Our group has developed several software packages. Some tools are listed / described below. Also see our [CompuTopoOSU] website (maintained by Dr. Dey and myself) for recent computational topology software.

Software


  • Denali [web-page]: A software package (developed by [Justin Eldridge]) for a terrain metaphor platform for general scalar trees, with a callback system for general data analysis applications. The algorithm behind the software is based on our earlier work [Harvey and Wang, CFG2010]. Our software Ayla below is a collaborative and integrative framework targeted at molecular simulation data sets, while Denali aims to serve as a generic framework for general data.
  • Per-Neuron [git hub page]: Code for comparing neuron structures via persistent homology summaries. The algorithm is described in our paper [Li, Wang, Ascoli, Mitra and Wang, PLOS One 2017], and the code is developed mainly by Yanjie Li, with some help from Justin Eldridge and Dayu Shi.
  • SimBa [download here]: A software package (developed by Dayu Shi) for approximating the persistence diagram induced by the Rips filtration of a set of points in both Euclidean space or more general metric space via batch collpase.
  • TopMapRecon [web-page]: The Morse-based map reconstruction software developed by [Suyi Wang]).
  • Simpers [download here]: A software package developed by Dayu Shi (with some earlier work by Fengtao Fan) for computing the persistent homology of a filtration connected by simplicial maps. It is based on the algorithm we proposed in [Dey, Fan, Wang, SoCG 2014].
  • Persistence-Distortion: [source-zip] and [exe-zip]. Code developed by Dayu Shi for comparing two metric graphs via the persistence distoriton distance that we proposed in [Dey, Shi, Wang, SoCG 2015].
  • Ayla [web-page]: A collaborative visual analytic platform (developed by W. Harvey) which produces a 2D-terrain metaphor for researchers to visualize and explore the high-dimensinoal molecular simulation data. The paper describing Ayla is available [here]. See a youtube video describing the tool [here], and also an image of the interface on the right and [here].
  • Smolign [web-server]: A complete software suite to compare multiple protein structures. It uses a novel method to extract and align spatial motifs from protein structures.
  • EPO [web-server]: An Enhanced Partial-Order Graph algorithm for comparing multiple (possibly high dimensional) curves. It aims at capturing low level of similarity.
  • LFM-Pro [download]: A tool for detecting significant local structural sites in proteins.