• Software

    jHoles

    jHoles is a new version of Holes and it implements the clique weight rank persistent homology algorithm. jHoles fills the lack of an efficient implementation of the filtering process for clique weight rank homology.

    boxedClique

    From Weighted Graph to Filtered Simplicial Complex

    For a complete description we refer to: Jacopo Binchi, Emanuela Merelli, Matteo Rucco, Giovanni Petri, and Francesco Vaccarino. jHoles: A tool for understanding biological complex networks via clique weight rank persistent homology. Electronic Notes in Theoretical Computer Science , 306:5–18, 2014

    jHoles is available at jHoles.eu. jHoles has been implemented by UNICAM and ISI.

    MyCwrph_incremental

    Example of computation of Persistent Homology from a filtered Simplicial Complex

    Holes

    A Python module for the preprocessing, computation and analyses of the results of persistent homology on weighted complex networks.  The  module wraps the homology calculations engines javaplex and Perseus in an environment designed to facilitate the analysis of large datasets.

    Holes is available at: http://lordgrilo.github.io/Holes/
    For a complete description we refer to: Petri, G., Scolamiero, M., Donato, I. & Vaccarino, F. Topological strata of weighted complex networks. Plos One 8, e66506 EP– (2013).

    JointPDF

    Firstly, this Python module implements the notion of a “joint probability distribution” among discrete stochastic variables, as well as many common operations for them. Secondly, it implements many information-theoretical quantities such as Shannon entropy, mutual information, information synergy, information-based optimization procedures, and robustness tests.

    For a complete description, please read here.

    JointPDF has been developed by Rick Quax and it is available at bitbucket.org.

    Non-Parametric Fisher Information (NPFI)

    This software package implements an algorithm to compute the Fisher Information matrix from non-parametric estimates of the underlying Probability Density Functions using a finite-difference scheme.

    For a complete description we refer to npfi.nl and to O. Har-Shemesh, R. Quax, B. Miñano, A.G. Hoekstra, P.M.A. Sloot, Non-parametric estimation of Fisher information from real data, (2015) arxiv:1507.00964.

    NPFI is available here: github.com.

    TPUniform

    TPUniform is a sampling framework for RNA structures of fixed topological genus. We introduce a novel, linear time, uniform sampling algorithm for RNA structures of fixed topological genus g, for arbitrary g>0.

    For a complete description we refer to: Fenix Huang, Markus Nebel and Christian Reidys. Generation of RNA structures with topological genus filtration. Math Biosci., (2013), 245(2), 216-225.

    TPUniform is available here: vbi.vt.