{"id":170,"date":"2015-09-02T14:12:16","date_gmt":"2015-09-02T18:12:16","guid":{"rendered":"https:\/\/people.clas.ufl.edu\/peterbubenik\/?page_id=170"},"modified":"2026-03-27T12:31:41","modified_gmt":"2026-03-27T16:31:41","slug":"software","status":"publish","type":"page","link":"https:\/\/people.clas.ufl.edu\/peterbubenik\/software\/","title":{"rendered":"Software"},"content":{"rendered":"\n<section class=\"fullwidth-text-block\"><div class=\"container px-0\"><div class=\"row align-items-start\"><div class=\"col-12\">\n<h1 class=\"wp-block-heading\">Software<\/h1>\n\n\n\n<h3 class=\"wp-block-heading\">My Software<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Topological Data Analysis with R. Code with examples: <a href=\"https:\/\/sites.google.com\/view\/peters-rmds\/home\/lab-1\">Lab 1<\/a>, <a href=\"https:\/\/sites.google.com\/view\/peters-rmds\/home\/lab-2\">Lab 2<\/a>, <a href=\"https:\/\/sites.google.com\/view\/peters-rmds\/home\/lab-3\">Lab 3<\/a>.<\/li>\n\n\n\n<li><a href=\"https:\/\/people.clas.ufl.edu\/peterbubenik\/files\/plt_source_bubenik.txt\">My version of Pawel Dlotko&#8217;s The Persistence Landscape Toolbox<\/a>. ComputePersistenceLandscape uses standard i\/o rather than file i\/o. Rename from .txt to .tgz.<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Software written or maintained by members or former members of my research group<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/github.com\/ZachTRoss\/MPHvect\">MPHvect<\/a>, by Zachariah Ross<\/li>\n\n\n\n<li>Topological Data Analysis for Python: <a href=\"https:\/\/github.com\/scikit-tda\">scikit-tda<\/a>, previously maintained by Michael Catanzaro<\/li>\n\n\n\n<li>Software for Topological Data Analysis of Images: <a href=\"https:\/\/github.com\/P-Edwards\/TDAExplore\">TDAExplore<\/a>, by Parker Edwards<\/li>\n\n\n\n<li>Software for Topological Data Analysis of Video:\u00a0<a href=\"https:\/\/github.com\/althomas\/tda-for-worm-behavior\">tda-for-worm-behavior<\/a>, by Ashleigh Thomas<\/li>\n\n\n\n<li>Jose Bouza&#8217;s R package <a href=\"https:\/\/github.com\/jjbouza\/tda-tools\">tda-tools<\/a>.<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Software by other researchers at the University of Florida<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/bitbucket.org\/hubwag\/workspace\/repositories\/\">Hubert Wagner<\/a><\/li>\n\n\n\n<li>Cory Brunson: <a href=\"https:\/\/github.com\/corybrunson\/plt\">plt: Persistence Landscapes Toolbox<\/a>, <a href=\"https:\/\/github.com\/tdaverse\/tdaverse\">tdaverse<\/a><\/li>\n\n\n\n<li>Hubert Wagner: <a href=\"https:\/\/github.com\/hubwag\/Mixup-SOCG26\">Mixup-SoCG2026<\/a><\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Other Software<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>The R package <a href=\"http:\/\/cran.r-project.org\/web\/packages\/TDA\/index.html\">TDA: Statistical Tools for Topological Data Analysis<\/a>, by Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria<\/li>\n\n\n\n<li><a href=\"http:\/\/gudhi.gforge.inria.fr\/doc\/latest\/\">GUDHI:\u00a0a generic open source\u00a0C++ library, with a\u00a0Python interface, for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding<\/a>\u00a0by INRIA<\/li>\n\n\n\n<li>Pawel Dlotko&#8217;s <a href=\"http:\/\/www.math.upenn.edu\/~dlotko\/persistenceLandscape.html\">The Persistence Landscape Toolbox<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/github.com\/jisuk1\/pllay\/\">PLLay: Efficient Topological Layer based on Persistence Landscapes<\/a>, by Kwangho Kim, Jisu Kim, Manzil Zaheer, Joon Sik Kim, Frederic Chazal, Larry Wasserman<\/li>\n\n\n\n<li><a href=\"https:\/\/github.com\/Ripser\">Ripser<\/a>, by Ulrich Bauer<\/li>\n\n\n\n<li><a href=\"http:\/\/gregoryhenselman.org\/eirene\/index.html\">Eirene<\/a>, by Gregory Henselman<\/li>\n\n\n\n<li><a href=\"http:\/\/www.mrzv.org\/software\/dionysus\/\">Dionysus: a C++ Library for computing persistent homology<\/a>, and <a href=\"https:\/\/mrzv.org\/software\/dionysus2\/\">Dionysus 2<\/a>, by Dmitriy Morozov<\/li>\n\n\n\n<li><a href=\"http:\/\/people.maths.ox.ac.uk\/nanda\/perseus\/\">The Perseus Software Project for Rapid Computation of Persistent Homology<\/a>, by Vidit Nanda<\/li>\n\n\n\n<li><a href=\"http:\/\/appliedtopology.github.io\/javaplex\/\">JavaPlex: the Persistent Homology and Topological Data Analysis Library<\/a>, by Andrew Tausz, Mikael Vejdemo-Johansson and Henry Adams<\/li>\n\n\n\n<li><a href=\"https:\/\/bitbucket.org\/phat-code\/phat\">PHAT: the Persistent Homology Algorithm Toolbox<\/a> by Ulrich Bauer, Michael Kerber, Jan Reininghaus<\/li>\n\n\n\n<li><a href=\"http:\/\/chomp.rutgers.edu\/index.html\">CHOMP: Computational Homology Project<\/a> by Konstantin Mischaikow&#8217;s group<\/li>\n\n\n\n<li><a href=\"http:\/\/web.cse.ohio-state.edu\/~tamaldey\/SimBa\/Simba.html\">SimBa<\/a>, by\u00a0Tamal K Dey , Dayu Shi , Yusu Wang<\/li>\n\n\n\n<li><a href=\"http:\/\/web.cse.ohio-state.edu\/~tamaldey\/SimPers\/Simpers.html\">SimPers<\/a>, by\u00a0Tamal K Dey , Fengtao Fan , Dayu Shi , Yusu Wang<\/li>\n<\/ul>\n<\/div><\/div><\/div><\/section>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":516,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"featured_post":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-170","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/people.clas.ufl.edu\/peterbubenik\/wp-json\/wp\/v2\/pages\/170","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/people.clas.ufl.edu\/peterbubenik\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/people.clas.ufl.edu\/peterbubenik\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/peterbubenik\/wp-json\/wp\/v2\/users\/516"}],"replies":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/peterbubenik\/wp-json\/wp\/v2\/comments?post=170"}],"version-history":[{"count":10,"href":"https:\/\/people.clas.ufl.edu\/peterbubenik\/wp-json\/wp\/v2\/pages\/170\/revisions"}],"predecessor-version":[{"id":1378,"href":"https:\/\/people.clas.ufl.edu\/peterbubenik\/wp-json\/wp\/v2\/pages\/170\/revisions\/1378"}],"wp:attachment":[{"href":"https:\/\/people.clas.ufl.edu\/peterbubenik\/wp-json\/wp\/v2\/media?parent=170"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}