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.
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.
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 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.