Difference between revisions of "List of Software"

Revision as of 20:49, 17 May 2019

In recent years, a whole landscape of software emerged that deals with computational topology tasks in different fashions. On this page, we provide starting points for the selection of software suited for the problem of interest.

Packages described here include the following:

CGAL (https://www.cgal.org/)
JavaPlex (https://github.com/appliedtopology/javaplex), Tutorial
GUDHI (http://gudhi.gforge.inria.fr/)
Ripser (https://github.com/Ripser)
PHAT (https://github.com/blazs/phat)
Dionysus (http://www.mrzv.org/software/dionysus)
R-TDA (https://cran.r-project.org/web/packages/TDA/index.html)
Persus (http://www.sas.upenn.edu/~vnanda/perseus/index.html)
Rivet (http://rivet.online/)

This collection has been created without any claim of comprehensiveness.

Overview

Comparison of some of these packages e.g. by Otter et al. ^[1]. Eventually we will put put the results of this comparison in a table somewhere on this page.

Details

CGAL

The basic design of CGAL is described in Fabri et al 2000^[2].

JavaPlex

The basic design of JavaPlex is described in Adams et al 2014^[3]. We provide an introductory tutorial to Javaplex on a different page.

GUDHI

The basic design of GUDHI is described in Maria et al 2014^[4]. We provide an introductory tutorial to using GUDHI on a different page.

Ripser

PHAT

Dionysus

R-TDA

Persus

Rivet

References

↑ Otter, Nina, et al. A roadmap for the computation of persistent homology. EPJ Data Science, 2017, 6. Jg., Nr. 1, S. 17. doi:10.1140/epjds/s13688-017-0109-5
↑ FABRI, Andreas, et al. On the design of CGAL a computational geometry algorithms library. Software: Practice and Experience, 2000, 30. Jg., Nr. 11, S. 1167-1202. doi:10.1002/1097-024X(200009)30:11<1167::AID-SPE337>3.0.CO;2-B
↑ ADAMS, Henry; TAUSZ, Andrew; VEJDEMO-JOHANSSON, Mikael. JavaPlex: A research software package for persistent (co) homology. In: International Congress on Mathematical Software. Springer, Berlin, Heidelberg, 2014. S. 129-136. doi:10.1007/978-3-662-44199-2_23
↑ MARIA, Clément, et al. The gudhi library: Simplicial complexes and persistent homology. In: International Congress on Mathematical Software. Springer, Berlin, Heidelberg, 2014. S. 167-174. doi:10.1007/978-3-662-44199-2_28

[1] Otter, Nina, et al. A roadmap for the computation of persistent homology. EPJ Data Science, 2017, 6. Jg., Nr. 1, S. 17. doi:10.1140/epjds/s13688-017-0109-5

[2] FABRI, Andreas, et al. On the design of CGAL a computational geometry algorithms library. Software: Practice and Experience, 2000, 30. Jg., Nr. 11, S. 1167-1202. doi:10.1002/1097-024X(200009)30:11<1167::AID-SPE337>3.0.CO;2-B

[3] ADAMS, Henry; TAUSZ, Andrew; VEJDEMO-JOHANSSON, Mikael. JavaPlex: A research software package for persistent (co) homology. In: International Congress on Mathematical Software. Springer, Berlin, Heidelberg, 2014. S. 129-136. doi:10.1007/978-3-662-44199-2_23

[4] MARIA, Clément, et al. The gudhi library: Simplicial complexes and persistent homology. In: International Congress on Mathematical Software. Springer, Berlin, Heidelberg, 2014. S. 167-174. doi:10.1007/978-3-662-44199-2_28

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-In recent years, a whole landscape of software emerged that deals with computational topology tasks in different fashions. On this page, we provide starting points for the selection of software suited for the problem of interest. This collection has been created without any claim of comprehensiveness.
+In recent years, a whole landscape of software emerged that deals with computational topology tasks in different fashions. On this page, we provide starting points for the selection of software suited for the problem of interest.
 Packages described here include the following:
@@ Line 12: / Line 12: @@
 * Rivet (http://rivet.online/)
+This collection has been created without any claim of comprehensiveness.
 == Overview ==
@@ Line 22: / Line 22: @@
 === CGAL ===
+The basic design of CGAL is described in Fabri et al 2000<ref>FABRI, Andreas, et al. On the design of CGAL a computational geometry algorithms library. ''Software: Practice and Experience'', 2000, 30. Jg., Nr. 11, S. 1167-1202. [https://doi.org/10.1002/1097-024X(200009)30:11&#x3C;1167::AID-SPE337&#x3E;3.0.CO;2-B doi:10.1002/1097-024X(200009)30:11<1167::AID-SPE337>3.0.CO;2-B]</ref>.
 === JavaPlex ===
-We provide an introductory tutorial to Javaplex on a different [[JavaPlex Tutorial|page]].
+The basic design of JavaPlex is described in Adams et al 2014<ref>ADAMS, Henry; TAUSZ, Andrew; VEJDEMO-JOHANSSON, Mikael. JavaPlex: A research software package for persistent (co) homology. In: ''International Congress on Mathematical Software''. Springer, Berlin, Heidelberg, 2014. S. 129-136. [https://doi.org/10.1007/978-3-662-44199-2_23 doi:10.1007/978-3-662-44199-2_23]</ref>. We provide an introductory tutorial to Javaplex on a different [[JavaPlex Tutorial|page]].
 === GUDHI ===
-We provide an introductory tutorial to using GUDHI on a different [[GUDHI Tutorial|page]].
+The basic design of GUDHI is described in Maria et al 2014<ref>MARIA, Clément, et al. The gudhi library: Simplicial complexes and persistent homology. In: ''International Congress on Mathematical Software''. Springer, Berlin, Heidelberg, 2014. S. 167-174. [https://doi.org/10.1007/978-3-662-44199-2_28 doi:10.1007/978-3-662-44199-2_28]</ref>. We provide an introductory tutorial to using GUDHI on a different [[GUDHI Tutorial|page]].
 === Ripser ===