Over the years I have been developing several programs/macros/scripts that I use to make my life easier. Some of this software became sufficiently user friendly so that others can perhaps use them without too much trouble.

Whenever appropriate, please acknowledge the use of the software posted here. I included the BibTeX entries to help you do this.

Send me note if any of these is useful to you. Enjoy…

**StochDynTools** – MATLAB
scripts to compute approximate moment dynamics for a stochastic network of
chemical reactions. This approximation is based on the moment closure
techniques described in the following references:

J. Hespanha. Moment closure for biochemical networks. In Proc. of the Third Int. Symp. on Control, Communications and Signal Processing, Mar. 2008. [pdf]

J. Hespanha, Abhyudai Singh. Stochastic Models for Chemically Reacting Systems Using Polynomial Stochastic Hybrid Systems.

, 15(15):669—689, Sep. 2005.Int. J. on Robust Control, Special Issue on Control at Small Scales: Issue 1A. Singh, J. Hespanha. LogNormal Moment Closures for Biochemical Reactions. In

, Dec. 2006.Proc. of the 45th Conf. on Decision and Contr.

* **Status:** Work in progress. The documentation is
fairly complete, but this software is still in its earlier stages of
development and perhaps not very user friendly. Please email me if you have
questions/problems using it. I’ll be happy to help.*

**TextVisTools** – This MATLAB toolbox permits the spatial visualization of large corpus of documents based on

1) Extraction of document features using Latent Dirichlet allocation

2) Locating documents in two-dimensional space using Self-Organizing Map's

3) Producing outputs that can be imported into ArcGIS, permitting the visualization of documents clusters.

* ** **Status:* *The code is fairly stable and each function has a detailed help, but the toolbox permits so many options that it is hard to get your hands around it without some help. The best is to start with the example included and work from there.*

**grPartition** – MATLAB
function to partition very large graphs very fast. This algorithm was used in
this paper:

C. Lim, S. Bohacek, __J. Hespanha__, K. Obraczka. Hierarchical Max-Flow
Routing. In * Proc. of the
IEEE GLOBECOM*, Nov. 2005.

* **Status:** Pretty stable, with a nice technical
report to explain the algorithm. *

**@graph** – MATLAB
graph class. It allows you to create, draw, and perform a few simple operations
on graphs.

Status: Work in progress. All scripts
have a nice help, but that is the extent of the documentation.

**bib2web** – Perl
script to automatically generate a web page from bibtex files.

Status: *Pretty stable. I have been using
this for several years to generate http://www.ece.ucsb.edu/~hespanha/published.html
and http://www.ece.ucsb.edu/~hespanha/techrep.html,
but as I keep adding “features” new bugs keep appearing.*

**FastTrack** – C
library to find and track specific landmarks in an image. This code was written
for speed.

It processes an entire image in just a few milliseconds so that it can be used
in robotics to process images at frame rate.

*Status:* *Work in
progess. Fairly complete documentation is available for all library functions.
Justin Pearson is currently working on interfacing this code with Simulink’s
Real-Time Workshop for feedback control.
*

To keep lawyers and such happy, the following paragraph applies to all software in this web site.

*This
program is free software; you can redistribute it and/or modify it under the
terms of the GNU General Public License as published by the Free Software
Foundation; either version 2 of the License, or (at your option) any later
version. This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details (http://www.gnu.org/copyleft/gpl.html)*