#===============================================================================
# README for ratespec 
#
# A python class library for computing rate spectra
#
# Please reference
# Voelz VA and Pande VS. 2011. "Calculation of Rate Spectra from Noisy Time Series Data"
# Proteins: Structure, Function and Bioinformatics, accepted (2011). 
#
# Written Feb 2011 by Vincent A. Voelz <vvoelz@stanford.edu>
# Pande group, Dept. of Chemistry, Stanford University
#
# Copyright (C) 2011  Stanford University

SVN REPOSITORY

For access to the SVN repository, please see: https://simtk.org/home/ratespec/

If you have permissions, you can check out this repository from svn using:
>>  svn checkout --username user https://simtk.org/svn/ratespec

INSTALLATION

    REQUIRED PATHNAMES

    Please put the ratespec directory in your PYTHONPATH environment variable

    REQUIRED PACKAGES

    * You will need a working installation of scipy and numpy (see http://www.scipy.org/ )
    * For PlottingTools.py, an installation of matplotlib is required (see http://matplotlib.sourceforge.net/ )
    * For computing rate spectra via the Lasso (L1-norm regularization), the scikits-learn package of
      machine learning tools is needed (see http://scikit-learn.sourceforge.net/ )

    NOTE: all of these packaged can be installed together using the Enthought Python Distribution, which
    is *highly* recommended: http://www.enthought.com/products/epd.php


---------------
Last Updated: September 14, 2011
--Vincent Voelz