javaPlex - an extensible platform for persistence. javaPlex is the newest member of the Stanford-based Plex family of persistent homology and cohomology software packages. Written in Java, it is optimized for easy interfacing with Matlab as well as anything running in the Java ecosystem - including Processing, Scala, Jython, and Mathematica. javaPlex was written to create a platform easier to extend and experiment with than its predecessor jPlex. In its last release, the platform support absolute and relative persistence (co)homology, as well as hom-complexes of simplicial complexes, cellular and simplicial complex constructions and fast Vietoris-Rips and witness complex constructions. We will demonstrate the architecture, usage, development and extension features of javaPlex, focusing on interoperability with Matlab as an interface to the library.

References in zbMATH (referenced in 12 articles )

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  1. Xia, Kelin; Li, Zhiming; Mu, Lin: Multiscale persistent functions for biomolecular structure characterization (2018)
  2. Bauer, Ulrich; Kerber, Michael; Reininghaus, Jan; Wagner, Hubert: Phat -- persistent homology algorithms toolbox (2017)
  3. Mittal, Khushboo; Gupta, Shalabh: Topological characterization and early detection of bifurcations and chaos in complex systems using persistent homology (2017)
  4. Toth, Csaba D. (ed.); Goodman, Jacob E. (ed.); O’Rourke, Joseph (ed.): Handbook of discrete and computational geometry (2017)
  5. Kovacev-Nikolic, Violeta; Bubenik, Peter; Nikolić, Dragan; Heo, Giseon: Using persistent homology and dynamical distances to analyze protein binding (2016)
  6. Wang, Bao; Wei, Guo-Wei: Object-oriented persistent homology (2016)
  7. Bubenik, Peter: Statistical topological data analysis using persistence landscapes (2015)
  8. Cang, Zixuan; Mu, Lin; Wu, Kedi; Opron, Kristopher; Xia, Kelin; Wei, Guo-Wei: A topological approach for protein classification (2015)
  9. Perea, Jose A.; Harer, John: Sliding windows and persistence: an application of topological methods to signal analysis (2015)
  10. Yogeshwaran, D.; Adler, Robert J.: On the topology of random complexes built over stationary point processes (2015)
  11. Adams, Henry; Tausz, Andrew; Vejdemo-Johansson, Mikael: Javaplex: a research software package for persistent (co)homology (2014)
  12. Binchi, Jacopo; Merelli, Emanuela; Rucco, Matteo; Petri, Giovanni; Vaccarino, Francesco: jHoles: a tool for understanding biological complex networks via clique weight rank persistent homology (2014)