dependence indices (mean phase coherence, mutual information, conditional probability),
- compute conditional mutual information (using the equiquantal binning method),
- construct surrogate time series (using phases or using amplitude time series),
- integrate various dynamical models and perform model testing experiments.

With the above toolbox the full range of weak interactions between a pair of systems can be analyzed. The toolbox is scheduled tp be extended with functions for multidimensional time series analysis in the near future.

## NDW-Graph Toolbox

The NDW-Graph Toolbox is C++ toolbox with interface to Matlab for analysis of large networks of several types (unweighted, weighted, ...). Among others functionalities one can use this toolbox for:

- compute basic graph characteristics like degree, density, strength, clustering coefficient, etc.,
- compute distance matrix and several other derived characteristics like characteristic path length, efficiency, transitivity, etc.,
- determine number of components and their actual structure,
- compute several centrality indices like closeness, betweenness centrality, etc.,
- compute some other characteristics like assortative coefficient, average nearest neighbors,
- compute small-wolrd coefficients.

Although the toolbox is already functional, it is still under development and some parts can be missing.