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Shawn Martin

Shawn Martin
(505) 845-9644


GENERAL NOTE: Some of the below files are *.tar.gz.  For some reason these files are sometimes altered when using Internet Explorer, e.g. unzipped.  If you have trouble try renaming the file *.tar or *.tar.gz or try a different browser. (source)

NMTRI: Non-Manifold Surface Reconstruction

I have implemented a toolbox for triangulating non-manifold point clouds in high dimensional vector spaces, as described in detail in "Non-Manifold Surface Reconstruction from High Dimensional Point Cloud Data" in publications.  The toolbox can handle 2-manifolds, 2-manifolds with boundary, and 2-manifolds with self-intersections (double curves, no cusps).  The code is written in Matlab.  Also included is code used in the cyclo-octane project "Topology of Cyclo-Octane Energy Landscape" in publications.  Please let me know if you have any problems.  (source, cyclo-octane example)

OpenOrd: Large-scale Graph Layout (formerly DrL)

We have developed a force-directed graph layout toolbox focused on real-world large-scale graphs.  This toolbox includes:

OpenOrd has been used on graphs up to 849k vertices.  It is written in C++ and can be used with Linux, Windows, and Mac, but has mostly been used in Linux.  Please email me with comments/problems.  (source)

Signature Products

We have developed a method for predicting protein-protein interactions (see "Predicting Protein-Protein Interactions using Signature Products" in publications) using amino acid sequences based on J.-L. Faulon's signature descriptor.  The software is written in C/C++ and is based on T. Joachim's SVM-light package V5.0.  The software has been compiled using gcc/g++ under Linux and Cygwin.  Please let me know if you have any problems compiling and/or using the software. (source)

IMPORTANT NOTE: You must use SVM-light version 5, otherwise the patch won't work.  SVM-light version 5 is available from T. Joachim's web page if you scroll down to the bottom.

Last Updated May 24, 2012.